Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 120 of 163
Found at i:33123985 original size:92 final size:92
Alignment explanation
Indices: 33123820--33124064 Score: 339
Period size: 92 Copynumber: 2.7 Consensus size: 92
33123810 TAAGAGCAAG
* * *
33123820 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
* * *
33123885 AAATAAGAGCAAGATGAAGCA-CCGAC
66 AAACAAGAGCAAGACGAAGCATCAGAC
*
33123911 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAGGCTGGATATCAAGTCTTTATCTCTCTGAAATT
1 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATT
* * *
33123976 GAAGCAAGAGCTAGACGAAGCATCAGAT
65 GAAACAAGAGCAAGACGAAGCATCAGAC
* * * * *
33124004 ATCACTTCCTATCCTCTTGAAATTGAAATAAAGTTGGATAGCAAGTCTTTATTTCTCTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
33124065 GAGCAAGACG
Statistics
Matches: 136, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 4 0.03
92 125 0.92
93 7 0.05
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (92 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTG
AAACAAGAGCAAGACGAAGCATCAGAC
Found at i:33124369 original size:17 final size:17
Alignment explanation
Indices: 33124333--33124404 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
33124323 GGTAAAGATA
*
33124333 TAAATTTAGTTTTAAA-T
1 TAAATTTA-TTATAAATT
*
33124350 TAAATTTATTATGAATT
1 TAAATTTATTATAAATT
33124367 TAAATTTGCA-TA-AAATT
1 TAAATTT--ATTATAAATT
*
33124384 TGAATTTATTATAAATT
1 TAAATTTATTATAAATT
33124401 TAAA
1 TAAA
33124405 CTTAAAACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.02
16 7 0.16
17 34 0.76
18 2 0.04
19 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (17 bp):
TAAATTTATTATAAATT
Found at i:33125178 original size:21 final size:22
Alignment explanation
Indices: 33125128--33125199 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 22
33125118 TAATGAGTAA
*
33125128 TAATAATAATGTTAATAATAAAG
1 TAATAATGAT-TTAATAATAAAG
* *
33125151 CAATAATGATTTAATAA-ATAG
1 TAATAATGATTTAATAATAAAG
** *
33125172 TAATAATGGCTTAATAAT-AAT
1 TAATAATGATTTAATAATAAAG
33125193 TAATAAT
1 TAATAAT
33125200 AATATTAACA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 25 0.62
22 7 0.17
23 8 0.20
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (22 bp):
TAATAATGATTTAATAATAAAG
Found at i:33126334 original size:30 final size:29
Alignment explanation
Indices: 33126299--33126597 Score: 87
Period size: 29 Copynumber: 10.2 Consensus size: 29
33126289 TTACATTTTG
33126299 ACCTCGAAAC-TTCCAAAGATTGCCATTTCA
1 ACCTCGAAACTTTCCAAA-ATT-CCATTTCA
* *
33126329 CCCTCG-AACTTTCCAAAATTCCATTTTA
1 ACCTCGAAACTTTCCAAAATTCCATTTCA
*
33126357 ACCTCG--A-TTTCACTAAAAATTACCATTTTA
1 ACCTCGAAACTTTC-C--AAAATT-CCATTTCA
* * *
33126387 CCCCCG-AACTTTCCAAAATTCCATTTTTA
1 ACCTCGAAACTTTCCAAAATTCCA-TTTCA
* *
33126416 ACCCCG--A-TTTCACCAAAATTACCATTT-T
1 ACCTCGAAACTTT--CCAAAATT-CCATTTCA
* * * * *
33126444 ACCCCCAAACCTTCTAAAATTCCATTTTTA
1 ACCTCGAAACTTTCCAAAATTCCA-TTTCA
*
33126474 ACCTCG--A-TTTCATCAAAAATTACCATTT-T
1 ACCTCGAAACTTTC--C-AAAATT-CCATTTCA
* *
33126503 A-CTCCCAAACTTTCCAAAATTCCATTTTTA
1 ACCT-CGAAACTTTCCAAAATTCCA-TTTCA
*
33126533 ACCTCG--A-TTTAACCAAAATTACCATTTTA
1 ACCTCGAAACTTT--CCAAAATT-CCATTTCA
* * * *
33126562 CCCTCG-AACCTTCTAAAATTCCATTTTTA
1 ACCTCGAAACTTTCCAAAATTCCA-TTTCA
33126591 ACCTCGA
1 ACCTCGA
33126598 TTTCATCAAA
Statistics
Matches: 212, Mismatches: 23, Indels: 68
0.70 0.08 0.22
Matches are distributed among these distances:
26 4 0.02
27 11 0.05
28 34 0.16
29 95 0.45
30 48 0.23
31 12 0.06
32 8 0.04
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (29 bp):
ACCTCGAAACTTTCCAAAATTCCATTTCA
Found at i:33126495 original size:117 final size:117
Alignment explanation
Indices: 33126311--33126685 Score: 567
Period size: 117 Copynumber: 3.2 Consensus size: 117
33126301 CTCGAAACTT
* * * *
33126311 CCAAAGATTGCCATTTCACCCTCGAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA-CTAAA
1 CCAAA-ATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATC-AAA
*
33126374 AATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
64 AATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
33126428 CCAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
1 CCAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
* * *
33126493 TTACCATTTTACTCCCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTAA
66 TTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
33126545 CCAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
1 CCAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
* * * *
33126610 TTACCATTTTACGCTCGAAGC-CTCAAAAATTCCATTTTTAACCTCGATTTCA
66 TTACCATTTTACCCCCGAA-CTTTCCAAAATTCCATTTTTAACCTCGATTTCA
*
33126662 CCAAAATTACCATTTTGCCCTCGA
1 CCAAAATTACCATTTTACCCTCGA
33126686 GTATCCAAAA
Statistics
Matches: 236, Mismatches: 19, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
116 29 0.12
117 205 0.87
118 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (117 bp):
CCAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCATCAAAAA
TTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:33126719 original size:58 final size:57
Alignment explanation
Indices: 33126312--33126685 Score: 482
Period size: 58 Copynumber: 6.4 Consensus size: 57
33126302 TCGAAACTTC
* * *
33126312 CAAAGATTGCCATTTCACCCTCGAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
33126369 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 C-AAAAATTACCATTTTACCCTCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCA
* * * *
33126428 CCAAAATTACCATTTTACCCCCAAACCTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCTCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
33126486 TCAAAAATTACCATTTTACTCC-CAAACTTTCCAAAATTCCATTTTTAACCTCGATTTAA
1 -CAAAAATTACCATTTTAC-CCTCGAAC-TTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
33126545 CCAAAATTACCATTTTACCCTCGAACCTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CAAAAATTACCATTTTACCCTCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
33126603 TCAAAAATTACCATTTTACGCTCGAAGCCTCAAAAATTCCATTTTTAACCTCGATTTCA
1 -CAAAAATTACCATTTTACCCTCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
33126662 CCAAAATTACCATTTTGCCCTCGA
1 CAAAAATTACCATTTTACCCTCGA
33126686 GTATCCAAAA
Statistics
Matches: 284, Mismatches: 24, Indels: 17
0.87 0.07 0.05
Matches are distributed among these distances:
57 3 0.01
58 157 0.55
59 122 0.43
60 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.34
Consensus pattern (57 bp):
CAAAAATTACCATTTTACCCTCGAACTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:33127986 original size:33 final size:33
Alignment explanation
Indices: 33127939--33128009 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
33127929 TTGTCGGGAC
* *
33127939 AACATAGAGTAATTGAATGAAATTGTAAGTAAT
1 AACACAGAGTAATTGAACGAAATTGTAAGTAAT
33127972 AACACAGAGTAATTGAACGAAATTGTAAGTAAT
1 AACACAGAGTAATTGAACGAAATTGTAAGTAAT
*
33128005 TACAC
1 AACAC
33128010 TTTCTTGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (33 bp):
AACACAGAGTAATTGAACGAAATTGTAAGTAAT
Found at i:33132388 original size:30 final size:29
Alignment explanation
Indices: 33132324--33132575 Score: 204
Period size: 30 Copynumber: 8.6 Consensus size: 29
33132314 AGGAATTTGA
*
33132324 GGTTAAAATGTAATTTTAGAAAAATTTAG
1 GGTTAAAATGTAATTTTAGAAAAGTTTAG
* *
33132353 GGTTAAAATGTGATTTTAGAAAAGTTTGGG
1 GGTTAAAATGTAATTTTAGAAAAGTTT-AG
* * * *
33132383 GGTTAAAATATGATTTTAGGAAAGTTTGG
1 GGTTAAAATGTAATTTTAGAAAAGTTTAG
*
33132412 AGGTTAAAATGTAATTTT-GGAAAGTTT-G
1 -GGTTAAAATGTAATTTTAGAAAAGTTTAG
* *
33132440 AGGTTAAAATGTAAATTTGGAAAAGTTTAG
1 -GGTTAAAATGTAATTTTAGAAAAGTTTAG
* *
33132470 GGTGAAAATATAATTTTA-AGAAAGTTTAAG
1 GGTTAAAATGTAATTTTAGA-AAAGTTT-AG
** * ** * *
33132500 GGCCAAAATGTAATTTTGGAGTAGGTTGG
1 GGTTAAAATGTAATTTTAGAAAAGTTTAG
* * *
33132529 TGGTTAAAATGTTATTTTGGAGAAGTTTAAG
1 -GGTTAAAATGTAATTTTAGAAAAGTTT-AG
* *
33132560 GGTCAAAATGTGATTT
1 GGTTAAAATGTAATTT
33132576 CTTAAAAGTT
Statistics
Matches: 185, Mismatches: 29, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
28 19 0.10
29 66 0.36
30 98 0.53
31 2 0.01
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTAGAAAAGTTTAG
Found at i:33132448 original size:117 final size:118
Alignment explanation
Indices: 33132319--33132575 Score: 295
Period size: 117 Copynumber: 2.2 Consensus size: 118
33132309 TTTTGAGGAA
* * * **
33132319 TTTGAGGTTAAAATGTAATTTTAGAAAAATTTAGGGTTAAAATGTGATTTT-AGAAAAGTTTGGG
1 TTTGAGGTTAAAATGTAATTTTAGAAAAATTTAGGGTGAAAATATAATTTTAAG-AAAGTTTAAG
** * *
33132383 GGTTAAAATATGATTTTAGGA-AAGTTTGGAGGTTAAAATGTAATTTTGGA-AAG
65 GGCCAAAATATAATTTT-GGAGAAGGTTGGAGGTTAAAATGTAATTTTGGAGAAG
* * *
33132436 TTTGAGGTTAAAATGTAAATTTGGAAAAGTTTAGGGTGAAAATATAATTTTAAGAAAGTTTAAGG
1 TTTGAGGTTAAAATGTAATTTTAGAAAAATTTAGGGTGAAAATATAATTTTAAGAAAGTTTAAGG
* * * *
33132501 GCCAAAATGTAATTTTGGAGTAGGTTGGTGGTTAAAATGTTATTTTGGAGAAG
66 GCCAAAATATAATTTTGGAGAAGGTTGGAGGTTAAAATGTAATTTTGGAGAAG
* * *
33132554 TTTAAGGGTCAAAATGTGATTT
1 TTTGA-GGTTAAAATGTAATTT
33132576 CTTAAAAGTT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
116 3 0.03
117 91 0.78
118 9 0.08
119 13 0.11
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (118 bp):
TTTGAGGTTAAAATGTAATTTTAGAAAAATTTAGGGTGAAAATATAATTTTAAGAAAGTTTAAGG
GCCAAAATATAATTTTGGAGAAGGTTGGAGGTTAAAATGTAATTTTGGAGAAG
Found at i:33134620 original size:50 final size:49
Alignment explanation
Indices: 33134206--33134637 Score: 357
Period size: 50 Copynumber: 8.7 Consensus size: 49
33134196 TTCGCTGTTA
* * *
33134206 CGGCCTAAACCTTTCCCTTTATATCTTCATGGTATCGGATTCACCGTTG
1 CGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTG
* * * ** * *
33134255 CGACCTTAACCCTT-CCTATCGCATCTTCTAAGGTATCGGGTTCGCCGTTG
1 CGGCCTCAACCTTTCCCT-TCATATCTTC-ATGGTATCGGGTTCACCGTTG
* * * * **
33134305 CGGCCTTAACCTTTCCCATC-TCATCTTCTTAGGTACCGGGTTCGTCGTTG
1 CGGCCTCAACCTTTCCCTTCAT-ATCTTCAT-GGTATCGGGTTCACCGTTG
* * ** ***
33134355 CGGCCTCAACCTTTCCATTCATATCTTCATGGTACCAAGTTTGTCGTTG
1 CGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTG
* * ** * *
33134404 TGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGAGTTCACCGTTG
1 CGGCCTCAACCTTTCCCTTCATATCTTCAT-GGTATCGGGTTCACCGTTG
* * * * * * **
33134454 CGGCCTTAATCATTCCCTTTAAATCGTCATGGTATCGGGTTCGTCGTTG
1 CGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTG
* * * * *
33134503 CGGCCTCAATCTTTCCCATT-AAATCTTCTTAGGTATTGGGTTTACCGTTG
1 CGGCCTCAACCTTTCCC-TTCATATCTTCAT-GGTATCGGGTTCACCGTTG
* *
33134553 TGGCCTCAACCTTTCCCTTCGTATCTTCATGGTATCGGGTTCACCGTTG
1 CGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTG
* *
33134602 CGGTCCTCAACCTTTCCCTTCATATCTCCAAGGTAT
1 CGG-CCTCAACCTTTCCCTTCATATCTTCATGGTAT
33134638 TAGATTTGCC
Statistics
Matches: 305, Mismatches: 67, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
48 3 0.01
49 118 0.39
50 181 0.59
51 3 0.01
ACGTcount: A:0.16, C:0.30, G:0.18, T:0.36
Consensus pattern (49 bp):
CGGCCTCAACCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTG
Found at i:33134638 original size:99 final size:99
Alignment explanation
Indices: 33134194--33134628 Score: 419
Period size: 99 Copynumber: 4.4 Consensus size: 99
33134184 TAAGATGCTA
* * * * * * *
33134194 GGTTCGCTGTTACGGCCTAAACCTTTCCCTTTATATCTTCAT-GGTATCGGATTCACCGTTGCGA
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCACCGTTGCGG
* * ** *
33134258 CCTTAACCCTT-CCTATCGCATCTTCTAAGGTATCG
66 CCTCAACCTTTCCCT-TCATATCTTC-ATGGTATCG
* * * **
33134293 GGTTCGCCGTTGCGGCCTTAACCTTTCCCATC-TCATCTTCTTAGGTACCGGGTTCGTCGTTGCG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCAT-ATCTTCTTAGGTATCGGGTTCACCGTTGCG
* * *
33134357 GCCTCAACCTTTCCATTCATATCTTCATGGTACCA
65 GCCTCAACCTTTCCCTTCATATCTTCATGGTATCG
* * * * * ** *
33134392 AGTTTGTCGTTGTGGCCTCAACCTTTCCCATCGCATCTTCTTAGGTATCGAGTTCACCGTTGCGG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCACCGTTGCGG
* * * * * *
33134457 CCTTAATCATTCCCTTTAAATCGTCATGGTATCG
66 CCTCAACCTTTCCCTTCATATCTTCATGGTATCG
* * * * * *
33134491 GGTTCGTCGTTGCGGCCTCAATCTTTCCCATT-AAATCTTCTTAGGTATTGGGTTTACCGTTGTG
1 GGTTCGCCGTTGCGGCCTCAACCTTTCCC-TTCATATCTTCTTAGGTATCGGGTTCACCGTTGCG
*
33134555 GCCTCAACCTTTCCCTTCGTATCTTCATGGTATCG
65 GCCTCAACCTTTCCCTTCATATCTTCATGGTATCG
*
33134590 GGTTCACCGTTGCGGTCCTCAACCTTTCCCTTCATATCT
1 GGTTCGCCGTTGCGG-CCTCAACCTTTCCCTTCATATCT
33134629 CCAAGGTATT
Statistics
Matches: 269, Mismatches: 60, Indels: 13
0.79 0.18 0.04
Matches are distributed among these distances:
98 1 0.00
99 213 0.79
100 53 0.20
101 2 0.01
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.36
Consensus pattern (99 bp):
GGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCTTAGGTATCGGGTTCACCGTTGCGG
CCTCAACCTTTCCCTTCATATCTTCATGGTATCG
Found at i:33140657 original size:239 final size:239
Alignment explanation
Indices: 33140238--33140703 Score: 923
Period size: 239 Copynumber: 1.9 Consensus size: 239
33140228 TTATCGAATG
33140238 AAATCGGTTTAGGGGGACACATTTCCCACATGTTTGCACGGAAGTGAAAACTTCACGAAAACATG
1 AAATCGGTTTAGGGGGACACATTTCCCACATGTTTGCACGGAAGTGAAAACTTCACGAAAACATG
33140303 GGTACGGATGTAATCTAGAAAGCGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGT
66 GGTACGGATGTAATCTAGAAAGCGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGT
*
33140368 AGTTTCTCGCTTCCACTTAAAGGGACAGAAATAGATGCATATGAATGCAAACTTATACTAGCAAT
131 AGTTTCCCGCTTCCACTTAAAGGGACAGAAATAGATGCATATGAATGCAAACTTATACTAGCAAT
33140433 AATATAGCATCACACAAAAATACAAAGGATCGTATATTAAACAA
196 AATATAGCATCACACAAAAATACAAAGGATCGTATATTAAACAA
33140477 AAATCGGTTTAGGGGGACACATTTCCCACATGTTTGCACGGAAGTGAAAACTTCACGAAAACATG
1 AAATCGGTTTAGGGGGACACATTTCCCACATGTTTGCACGGAAGTGAAAACTTCACGAAAACATG
33140542 GGTACGGATGTAATCTAGAAAGCGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGT
66 GGTACGGATGTAATCTAGAAAGCGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGT
33140607 AGTTTCCCGCTTCCACTTAAAGGGACAGAAATAGATGCATATGAATGCAAACTTATACTAGCAAT
131 AGTTTCCCGCTTCCACTTAAAGGGACAGAAATAGATGCATATGAATGCAAACTTATACTAGCAAT
33140672 AATATAGCATCACACAAAAATACAAAGGATCG
196 AATATAGCATCACACAAAAATACAAAGGATCG
33140704 AGTAAAACTT
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
239 226 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (239 bp):
AAATCGGTTTAGGGGGACACATTTCCCACATGTTTGCACGGAAGTGAAAACTTCACGAAAACATG
GGTACGGATGTAATCTAGAAAGCGATCCACTATCCTGCACGGAGGTGAAAACCTCACGAAGGAGT
AGTTTCCCGCTTCCACTTAAAGGGACAGAAATAGATGCATATGAATGCAAACTTATACTAGCAAT
AATATAGCATCACACAAAAATACAAAGGATCGTATATTAAACAA
Found at i:33141347 original size:59 final size:59
Alignment explanation
Indices: 33141281--33141563 Score: 263
Period size: 59 Copynumber: 4.8 Consensus size: 59
33141271 AAAGAATTTG
*
33141281 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTTATTTTAAGAAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAAGAAAGTTTAA
* * * * * *
33141340 AGGTTAAAATGTGATTTTGGGAAAG-TTAGGGGTTAAAATATAATTTTAGGAAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTA-GGGTTAAAATGTAATTTTAAGAAAGTTTAA
* ** *
33141399 GGGTCAAAATGTAATTTTAGAGTAGTTTAGGGTTAAAATGTAATTTT-GGAAAAGTTT-A
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAAG-AAAGTTTAA
* * * * * *
33141457 GGAGTTAAAATGTGATTTTA-AGAAAGTTTGGGGGTCAAATGTGATTTTATA-AAAGTTCAA
1 GG-GTTAAAATGTAATTTTAGA-AAAGTTTAGGGTTAAAATGTAATTTTA-AGAAAGTTTAA
* * * * *
33141517 GGGTTAAAATGTTATTGTA-AAGAAGTTTGCGGGTCAAAATGTGATTT
1 GGGTTAAAATGTAATTTTAGAA-AAGTTT-AGGGTTAAAATGTAATTT
33141564 CTATAAAGTT
Statistics
Matches: 183, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
58 10 0.05
59 153 0.84
60 20 0.11
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (59 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAAGAAAGTTTAA
Found at i:33141434 original size:118 final size:118
Alignment explanation
Indices: 33141281--33141563 Score: 320
Period size: 118 Copynumber: 2.4 Consensus size: 118
33141271 AAAGAATTTG
*
33141281 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTTATTTTA-AGAAAGTTTAA-AGGT
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGA-AAAGTTTAAGA-GT
** * * *
33141344 TAAAATGTGATTTTGGGAAAGTTAGGGGTTAAAATATAATTTTAGGAAAGTTTAA
64 TAAAATGTGATTTTAAGAAAGTTAGGGGGTAAAATATAATTTTAGAAAAGTTCAA
* ** * *
33141399 GGGTCAAAATGTAATTTTAGAGTAGTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGAGTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGAGTTA
* * * * *
33141464 AAATGTGATTTTAAGAAAGTTTGGGGGTCAAATGTGATTTTATAAAAGTTCAA
66 AAATGTGATTTTAAGAAAGTTAGGGGGTAAAATATAATTTTAGAAAAGTTCAA
* * * * *
33141517 GGGTTAAAATGTTATTGTA-AAGAAGTTTGCGGGTCAAAATGTGATTT
1 GGGTTAAAATGTAATTTTAGAA-AAGTTT-AGGGTTAAAATGTAATTT
33141564 CTATAAAGTT
Statistics
Matches: 137, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
117 1 0.01
118 119 0.87
119 17 0.12
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (118 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTAGGGTTAAAATGTAATTTTAGAAAAGTTTAAGAGTTA
AAATGTGATTTTAAGAAAGTTAGGGGGTAAAATATAATTTTAGAAAAGTTCAA
Found at i:33141573 original size:30 final size:29
Alignment explanation
Indices: 33141277--33141573 Score: 149
Period size: 30 Copynumber: 10.1 Consensus size: 29
33141267 TTTCAAAGAA
* * *
33141277 TTTG-GGGTTAAAATGTAATTTTAGAAAAG
1 TTTGAGGGTCAAAATGTGATTTTA-TAAAG
* * *
33141306 TTT-AGGGTTAAAATGTTATTTTAAGAAAG
1 TTTGAGGGTCAAAATGTGATTTT-ATAAAG
* * * **
33141335 TTTAAAGGTTAAAATGTGATTTTGGGAAAG
1 TTTGAGGGTCAAAATGTGATTTT-ATAAAG
* * * * *
33141365 TTAG-GGGTTAAAATATAATTTTAGGAAAG
1 TTTGAGGGTCAAAATGTGATTTTA-TAAAG
* * * *
33141394 TTTAAGGGTCAAAATGTAATTTTAGAGTAG
1 TTTGAGGGTCAAAATGTGATTTTATA-AAG
* *
33141424 TTT-AGGGTTAAAATGTAATTTTGGA-AAAG
1 TTTGAGGGTCAAAATGTGATTTT--ATAAAG
* *
33141453 TTT-AGGAGTTAAAATGTGATTTTAAGAAAG
1 TTTGAGG-GTCAAAATGTGATTTT-ATAAAG
*
33141483 TTTGGGGGTC-AAATGTGATTTTATAAAAG
1 TTTGAGGGTCAAAATGTGATTTTAT-AAAG
** * * * *
33141512 TTCAAGGGTTAAAATGTTATTGTAAAGAAG
1 TTTGAGGGTCAAAATGTGATTTTATA-AAG
*
33141542 TTTGCGGGTCAAAATGTGATTTCTATAAAG
1 TTTGAGGGTCAAAATGTGATTT-TATAAAG
33141572 TT
1 TT
33141574 CAAGGACTTA
Statistics
Matches: 215, Mismatches: 38, Indels: 29
0.76 0.13 0.10
Matches are distributed among these distances:
28 1 0.00
29 101 0.47
30 107 0.50
31 6 0.03
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
TTTGAGGGTCAAAATGTGATTTTATAAAG
Found at i:33142540 original size:17 final size:17
Alignment explanation
Indices: 33142517--33142606 Score: 108
Period size: 17 Copynumber: 5.3 Consensus size: 17
33142507 ACCAAATCAT
33142517 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
33142534 ATTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
33142551 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
* * *
33142568 CTTGAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
* *
33142585 TTTAAAGTTATTATAAA
1 TTTAAATTTATTTTAAA
33142602 TTTAA
1 TTTAA
33142607 TAAAATGTCC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:33143238 original size:26 final size:25
Alignment explanation
Indices: 33143189--33143242 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
33143179 TTGCCTCTTC
*
33143189 ATATTAATAAATATCCTTAATAATA
1 ATATTAATAAATATCATTAATAATA
* *
33143214 ATATTAATAAAATATTATTATTAATA
1 ATATTAAT-AAATATCATTAATAATA
33143240 ATA
1 ATA
33143243 AGCATAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATTAATAAATATCATTAATAATA
Found at i:33144039 original size:29 final size:30
Alignment explanation
Indices: 33143971--33144198 Score: 216
Period size: 29 Copynumber: 7.7 Consensus size: 30
33143961 GGAGGTCCCT
* *
33143971 AAACTATCCAAAAATTATA-TTTTGACCCC-
1 AAACT-TCCAAAAATTACATTTTTAACCCCG
* * *
33144000 AAACTTCTCCAAAATTATATTTTTAACCTCG
1 AAACTTC-CAAAAATTACATTTTTAACCCCG
* *
33144031 AAACTTCCAAAAATTACA-TTTCACCCCCG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * *
33144060 -AACTTTCAAAAATTCCATTTTT-ACCCCC
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * **
33144088 AAACTTCTAAAAATTCCATTTTTAACCTTG
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* * *
33144118 AAACTTCCAAAAATTGCATTTTT-ACCTCT
1 AAACTTCCAAAAATTACATTTTTAACCCCG
* *
33144147 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTACATTTTTAACCCCG
*
33144177 AAACTTCCAAAAATTACGTTTT
1 AAACTTCCAAAAATTACATTTT
33144199 ACCCTGGATA
Statistics
Matches: 165, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
28 21 0.13
29 72 0.44
30 65 0.39
31 7 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
AAACTTCCAAAAATTACATTTTTAACCCCG
Found at i:33144064 original size:59 final size:58
Alignment explanation
Indices: 33143971--33144198 Score: 194
Period size: 59 Copynumber: 3.9 Consensus size: 58
33143961 GGAGGTCCCT
* * * * * *
33143971 AAACTATCCAAAAATTATATTTTGACCCCAAACTTCTCCAAAATTATATTTTTAACCTCG
1 AAACT-TCCAAAAATTACATTTTCACCCCGAACTTCTCAAAAATTACATTTTT-ACCTCC
* *
33144031 AAACTTCCAAAAATTACA-TTTCACCCCCGAACTT-TCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTACATTTTCA-CCCCGAACTTCTCAAAAATTACATTTTTACCTCC
* * * ** * *
33144088 AAACTTCTAAAAATTCCATTTTTAACCTTGAAACTTC-CAAAAATTGCATTTTTACCTCT
1 AAACTTCCAAAAATTACA-TTTTCACCCCG-AACTTCTCAAAAATTACATTTTTACCTCC
* * * *
33144147 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTC-CAAAAATTACGTTTT
1 AAACTTCCAAAAATTACA-TTTTCACCCC-GAACTTCTCAAAAATTACATTTT
33144199 ACCCTGGATA
Statistics
Matches: 140, Mismatches: 22, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
57 20 0.14
58 21 0.15
59 94 0.67
60 5 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCCAAAAATTACATTTTCACCCCGAACTTCTCAAAAATTACATTTTTACCTCC
Found at i:33144566 original size:97 final size:100
Alignment explanation
Indices: 33144424--33144617 Score: 236
Period size: 97 Copynumber: 2.0 Consensus size: 100
33144414 TTCATAAAAA
* * * *
33144424 CTTTAAAATCGAGGCAATATTCTTTTATTTCGAATTTTAAAAATTTGTGCCTTAACTTACTAGGC
1 CTTTAAAATCGAGGCAATATTCTCTTATTTCGAATTTTAAAAATTTGTACCTAAAATTACTAGGC
*
33144489 ACGA-ATTTT-TTTCAAATCAAAATAATCGAATAT
66 ACGACATTTTCTTTAAAATCAAAATAATCGAATAT
* *
33144522 CTTT-AAATCGAGGCAATGTT-TCTTATCTTTG-ATTTTGAAAAATTTGTACCTAAAATTACTAG
1 CTTTAAAATCGAGGCAATATTCTCTTAT-TTCGAATTTT-AAAAATTTGTACCTAAAATTACTAG
** * *
33144584 GTGCGACTTTTTCTTTAAAATCAAGATAATCGAA
64 GCACGACATTTTCTTTAAAATCAAAATAATCGAA
33144618 CATCCTTTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
96 10 0.12
97 44 0.54
98 8 0.10
99 19 0.23
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (100 bp):
CTTTAAAATCGAGGCAATATTCTCTTATTTCGAATTTTAAAAATTTGTACCTAAAATTACTAGGC
ACGACATTTTCTTTAAAATCAAAATAATCGAATAT
Found at i:33156352 original size:92 final size:92
Alignment explanation
Indices: 33156195--33156423 Score: 379
Period size: 92 Copynumber: 2.5 Consensus size: 92
33156185 AAAATAACAA
* * * *
33156195 TAAGTCTTTATCTCTTTGAAGTTGTAGTAAGACCAAGATGAACCTTCAAATATCAATTCCTATCC
1 TAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTCCAAATATCAATTCCTATCC
33156260 TCTTGAAGTTGCAGTAAAGTTGGATAG
66 TCTTGAAGTTGCAGTAAAGTTGGATAG
*
33156287 TAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTCCAAA-ATTCAATTCCTATC
1 TAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTCCAAATA-TCAATTCCTATC
33156351 CTCTTGAAGTTGCAGTAAAGTTGGATAG
65 CTCTTGAAGTTGCAGTAAAGTTGGATAG
* *
33156379 CAAGTCTTTATCTCTCTGATGTTGTAGTAAGAGCAAGATGAAGCT
1 TAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCT
33156424 TCGATACCAA
Statistics
Matches: 128, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
91 1 0.01
92 127 0.99
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (92 bp):
TAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTCCAAATATCAATTCCTATCC
TCTTGAAGTTGCAGTAAAGTTGGATAG
Found at i:33156468 original size:92 final size:91
Alignment explanation
Indices: 33156196--33156450 Score: 375
Period size: 92 Copynumber: 2.8 Consensus size: 91
33156186 AAATAACAAT
* * *
33156196 AAGTCTTTATCTCTTTGAAGTTGTAGTAAGACCAAGATGAACCTTCAAATATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTC-AATATCAATTCCTATCCT
*
33156261 CTTGAAGTTGCAGTAAAGTTGGATAGT
65 CTTGAAGTTGCAGTAAAGTTGGATAGC
* * *
33156288 AAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTCCAAAATTCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAATA-TCAATTCCTATCCT
33156353 CTTGAAGTTGCAGTAAAGTTGGATAGC
65 CTTGAAGTTGCAGTAAAGTTGGATAGC
* * * * *
33156380 AAGTCTTTATCTCTCTGATGTTGTAGTAAGAGCAAGATGAAGCTTCGATACCAAATCCTATCTTC
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAATATCAATTCCTATCCTC
*
33156445 ATGAAG
66 TTGAAG
33156451 ATGTAGTGGA
Statistics
Matches: 146, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 20 0.14
92 126 0.86
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (91 bp):
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAATATCAATTCCTATCCTC
TTGAAGTTGCAGTAAAGTTGGATAGC
Found at i:33157124 original size:6 final size:6
Alignment explanation
Indices: 33157104--33157164 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
33157094 ACCAAACCAT
* * * *
33157104 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG CTTGAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33157149 TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTA
33157165 CTATAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 14 0.31
6 31 0.69
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:33157126 original size:17 final size:17
Alignment explanation
Indices: 33157104--33157176 Score: 92
Period size: 17 Copynumber: 4.3 Consensus size: 17
33157094 ACCAAACCAT
*
33157104 TTTAAATTTATTTTAAA
1 TTTAAATTTAATTTAAA
*
33157121 TTTAAATTTAATTTAAG
1 TTTAAATTTAATTTAAA
* *
33157138 CTTGAATTTAATTTAAA
1 TTTAAATTTAATTTAAA
* *
33157155 TTTAAATTTACTATAAA
1 TTTAAATTTAATTTAAA
33157172 TTTAA
1 TTTAA
33157177 TAAAATGTCC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:33157133 original size:11 final size:11
Alignment explanation
Indices: 33157104--33157164 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
33157094 ACCAAACCAT
*
33157104 TTTAAATTTAT
1 TTTAAATTTAA
33157115 TTTAAATTTAAA
1 TTTAAATTT-AA
33157127 TTT-AATTTAA
1 TTTAAATTTAA
* *
33157137 GCTTGAATTTAA
1 -TTTAAATTTAA
33157149 TTTAAATTTAAA
1 TTTAAATTT-AA
33157161 TTTA
1 TTTA
33157165 CTATAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 2 0.05
11 23 0.55
12 17 0.40
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:33157173 original size:28 final size:28
Alignment explanation
Indices: 33157119--33157177 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
33157109 ATTTATTTTA
*
33157119 AATTTAAATTTAATTTAAGCTTGAATTT
1 AATTTAAATTTAATTTAAGCTTAAATTT
33157147 AATTTAAATTTAAATTT-A-CTATAAATTT
1 AATTTAAATTT-AATTTAAGCT-TAAATTT
33157175 AAT
1 AAT
33157178 AAAATGTCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 21 0.75
29 5 0.18
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTTAAATTTAATTTAAGCTTAAATTT
Found at i:33157319 original size:21 final size:21
Alignment explanation
Indices: 33157295--33157356 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
33157285 AAAGGACCCA
33157295 AACCCTATGACCCATATCCTT
1 AACCCTATGACCCATATCCTT
* **
33157316 AACCC-ATTA--C--A-CCCA
1 AACCCTATGACCCATATCCTT
33157331 AACCCTATGACCCATATCCTT
1 AACCCTATGACCCATATCCTT
33157352 AACCC
1 AACCC
33157357 ATTACACCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
18 2 0.07
20 4 0.14
21 12 0.41
ACGTcount: A:0.32, C:0.42, G:0.03, T:0.23
Consensus pattern (21 bp):
AACCCTATGACCCATATCCTT
Found at i:33157331 original size:36 final size:36
Alignment explanation
Indices: 33157290--33157372 Score: 166
Period size: 36 Copynumber: 2.3 Consensus size: 36
33157280 ACAAAAAAGG
33157290 ACCCAAACCCTATGACCCATATCCTTAACCCATTAC
1 ACCCAAACCCTATGACCCATATCCTTAACCCATTAC
33157326 ACCCAAACCCTATGACCCATATCCTTAACCCATTAC
1 ACCCAAACCCTATGACCCATATCCTTAACCCATTAC
33157362 ACCCAAACCCT
1 ACCCAAACCCT
33157373 GAAGCACCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.34, C:0.43, G:0.02, T:0.20
Consensus pattern (36 bp):
ACCCAAACCCTATGACCCATATCCTTAACCCATTAC
Found at i:33157860 original size:12 final size:12
Alignment explanation
Indices: 33157845--33157871 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
33157835 ATAAATATCC
33157845 TTAATAATAATA
1 TTAATAATAATA
33157857 TTAATAATAATA
1 TTAATAATAATA
33157869 TTA
1 TTA
33157872 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAATAATAATA
Found at i:33159095 original size:30 final size:30
Alignment explanation
Indices: 33159028--33159095 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
33159018 ATAAACTGTC
* *
33159028 CAAAAATTATATTTTGACCCCAAACTTCTT
1 CAAAAATTATATTTTAACCCCAAAATTCTT
* *
33159058 C-AAAATTATGTTTTTAACCCTAAAATT-TT
1 CAAAAATTAT-ATTTTAACCCCAAAATTCTT
33159087 CAAAAATTA
1 CAAAAATTA
33159096 CATGTTCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (30 bp):
CAAAAATTATATTTTAACCCCAAAATTCTT
Found at i:33159135 original size:29 final size:28
Alignment explanation
Indices: 33159020--33159221 Score: 129
Period size: 29 Copynumber: 6.9 Consensus size: 28
33159010 GGAGGTCCAT
* *
33159020 AAACTGTCCAAAAATTATATTTTGACCCC-
1 AAACT-TCC-AAAATTACATTTTTACCCCA
** *
33159049 AAACTTCTTCAAAATTATGTTTTTAACCCTA
1 AAACTTC--CAAAATTACATTTTT-ACCCCA
* * * * *
33159080 AAATTTTCAAAAATTACATGTTCACCCCC
1 AAA-CTTCCAAAATTACATTTTTACCCCA
* **
33159109 GAACTTCCAAGAATTACATTTTTACCCTT
1 AAACTTCCAA-AATTACATTTTTACCCCA
*
33159138 AAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCC-AAAATTACATTTTT-ACCCCA
* * *
33159168 AAACTTTCAAAATTCCATTTTTACCCTA
1 AAACTTCCAAAATTACATTTTTACCCCA
* *
33159196 AAACTTCTAAAAATTCCA-TTTTACCC
1 AAACTTC-CAAAATTACATTTTTACCC
33159222 GCGAATATCC
Statistics
Matches: 138, Mismatches: 26, Indels: 19
0.75 0.14 0.10
Matches are distributed among these distances:
28 26 0.19
29 78 0.57
30 28 0.20
31 3 0.02
32 3 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
AAACTTCCAAAATTACATTTTTACCCCA
Found at i:33159187 original size:58 final size:57
Alignment explanation
Indices: 33159020--33159217 Score: 193
Period size: 58 Copynumber: 3.4 Consensus size: 57
33159010 GGAGGTCCAT
* **
33159020 AAACTGTCCAAAAATT--ATATTTTGACCCCAAACTTCTTCAAAATTATGTTTTTAACCCTA
1 AAACT-TCCAAAAATTCCAT-TTTTAACCCCAAAC-T-TTCAAAATTACATTTTT-ACCCTA
* * * * * * * * *
33159080 AAATTTTCAAAAATTACATGTTCACCCCCGAACTTCCAAGAATTACATTTTTACCCTT
1 AAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCAA-AATTACATTTTTACCCTA
*
33159138 AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCAAAATTCCATTTTTACCCTA
1 AAACTTCCAAAAATTCCATTTTTAACCCC-AAACTTTCAAAATTACATTTTTACCCTA
*
33159196 AAACTTCTAAAAATTCCATTTT
1 AAACTTCCAAAAATTCCATTTT
33159218 ACCCGCGAAT
Statistics
Matches: 112, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
58 69 0.62
59 28 0.25
60 13 0.12
61 2 0.02
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTAACCCCAAACTTTCAAAATTACATTTTTACCCTA
Found at i:33162573 original size:14 final size:15
Alignment explanation
Indices: 33162534--33162571 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
33162524 GTATTAAGTG
*
33162534 TTAATTGTTTAGTGT
1 TTAATTGTTTAATGT
*
33162549 TT-AGTGTTTAATGT
1 TTAATTGTTTAATGT
33162563 TTAATTGTT
1 TTAATTGTT
33162572 AAAAGAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (15 bp):
TTAATTGTTTAATGT
Found at i:33167069 original size:2 final size:2
Alignment explanation
Indices: 33167062--33167086 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
33167052 GATGAAATAC
33167062 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
33167087 AATTAACAGC
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:33173716 original size:36 final size:36
Alignment explanation
Indices: 33173669--33173741 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
33173659 AGTTGAATTA
* * *
33173669 ACAGTATGTTGTTAGAGTGCTGTTATCACTTCTTGT
1 ACAGTACGTTGTTAGAGTGCAGTTACCACTTCTTGT
33173705 ACAGTACGTTGTTAGAGTGCAGTTACCACTTCTTGT
1 ACAGTACGTTGTTAGAGTGCAGTTACCACTTCTTGT
33173741 A
1 A
33173742 TATACAAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (36 bp):
ACAGTACGTTGTTAGAGTGCAGTTACCACTTCTTGT
Found at i:33175849 original size:22 final size:20
Alignment explanation
Indices: 33175801--33175850 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
33175791 TGCTTATATA
33175801 TTTTTTATTTCAGTTTTACT
1 TTTTTTATTTCAGTTTTACT
*
33175821 TAATTTTTATTTACTAGTTTTAGT
1 T--TTTTTATTT-C-AGTTTTACT
33175845 TTTTTT
1 TTTTTT
33175851 TTTTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 14 0.56
23 1 0.04
24 9 0.36
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (20 bp):
TTTTTTATTTCAGTTTTACT
Found at i:33175851 original size:24 final size:22
Alignment explanation
Indices: 33175799--33175852 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
33175789 TTTGCTTATA
33175799 TATTTTTTATTTCAGTTTTACT
1 TATTTTTTATTTCAGTTTTACT
* *
33175821 TAATTTTTATTTACTAGTTTTAGT
1 TATTTTTTATTT-C-AGTTTTACT
*
33175845 TTTTTTTT
1 TATTTTTT
33175853 TTGAATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 11 0.42
23 1 0.04
24 14 0.54
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.70
Consensus pattern (22 bp):
TATTTTTTATTTCAGTTTTACT
Found at i:33176373 original size:22 final size:22
Alignment explanation
Indices: 33176345--33176387 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
33176335 TAGTGGTGCT
33176345 TTTCCCACAAACGCCGCTAAAA
1 TTTCCCACAAACGCCGCTAAAA
*
33176367 TTTCCCACAAATGCCGCTAAA
1 TTTCCCACAAACGCCGCTAAA
33176388 GAACATGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.35, G:0.09, T:0.21
Consensus pattern (22 bp):
TTTCCCACAAACGCCGCTAAAA
Found at i:33176827 original size:66 final size:66
Alignment explanation
Indices: 33176704--33176828 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
33176694 CTGTAGCTAT
* * *
33176704 AGTTCGTCATACTTTCTTTGAGACTCTGCTTCCTTCGCTGCTATCTTGGCTTCAAGTTGTAGTTG
1 AGTTCATCATACTTTCTTTGAGACTCTGCTTCCTTCGCTGCTACCTTCGCTTCAAGTTGTAGTTG
33176769 A
66 A
* * * * *
33176770 AGTTCATCATATTTTCTTTGAGCCTCTGCTTCTCTT-GTTGCTGCCTTCGCTTTAAGTTG
1 AGTTCATCATACTTTCTTTGAGACTCTGCTTC-CTTCGCTGCTACCTTCGCTTCAAGTTG
33176829 AGCAATTTGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 47 0.94
67 3 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (66 bp):
AGTTCATCATACTTTCTTTGAGACTCTGCTTCCTTCGCTGCTACCTTCGCTTCAAGTTGTAGTTG
A
Found at i:33180430 original size:27 final size:25
Alignment explanation
Indices: 33180369--33180432 Score: 110
Period size: 25 Copynumber: 2.5 Consensus size: 25
33180359 ATTATTTTGA
33180369 TTTTAAAATTAATTTGTTATTACTT
1 TTTTAAAATTAATTTGTTATTACTT
33180394 TTTTAAAATTAATTTGTTATTACTTTT
1 TTTTAAAATTAATTTGTTATTAC--TT
33180421 TTTTAAAATTAA
1 TTTTAAAATTAA
33180433 ATTAAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 23 0.62
27 14 0.38
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTTAAAATTAATTTGTTATTACTT
Found at i:33198501 original size:9 final size:9
Alignment explanation
Indices: 33198487--33198515 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
33198477 GTTAATTGAA
33198487 TCGAGTTAT
1 TCGAGTTAT
33198496 TCGAGTTAT
1 TCGAGTTAT
33198505 TCGAGTTAT
1 TCGAGTTAT
33198514 TC
1 TC
33198516 AAATTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.45
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:33198522 original size:18 final size:18
Alignment explanation
Indices: 33198487--33198524 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33198477 GTTAATTGAA
* *
33198487 TCGAGTTATTCGAGTTAT
1 TCGAGTTATTCAAATTAT
33198505 TCGAGTTATTCAAATTAT
1 TCGAGTTATTCAAATTAT
33198523 TC
1 TC
33198525 AAGTCAACTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (18 bp):
TCGAGTTATTCAAATTAT
Found at i:33198664 original size:31 final size:31
Alignment explanation
Indices: 33198626--33198689 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
33198616 ACCCCTATAA
*
33198626 TAGATGTAACATATTCCTTTATGGTTTTGTC
1 TAGATGTAACATATTCCTTTAAGGTTTTGTC
*
33198657 TAGATGTAACATATTCCTTTAAGTTTTTGTC
1 TAGATGTAACATATTCCTTTAAGGTTTTGTC
33198688 TA
1 TA
33198690 TGTAAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.48
Consensus pattern (31 bp):
TAGATGTAACATATTCCTTTAAGGTTTTGTC
Found at i:33202075 original size:27 final size:27
Alignment explanation
Indices: 33202040--33202103 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
33202030 TTTCTTATTA
* *
33202040 GCCATAAAGGCTTCCTTTATAAAGATT
1 GCCACAAAGGCTTCCTTTACAAAGATT
*
33202067 GTCACAAAGGCTTCCTTTACAAAGATT
1 GCCACAAAGGCTTCCTTTACAAAGATT
33202094 GCCACAAAGG
1 GCCACAAAGG
33202104 TATTTCCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (27 bp):
GCCACAAAGGCTTCCTTTACAAAGATT
Found at i:33203916 original size:74 final size:74
Alignment explanation
Indices: 33203795--33203940 Score: 249
Period size: 74 Copynumber: 2.0 Consensus size: 74
33203785 ACTCGCCATG
*
33203795 AAGCTCCACAGTGGACCAATCCTCTAACTTCTTTTTATTTGTCAGCAACTCTTTTAAAAATTTTG
1 AAGCTCCACAGTGGACCAATCCTCTAACTTCCTTTTATTTGTCAGCAACTCTTTTAAAAATTTTG
33203860 CATAAGTTT
66 CATAAGTTT
* *
33203869 AAGCTCCACAGTGGA-CAACTCCTCTCACTTCCTTTTATTTTTCAGCAACTCTTTTAAAAATTTT
1 AAGCTCCACAGTGGACCAA-TCCTCTAACTTCCTTTTATTTGTCAGCAACTCTTTTAAAAATTTT
33203933 GCATAAGT
65 GCATAAGT
33203941 GGGCATCTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 3 0.04
74 65 0.96
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (74 bp):
AAGCTCCACAGTGGACCAATCCTCTAACTTCCTTTTATTTGTCAGCAACTCTTTTAAAAATTTTG
CATAAGTTT
Found at i:33205660 original size:19 final size:19
Alignment explanation
Indices: 33205618--33205678 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
33205608 TAAAAGGGAA
*
33205618 AAAATT-AAAATAGAAAAAT
1 AAAATTAAAAAT-GAATAAT
*
33205637 TAAATTAAAAATGAATAAT
1 AAAATTAAAAATGAATAAT
*
33205656 AAAA-TAAAAATAAATAACT
1 AAAATTAAAAATGAATAA-T
33205675 AAAA
1 AAAA
33205679 ATATGACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 12 0.33
19 19 0.53
20 5 0.14
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATTAAAAATGAATAAT
Found at i:33205663 original size:18 final size:19
Alignment explanation
Indices: 33205618--33205678 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
33205608 TAAAAGGGAA
* * *
33205618 AAAATTAAAATAGAAAAATT
1 AAAATAAAAAT-GAATAACT
*
33205638 AAATTAAAAATGAATAA-T
1 AAAATAAAAATGAATAACT
*
33205656 AAAATAAAAATAAATAACT
1 AAAATAAAAATGAATAACT
33205675 AAAA
1 AAAA
33205679 ATATGACTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 16 0.46
19 10 0.29
20 9 0.26
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATAAAAATGAATAACT
Found at i:33206685 original size:25 final size:23
Alignment explanation
Indices: 33206657--33206702 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
33206647 GTTGGATCCA
33206657 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
33206682 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
33206703 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:33206794 original size:13 final size:13
Alignment explanation
Indices: 33206773--33206806 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33206763 ACAATATAAC
33206773 AATAATAATCTTA
1 AATAATAATCTTA
*
33206786 AATATTAATCTTA
1 AATAATAATCTTA
*
33206799 AAAAATAA
1 AATAATAA
33206807 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (13 bp):
AATAATAATCTTA
Found at i:33207354 original size:20 final size:19
Alignment explanation
Indices: 33207329--33207380 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
33207319 AATTACAAAA
* *
33207329 AAAAATTTAATATATTTTT
1 AAAAATTTAAAATATTTAT
*
33207348 CAAAAATTCAAAATATTTAT
1 -AAAAATTTAAAATATTTAT
33207368 AAAAATTTCAAAA
1 AAAAATTT-AAAA
33207381 AAAATCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 7 0.26
20 20 0.74
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:33210928 original size:21 final size:20
Alignment explanation
Indices: 33210904--33210950 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
33210894 TTAACTAATT
33210904 TTTTTAAATATTTTTTTATA
1 TTTTTAAATATTTTTTTATA
* *
33210924 ATTTTATAATATAGTTTTTATA
1 TTTTTA-AATAT-TTTTTTATA
33210946 TTTTT
1 TTTTT
33210951 GAATTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTAAATATTTTTTTATA
Found at i:33220683 original size:173 final size:174
Alignment explanation
Indices: 33220338--33220689 Score: 390
Period size: 173 Copynumber: 2.0 Consensus size: 174
33220328 CAGTCACTCT
*
33220338 AGTTTCAATTCAGTCACTCAATTTTAAAAAAAATAATAAAATAATCACTAACGTTATCAAAAAAT
1 AGTTTCAATTCAGTCACTCAACTTTAAAAAAAATAATAAAATAATCACTAACGTTATCAAAAAAT
* * *
33220403 GACAAATCAATCACCCATTAACATTTTTCATTACCAGCCTAACGGGACAACTGACGTGACCAATT
66 GACAAATCAATCACCCATTAACATTTTTCATTACCAGCCTAACGAGACAACTGACATGACCAATA
* ** **
33220468 AACTACCTGACATAGTCAATTAACTTGCCATGTTGGACGAGGCAA
131 AACTACCTGA-ATAGCCAATTAACTTGCCACATCAGACGAGGCAA
* * *
33220513 AGTTTCAATTCAGTCACTCAACTTT-CAAAAAATAA-CAAATCAAT-ACTAACGTTATCAAAAAG
1 AGTTTCAATTCAGTCACTCAACTTTAAAAAAAATAATAAAAT-AATCACTAACGTTATCAAAAAA
* * ** * ** **
33220575 TGACAAATCAGTCACTCATTAACATTTTTTGTTA-TAGGCCTAACGAGACAGGTGACATGGTCAA
65 TGACAAATCAATCACCCATTAACATTTTTCATTACCA-GCCTAACGAGACAACTGACATGACCAA
* ** * *
33220639 TAAATTAGTTG-ATGAGGCCAGTTAACTTGCCACATCATACGAGGCAA
129 TAAACTACCTGAAT-A-GCCAATTAACTTGCCACATCAGACGAGGCAA
33220686 AGTT
1 AGTT
33220690 GAGTGATTGT
Statistics
Matches: 147, Mismatches: 26, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
171 2 0.01
172 2 0.01
173 107 0.73
174 12 0.08
175 24 0.16
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (174 bp):
AGTTTCAATTCAGTCACTCAACTTTAAAAAAAATAATAAAATAATCACTAACGTTATCAAAAAAT
GACAAATCAATCACCCATTAACATTTTTCATTACCAGCCTAACGAGACAACTGACATGACCAATA
AACTACCTGAATAGCCAATTAACTTGCCACATCAGACGAGGCAA
Found at i:33228789 original size:13 final size:13
Alignment explanation
Indices: 33228767--33228804 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
33228757 AACTGATACT
33228767 TAACAGACTTAAC
1 TAACAGACTTAAC
*
33228780 TAACAAACTTAAC
1 TAACAGACTTAAC
33228793 TAACAGACTTAA
1 TAACAGACTTAA
33228805 TTGCTAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (13 bp):
TAACAGACTTAAC
Found at i:33229908 original size:29 final size:28
Alignment explanation
Indices: 33229876--33229937 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
33229866 TCACTTGTAT
*
33229876 AATTG-CATCAAATTAAAGTTCATGTATAC
1 AATTGACATCAAATCAAAGTTCATG-A-AC
*
33229905 AATTGCACATTAAATCAAAGTTCATGAAC
1 AATTG-ACATCAAATCAAAGTTCATGAAC
33229934 AATT
1 AATT
33229938 TTGAGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.38
30 1 0.03
31 17 0.59
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (28 bp):
AATTGACATCAAATCAAAGTTCATGAAC
Found at i:33230907 original size:28 final size:29
Alignment explanation
Indices: 33230846--33230912 Score: 109
Period size: 28 Copynumber: 2.3 Consensus size: 29
33230836 AATATAACAA
*
33230846 TTGGCATCTGAACTTAACATTTTTTTTAAT
1 TTGGTATCTGAACTTAACA-TTTTTTTAAT
33230876 TTGGTATCTGAACTTAACA-TTTTTTAAT
1 TTGGTATCTGAACTTAACATTTTTTTAAT
33230904 TTGGTATCT
1 TTGGTATCT
33230913 TTGGTATCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 18 0.50
30 18 0.50
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (29 bp):
TTGGTATCTGAACTTAACATTTTTTTAAT
Found at i:33231013 original size:59 final size:57
Alignment explanation
Indices: 33230912--33231049 Score: 136
Period size: 59 Copynumber: 2.4 Consensus size: 57
33230902 ATTTGGTATC
* ** *
33230912 TTTGGTATCTAAACTTTTTTTATCCAATTTAGTATTTAAACTTGACACTT-TTTCTTAA
1 TTTGGTACCTAAA-TTTTTTTATCCAATTTAGTACCTAAACTTGACA-TTCTTTCCTAA
*
33230970 TTTGGTACCTAAATTTTTTTGGATCCAATTT-GATACCTGAACTTGACATTCTTTCCTAA
1 TTTGGTACCTAAATTTTTTT--ATCCAATTTAG-TACCTAAACTTGACATTCTTTCCTAA
** *
33231029 TTAAGTACCTAAGCTTTTTTT
1 TTTGGTACCTAA-ATTTTTTT
33231050 TAGATTTAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
57 7 0.10
58 15 0.22
59 38 0.57
60 7 0.10
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (57 bp):
TTTGGTACCTAAATTTTTTTATCCAATTTAGTACCTAAACTTGACATTCTTTCCTAA
Found at i:33231285 original size:60 final size:59
Alignment explanation
Indices: 33231211--33231342 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 59
33231201 TAAAAAAAGA
*** *
33231211 TTAGGTACCAAATTGAACCCCAAAAAGTCTAAG-TACCAACTTAAAAAAAAAGTGTCAAGT
1 TTAGGTACCAAATTGAACAAAAAAAAGT-TAAGATACCAAATTAAAAAAAAA-TGTCAAGT
* * * *
33231271 TTAGGTAACAAATTGGACAAAAAAAAGTTTAGATACCAAATTAAGAAAAAATGTCAAGT
1 TTAGGTACCAAATTGAACAAAAAAAAGTTAAGATACCAAATTAAAAAAAAATGTCAAGT
*
33231330 TTAAGTACCAAAT
1 TTAGGTACCAAAT
33231343 ATTATATTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 22 0.36
60 39 0.64
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (59 bp):
TTAGGTACCAAATTGAACAAAAAAAAGTTAAGATACCAAATTAAAAAAAAATGTCAAGT
Found at i:33231320 original size:28 final size:28
Alignment explanation
Indices: 33231267--33231321 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
33231257 AAAAAGTGTC
* *
33231267 AAGTTTAGGTAACAAATTGGACAAAAAA
1 AAGTTTAGATAACAAATTAGACAAAAAA
* *
33231295 AAGTTTAGATACCAAATTA-AGAAAAAA
1 AAGTTTAGATAACAAATTAGACAAAAAA
33231322 TGTCAAGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (28 bp):
AAGTTTAGATAACAAATTAGACAAAAAA
Found at i:33234470 original size:29 final size:28
Alignment explanation
Indices: 33234367--33234469 Score: 102
Period size: 28 Copynumber: 3.6 Consensus size: 28
33234357 GGATACTTGG
* **
33234367 GGGTAAAATGGTAATTTTGGACTTTTAA
1 GGGTAAAATGGTAATTTTAGACAATTAA
* **
33234395 GGGTAAAATGGTAATTTTAGAAAATTTG
1 GGGTAAAATGGTAATTTTAGACAATTAA
*
33234423 GGGTTAAAAAT-G-ACATTTTAGACACTTAA
1 GGG-T-AAAATGGTA-ATTTTAGACAATTAA
33234452 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
33234470 TGAAAGAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
27 5 0.08
28 33 0.55
29 17 0.28
30 5 0.08
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGACAATTAA
Found at i:33234657 original size:145 final size:144
Alignment explanation
Indices: 33234367--33234672 Score: 357
Period size: 145 Copynumber: 2.1 Consensus size: 144
33234357 GGATACTTGG
* * * *
33234367 GGGTAAAATGGTAATTTTGGACTTTTAAGGGTAAAATGGTAATTTTAGAAAATTTGGGGTTAAAA
1 GGGTAAAATGGTAATTTTGGACTCTCAAGGGCAAAATGGTAATTTTAGAAAATTTAGGGTTAAAA
* * * *
33234432 ATGACATTTTAGACACTTAAGGGTAAAATGGTAATTTTTGAAAGAATCGAGATAAAAACGGGACT
66 ATGAAATTTTAGACAATCAAGGGTAAAATAGTAATTTTTGAAAGAATCGAGATAAAAACGGGACT
* **
33234497 TTTTGGATGCCCGA
131 TTATGGACACCCGA
* *
33234511 GGGTAAAATGGTAATTTTGGACTCTCGA-GGCAAAATGGTAATTTTAGGAAAATTTTAGTGTTAA
1 GGGTAAAATGGTAATTTTGGACTCTCAAGGGCAAAATGGTAATTTTA-GAAAA-TTTAGGGTTAA
* * * * * **
33234575 AAATGAAATTTTAGATAATCGAGGGTAAAGTAGTAATTTTTAGAAA-AATTGGGATAAAAAATTG
64 AAATGAAATTTTAGACAATCAAGGGTAAAATAGTAATTTTT-GAAAGAATCGAGAT-AAAAACGG
**
33234639 G-CTTTATGGACATTCGA
127 GACTTTATGGACACCCGA
33234656 GGGTAAAATGGTAATTT
1 GGGTAAAATGGTAATTT
33234673 CAAGAGTTTC
Statistics
Matches: 136, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
143 17 0.12
144 30 0.22
145 78 0.57
146 11 0.08
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (144 bp):
GGGTAAAATGGTAATTTTGGACTCTCAAGGGCAAAATGGTAATTTTAGAAAATTTAGGGTTAAAA
ATGAAATTTTAGACAATCAAGGGTAAAATAGTAATTTTTGAAAGAATCGAGATAAAAACGGGACT
TTATGGACACCCGA
Found at i:33234811 original size:59 final size:59
Alignment explanation
Indices: 33234684--33234888 Score: 166
Period size: 59 Copynumber: 3.4 Consensus size: 59
33234674 AAGAGTTTCA
* *
33234684 AGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAGTGTAATTTTTGGAAGTTTTAGG
1 AGGT-AAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGAATTTTTGGAAG-TTTAGG
* * * * *
33234745 -GGCAAAATTGGAATTTTTGGAAGCTT-GGGGGTAAAAATGGAATTTTTGGAAG-TTCGG
1 AGGTAAAAATGGAATTTTTGGAAG-TTCGAGGGCAAAAATGGAATTTTTGGAAGTTTAGG
*** * * * * *
33234802 AGGTAAAAATGGAATTTTCAAAAGTTTCAAGGTCAAAAATGTAATTTTGGAGAAG-TTCGG
1 AGGTAAAAATGGAATTTTTGGAAG-TTCGAGGGCAAAAATGGAATTTTTG-GAAGTTTAGG
* **
33234862 AGGTCAAAATATAATTTTTGGACAGTT
1 AGGTAAAAATGGAATTTTTGGA-AGTT
33234889 TAGAGACCTT
Statistics
Matches: 114, Mismatches: 25, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
57 4 0.04
58 20 0.18
59 57 0.50
60 31 0.27
61 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (59 bp):
AGGTAAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTAGG
Found at i:33234839 original size:88 final size:88
Alignment explanation
Indices: 33234689--33234849 Score: 207
Period size: 88 Copynumber: 1.8 Consensus size: 88
33234679 TTTCAAGGTC
* * *** * * *
33234689 AAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAGTGTAATTTTTGGAAGTTTTAGGGGCAAAATT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGAATTTTCAAAAGTTTCAAGGGCAAAAAT
33234754 GGAATTTTTGGAAGCTTGGGGGT
66 GGAATTTTTGGAAGCTTGGGGGT
* *
33234777 AAAAATGGAATTTTTGGAAGTTCG-GAGGTAAAAATGGAATTTTCAAAAGTTTCAAGGTCAAAAA
1 AAAAATGGAATTTTTGGAAGTTCGAG-GGCAAAAATGGAATTTTCAAAAGTTTCAAGGGCAAAAA
*
33234841 TGTAATTTT
65 TGGAATTTT
33234850 GGAGAAGTTC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
87 1 0.02
88 60 0.98
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (88 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGCAAAAATGGAATTTTCAAAAGTTTCAAGGGCAAAAAT
GGAATTTTTGGAAGCTTGGGGGT
Found at i:33234842 original size:30 final size:30
Alignment explanation
Indices: 33234677--33234889 Score: 161
Period size: 29 Copynumber: 7.2 Consensus size: 30
33234667 TAATTTCAAG
33234677 AGTTTCAAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGA
* * * *
33234707 AG-TTCGAGGGCAAAAGTGTAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGA
* * * *
33234736 AGTTTTAGGGGCAAAATTGGAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGA
* ***
33234766 AGCTTGGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTGGA
* ***
33234795 AG-TTCGGAGGT-AAAAATGGAATTTTCAAA
1 AGTTTC-AAGGTCAAAAATGGAATTTTTGGA
* *
33234824 AGTTTCAAGGTCAAAAATGTAATTTTGGAGA
1 AGTTTCAAGGTCAAAAATGGAATTTTTG-GA
*
33234855 AG-TTCGGAGGTCAAAATAT--AATTTTTGGA
1 AGTTTC-AAGGTCAAAA-ATGGAATTTTTGGA
33234884 CAGTTT
1 -AGTTT
33234890 AGAGACCTTC
Statistics
Matches: 148, Mismatches: 26, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 71 0.48
30 59 0.40
31 14 0.09
32 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (30 bp):
AGTTTCAAGGTCAAAAATGGAATTTTTGGA
Found at i:33236158 original size:3 final size:3
Alignment explanation
Indices: 33236111--33236142 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
33236101 ATAATAATAA
*
33236111 TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
33236143 GTAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:33236932 original size:17 final size:17
Alignment explanation
Indices: 33236912--33236958 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
33236902 AAATTTTATT
33236912 AAATTTAAATTCAAAAC
1 AAATTTAAATTCAAAAC
* *
33236929 AAATTTAAATT-TAAAT
1 AAATTTAAATTCAAAAC
*
33236945 AAATTTAAAATCAA
1 AAATTTAAATTCAA
33236959 TTCAAACTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (17 bp):
AAATTTAAATTCAAAAC
Found at i:33236947 original size:27 final size:28
Alignment explanation
Indices: 33236917--33236987 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
33236907 TTATTAAATT
* *
33236917 TAAATTCAAAA-CAAATTTAAATTTAA-A
1 TAAATTCAAAATC-AATTCAAACTTAATA
*
33236944 TAAATTTAAAATCAATTCAAACTTAATA
1 TAAATTCAAAATCAATTCAAACTTAATA
33236972 TAAATTCAAAAATCAA
1 TAAATTC-AAAATCAA
33236988 AAATTTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 21 0.57
28 8 0.22
29 8 0.22
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAATTCAAAATCAATTCAAACTTAATA
Found at i:33236950 original size:16 final size:16
Alignment explanation
Indices: 33236899--33236953 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
33236889 TTGAAACCAT
* *
33236899 TTTAAATTTTATTAAA
1 TTTAAATTTAAATAAA
* *
33236915 TTTAAATTCAAAACAAA
1 TTTAAATT-TAAATAAA
33236932 TTTAAATTTAAATAAA
1 TTTAAATTTAAATAAA
33236948 TTTAAA
1 TTTAAA
33236954 ATCAATTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 20 0.62
17 12 0.38
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:33239766 original size:36 final size:36
Alignment explanation
Indices: 33239712--33239780 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
33239702 AATCATATGA
33239712 CATGAAGAAAATACCCACATATTTTCTGTCACATGG
1 CATGAAGAAAATACCCACATATTTTCTGTCACATGG
* * * *
33239748 CATGAATAACATATCCACATATTTTCTTTCACA
1 CATGAAGAAAATACCCACATATTTTCTGTCACA
33239781 ACAATTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (36 bp):
CATGAAGAAAATACCCACATATTTTCTGTCACATGG
Found at i:33241767 original size:28 final size:28
Alignment explanation
Indices: 33241735--33241796 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
33241725 AAAACGGGAC
*
33241735 TTTTGGATACCCGGGGGCAAAATGGTAA
1 TTTTGGACACCCGGGGGCAAAATGGTAA
* **
33241763 TTTTGGACGCGTGGGGGCAAAATGGTAA
1 TTTTGGACACCCGGGGGCAAAATGGTAA
33241791 TTTTGG
1 TTTTGG
33241797 TTAAACCAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.35, T:0.29
Consensus pattern (28 bp):
TTTTGGACACCCGGGGGCAAAATGGTAA
Found at i:33241851 original size:38 final size:38
Alignment explanation
Indices: 33241792--33241869 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
33241782 AAATGGTAAT
* *
33241792 TTTGGTTAAACCAGGGTTAAAAATGGAATTTTGGAAAC
1 TTTGGTGAAACCAGGGCTAAAAATGGAATTTTGGAAAC
*
33241830 TTTGGTGAAACTAGGGCTAAAAATGGAATTTTGGAAAC
1 TTTGGTGAAACCAGGGCTAAAAATGGAATTTTGGAAAC
33241868 TT
1 TT
33241870 CGGGGGGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (38 bp):
TTTGGTGAAACCAGGGCTAAAAATGGAATTTTGGAAAC
Found at i:33241958 original size:59 final size:59
Alignment explanation
Indices: 33241830--33242189 Score: 444
Period size: 59 Copynumber: 6.1 Consensus size: 59
33241820 TTTTGGAAAC
* * ** *
33241830 TTTGGTGAAA-CTAGGGCTAAAAATGGAATTTTGGAAACTTCGGGGGGTAAAATGGTGATT
1 TTTGGTGAAATC-AGGGTTAAAAATGGAATTTTGGAAAGTT-TAGGGGTAAAATGGTAATT
* *
33241890 TTTGGTGAAACCAGGGTTAAAGATAGG-ATTTTGGAAAGTTCTA-GGGTAAAATGGTAATT
1 TTTGGTGAAATCAGGGTTAAAAAT-GGAATTTTGGAAAGTT-TAGGGGTAAAATGGTAATT
* *
33241949 TTTGATGAAATC-GAGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
1 TTTGGTGAAATCAG-GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TT
* * *
33242009 TTTGGTGAAATTAGGGTT-AAAATGGAATTTTGAAAAGTTTAGGGGTAAAATTGTAATT
1 TTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
* * ** *
33242067 TTTGGTGAAATCGGGGTTAAATATGGAATTTTGGAAAGTTCGGGGGTAAATTGGTAATT
1 TTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
* *
33242126 TTTGATGAAA-CAGGGGTTAAAAATGGAATTTTGGAAAGTTTATGGGTAAAATGGTAATT
1 TTTGGTGAAATCA-GGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
33242185 TTTGG
1 TTTGG
33242190 AGACACGTGG
Statistics
Matches: 260, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
58 23 0.09
59 184 0.71
60 49 0.19
61 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
TTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATT
Found at i:33242070 original size:177 final size:179
Alignment explanation
Indices: 33241830--33242187 Score: 517
Period size: 177 Copynumber: 2.0 Consensus size: 179
33241820 TTTTGGAAAC
* * *
33241830 TTTGGTGAAACTAGGGCTAAAAATGGAATTTTGGAAACTTCGGGGGGTAAAATGGTGATTTTTGG
1 TTTGGTGAAACTAGGGCTAAAAATGGAATTTTGAAAACTTCGAGGGGTAAAATGGTAATTTTTGG
*
33241895 TGAAACCAGGGTTAAAGATAGG-ATTTTGGAAAGTTCTAGGGTAAAATGGTAATTTTTGATGAAA
66 TGAAACCAGGGTTAAAGAT-GGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAA
33241959 TC-GAGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
130 -CAGAGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
* * * * *
33242009 TTTGGTGAAATTAGGG-TTAAAATGGAATTTTGAAAAGTT-TAGGGGTAAAATTGTAATTTTTGG
1 TTTGGTGAAACTAGGGCTAAAAATGGAATTTTGAAAACTTCGAGGGGTAAAATGGTAATTTTTGG
* * * * *
33242072 TGAAATCGGGGTTAAATATGGAATTTTGGAAAGTTCGGGGGTAAATTGGTAATTTTTGATGAAAC
66 TGAAACCAGGGTTAAAGATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAAC
* * *
33242137 AGGGGTTAAAAATGGAATTTTGGAAAGTTTATGGGTAAAATGGTAATTT
131 AGAGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
33242186 TT
1 TT
33242188 GGAGACACGT
Statistics
Matches: 160, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
176 3 0.02
177 122 0.76
178 20 0.12
179 15 0.09
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (179 bp):
TTTGGTGAAACTAGGGCTAAAAATGGAATTTTGAAAACTTCGAGGGGTAAAATGGTAATTTTTGG
TGAAACCAGGGTTAAAGATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGATGAAAC
AGAGGTTAAAAATAGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTT
Found at i:33242422 original size:161 final size:160
Alignment explanation
Indices: 33242220--33242554 Score: 564
Period size: 161 Copynumber: 2.1 Consensus size: 160
33242210 GGTACCCCGA
* *
33242220 AGTCAAAAGACTAATTATAAATCTTGAAAATTCTCGGGCCAATTTTGTAATTAAAGAAAAGTTGA
1 AGTCAAAGGACTAATTATAAATCTTAAAAATTCTCGGGCCAATTTTGTAATTAAAGAAAAGTTGA
33242285 TTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCC-AAAAGT
66 TTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAAAGT
33242349 GACACATGGCAGCCTCTGGTGCAATCAAAC
131 GACACATGGCAGCCTCTGGTGCAATCAAAC
* *
33242379 AGTCAAAGGACTAATTTATAAATCTTAAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAA-TTATAAATCTT-AAAAATTCTCGGGCCAATTTTGTAATTAAAGAAAAGTT
* * *
33242444 GGTTTAAGGATTAAATTAAAACAAATTAAAAATGATAGGGACTAGATACATAAATAAGCCAAAAA
64 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAAA
* *
33242509 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
129 GTGACACATGGCAGCCTCTGGTGCAATCAAAC
33242541 AGTCAAAGGACTAA
1 AGTCAAAGGACTAA
33242555 ATTGAAAAGT
Statistics
Matches: 164, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
159 13 0.08
160 11 0.07
161 92 0.56
162 48 0.29
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (160 bp):
AGTCAAAGGACTAATTATAAATCTTAAAAATTCTCGGGCCAATTTTGTAATTAAAGAAAAGTTGA
TTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAAAGT
GACACATGGCAGCCTCTGGTGCAATCAAAC
Found at i:33242603 original size:161 final size:161
Alignment explanation
Indices: 33242220--33242635 Score: 483
Period size: 161 Copynumber: 2.6 Consensus size: 161
33242210 GGTACCCCGA
* * * ** * *
33242220 AGTCAAAAGACTAATT-ATAAATCTTG--AAAATTCTCGGGCCAATTTTGTAATTAAAGAAAAGT
1 AGTCAAAGGACTAATTGATAAATC-TGAAAAAATTCTTGGGCCAATATTAAAAATAAATAAAAGT
33242282 TGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAA
65 TGATTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAA
33242347 GTGACACATGGCAGCCTCTGGTGCAATCAAAC
130 GTGACACATGGCAGCCTCTGGTGCAATCAAAC
* * * ** *
33242379 AGTCAAAGGACTAATTTATAAATCTTAAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTGATAAATCTGAAAAAATTCTTGGGCCAATATTAAAAATAAATAAAAGTT
* * *
33242444 GGTTTAAGGATTAAATTAAAACAAATTAAAAATGATAGGGACTAGATACATAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCC-AAAA
* *
33242509 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
130 GTGACACATGGCAGCCTCTGGTGCAATCAAAC
* * * *
33242541 AGTCAAAGGACTAAATTGA-AAA-GTGAATCAAGTTAC-TGGGCCAA-ATTAAAAATAATTAAAA
1 AGTCAAAGGACT-AATTGATAAATCTGAA-AAAATT-CTTGGGCCAATATTAAAAATAAATAAAA
* * *
33242602 GTATGA--AAAGGACTAAATTAAAAC-AATAAAAAAT
63 GT-TGATTTAAGGATTAAATTAAAACAAATTAAAAAT
33242636 ACGGAAAGAC
Statistics
Matches: 226, Mismatches: 23, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
159 25 0.11
160 23 0.10
161 109 0.48
162 63 0.28
163 6 0.03
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (161 bp):
AGTCAAAGGACTAATTGATAAATCTGAAAAAATTCTTGGGCCAATATTAAAAATAAATAAAAGTT
GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAAGGACTAGATACATAAATAAGCCAAAAG
TGACACATGGCAGCCTCTGGTGCAATCAAAC
Found at i:33243412 original size:16 final size:15
Alignment explanation
Indices: 33243392--33243430 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
33243382 CATTTATTGG
* *
33243392 TATTATTTATTATTA
1 TATTATTAATAATTA
33243407 TAATTATTAATAATTA
1 T-ATTATTAATAATTA
33243423 TATTATTA
1 TATTATTA
33243431 GTAGCAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTAATAATTA
Found at i:33244175 original size:17 final size:16
Alignment explanation
Indices: 33244142--33244212 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 16
33244132 ATATTTAAAC
*
33244142 ATTTAAATTCAAAATAA
1 ATTTAAATT-TAAATAA
*
33244159 ATTCAAATTTAACATAA
1 ATTTAAATTTAA-ATAA
* *
33244176 ATTTATATTCTAAATGA
1 ATTTAAATT-TAAATAA
33244193 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
33244210 ATT
1 ATT
33244213 AAGGTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
16 3 0.07
17 38 0.86
18 3 0.07
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:33244201 original size:34 final size:34
Alignment explanation
Indices: 33244142--33244212 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
33244132 ATATTTAAAC
*
33244142 ATTTAAATTCAAAATAAATTCAAATTTAACATAA
1 ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
* * * *
33244176 ATTTATATTCTAAATGAATTTAAATTTAAAATAA
1 ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
33244210 ATT
1 ATT
33244213 AAGGTTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (34 bp):
ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
Found at i:33244659 original size:38 final size:38
Alignment explanation
Indices: 33244617--33244812 Score: 132
Period size: 38 Copynumber: 5.3 Consensus size: 38
33244607 TATCCAACTC
*
33244617 TACTTCAATTTCAAGAGGATAGGAGATGACGTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
* *
33244655 TACTTCAATTTC-AGA-GAT---AAA-GACTTGTTATCCAACT
1 TACTTCAATTTCAAGAGGATAGGAAATGAC--G-T-TGC-TCT
*
33244692 CAACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
* * ** ***
33244731 TACTTCAATAT-AA-A-GACT-TGTTAT--C-CAACTC-
1 TACTTCAATTTCAAGAGGA-TAGGAAATGACGTTGCTCT
33244762 TACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
1 TACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
33244800 TACTTCAATTTCA
1 TACTTCAATTTCA
33244813 GAGATAAAGA
Statistics
Matches: 116, Mismatches: 21, Indels: 42
0.65 0.12 0.23
Matches are distributed among these distances:
31 10 0.09
32 8 0.07
33 5 0.04
34 6 0.05
35 6 0.05
36 8 0.07
37 10 0.09
38 45 0.39
39 5 0.04
40 5 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (38 bp):
TACTTCAATTTCAAGAGGATAGGAAATGACGTTGCTCT
Found at i:33244676 original size:76 final size:76
Alignment explanation
Indices: 33244499--33244857 Score: 564
Period size: 76 Copynumber: 4.9 Consensus size: 76
33244489 AGGCTTCATC
* *
33244499 TTGCTCTTACTTCAATTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTC-----G
1 TTGCTCTTACTTCAATTTC--AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
33244559 ATAGGAAATGATC-
64 ATAGGAAATGA-CG
33244572 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
*
33244637 AGGAGATGACG
66 AGGAAATGACG
*
33244648 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCAACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
33244713 AGGAAATGACG
66 AGGAAATGACG
33244724 TTGCTCTTACTTCAA--T-----ATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
33244782 AGGAAATGACG
66 AGGAAATGACG
33244793 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
33244858 CTTACTTCAA
Statistics
Matches: 267, Mismatches: 6, Indels: 23
0.90 0.02 0.08
Matches are distributed among these distances:
69 67 0.25
71 37 0.14
73 19 0.07
74 1 0.00
75 1 0.00
76 142 0.53
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (76 bp):
TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
AGGAAATGACG
Found at i:33244842 original size:38 final size:39
Alignment explanation
Indices: 33244740--33244857 Score: 115
Period size: 38 Copynumber: 3.1 Consensus size: 39
33244730 TTACTTCAAT
33244740 ATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 ATAAAGACTTGTTATCCAACTCTACTTCAATTTC-AGAGG
* *
33244780 ATAGGAAATGAC--G-T-TGC-TCT-TACTTCAATTTCAGA-G
1 AT---AAA-GACTTGTTATCCAACTCTACTTCAATTTCAGAGG
33244816 ATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGG
1 ATAAAGACTTGTTATCCAACTCTACTTCAATTTC-AGAGG
33244856 AT
1 AT
33244858 CTTACTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
32 3 0.05
33 3 0.05
34 1 0.02
35 1 0.02
36 5 0.08
37 5 0.08
38 24 0.39
39 5 0.08
40 7 0.11
41 1 0.02
42 1 0.02
43 3 0.05
44 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (39 bp):
ATAAAGACTTGTTATCCAACTCTACTTCAATTTCAGAGG
Found at i:33244890 original size:60 final size:60
Alignment explanation
Indices: 33244797--33244914 Score: 236
Period size: 60 Copynumber: 2.0 Consensus size: 60
33244787 ATGACGTTGC
33244797 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
33244857 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAG
33244915 ATAGGAAATG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (60 bp):
TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGA
Found at i:33245040 original size:76 final size:76
Alignment explanation
Indices: 33244857--33245310 Score: 856
Period size: 76 Copynumber: 6.0 Consensus size: 76
33244847 TTCAAGAGGA
33244857 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGA-GATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
33244921 AATGACGTTGC
66 AATGACGTTGC
*
33244932 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAGTTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
33244997 AATGACGTTGC
66 AATGACGTTGC
33245008 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
33245073 AATGACGTTGC
66 AATGACGTTGC
33245084 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
*
33245149 GATGACGTTGC
66 AATGACGTTGC
33245160 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
33245225 AATGACGTTGC
66 AATGACGTTGC
* *
33245236 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACGTCAATTTCAAGAGGGTAGGA
1 TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
*
33245301 AATGATGTTG
66 AATGACGTTG
33245311 GATTGATGTG
Statistics
Matches: 371, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
75 56 0.15
76 315 0.85
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (76 bp):
TCTTACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGA
AATGACGTTGC
Found at i:33257492 original size:29 final size:28
Alignment explanation
Indices: 33257468--33257803 Score: 185
Period size: 29 Copynumber: 11.5 Consensus size: 28
33257458 ACCGGGGCTA
*
33257468 AAAATGGAATTTTGGAAAGTTCGGGGGGT
1 AAAATGGAATTTTGGAAAGTTC-GGGGTT
*
33257497 AAAATGGTGATTTTTGGTGAAA--TCGGGGTT
1 AAAAT-G-GAATTTT-G-GAAAGTTCGGGGTT
33257527 AAAGATAGG-ATTTTGGAAAGTTCGAGGG-T
1 AAA-AT-GGAATTTTGGAAAGTTCG-GGGTT
* *
33257556 AAATTGGTAATTTTTGATGAAA--TCAGGGTT
1 AAAATGG-AA-TTTTG--GAAAGTTCGGGGTT
*
33257586 AAAACTGGAATTTT-GAAAGGTTTAGGGG-T
1 AAAA-TGGAATTTTGGAAA-G-TTCGGGGTT
*
33257615 AAAATGGTAATTTTTGGTAAA-ATCGGGGTT
1 AAAATGG-AA-TTTTGG-AAAGTTCGGGGTT
* * *
33257645 AAAAATGAAATTTTGTAAAGTTCGGGGGT
1 -AAAATGGAATTTTGGAAAGTTCGGGGTT
* *
33257674 -AAATGGTAATTTTTAGTAAA-ATCGGGGTT
1 AAAATGG-AA-TTTT-GGAAAGTTCGGGGTT
*
33257703 AAAATGGAATTTTGGAAAGTTCGGGGGT
1 AAAATGGAATTTTGGAAAGTTCGGGGTT
*
33257731 AAAATGGTAATTTTTGGTGAAA-CT-GGGGTT
1 AAAATGG-AA-TTTT-G-GAAAGTTCGGGGTT
** *
33257761 AAAAATGGAATTTTGGAAAGTTTAGGGAT
1 -AAAATGGAATTTTGGAAAGTTCGGGGTT
33257790 AAAATGGTAATTTT
1 AAAATGG-AATTTT
33257804 TGGATAGTCC
Statistics
Matches: 242, Mismatches: 26, Indels: 78
0.70 0.08 0.23
Matches are distributed among these distances:
26 4 0.02
27 19 0.08
28 37 0.15
29 77 0.32
30 59 0.24
31 30 0.12
32 12 0.05
33 4 0.02
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTGGAAAGTTCGGGGTT
Found at i:33257698 original size:58 final size:59
Alignment explanation
Indices: 33257449--33257806 Score: 465
Period size: 59 Copynumber: 6.1 Consensus size: 59
33257439 TTTTGGAAAC
* * * *
33257449 TTTGGCGAAACCGGGGCTAAAAATGGAATTTTGGAAAGTTCGGGGGGTAAAATGGTGATT
1 TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTC-GGGGGTAAAATGGTAATT
* * *
33257509 TTTGGTGAAATCGGGGTTAAAGATAGG-ATTTTGGAAAGTTCGAGGGTAAATTGGTAATT
1 TTTGGTGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* * * **
33257568 TTTGATGAAATCAGGGTTAAAACTGGAATTTT-GAAAGGTTTAGGGGTAAAATGGTAATT
1 TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAA-GTTCGGGGGTAAAATGGTAATT
* * *
33257627 TTTGGTAAAATCGGGGTTAAAAATGAAATTTTGTAAAGTTCGGGGGT-AAATGGTAATT
1 TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
* *
33257685 TTTAGTAAAATCGGGGTT-AAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
1 TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
** *
33257743 TTTGGTGAAA-CTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGATAAAATGGTAATT
1 TTTGGTGAAATC-GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
33257802 TTTGG
1 TTTGG
33257807 ATAGTCCAGG
Statistics
Matches: 260, Mismatches: 31, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
57 27 0.10
58 59 0.23
59 135 0.52
60 37 0.14
61 2 0.01
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
TTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATT
Found at i:33257818 original size:30 final size:28
Alignment explanation
Indices: 33257702--33257818 Score: 76
Period size: 30 Copynumber: 4.0 Consensus size: 28
33257692 AAATCGGGGT
* * *
33257702 TAAAATGGAATTTTGGAAAGTTCGGGGG
1 TAAAATGGAATTTTGGAAAGTCCAGGGA
** *
33257730 TAAAATGGTAATTTTTGGTGAAA--CTGGGGT
1 TAAAATGG-AA-TTTT-G-GAAAGTCCAGGGA
**
33257760 TAAAAATGGAATTTTGGAAAGTTTAGGGA
1 T-AAAATGGAATTTTGGAAAGTCCAGGGA
*
33257789 TAAAATGGTAATTTTTGGATAGTCCAGGGA
1 TAAAATGG-AA-TTTTGGAAAGTCCAGGGA
33257819 CTTATAAAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
27 4 0.06
28 16 0.23
29 13 0.18
30 26 0.37
31 8 0.11
32 4 0.06
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (28 bp):
TAAAATGGAATTTTGGAAAGTCCAGGGA
Found at i:33258054 original size:162 final size:162
Alignment explanation
Indices: 33257877--33258210 Score: 632
Period size: 162 Copynumber: 2.1 Consensus size: 162
33257867 GGTACCCAGA
*
33257877 AGTCAAAGGACTAATTTATAAATCTTAAAAAATTCTCGAGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTAAAAAACTCTCGAGCCAATTTTGTAATTAAATAAAAGTT
33257942 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
33258007 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
131 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
* * *
33258039 AGTCAAAGGACTAATTTATAAATCTTGAAAAACTCTTGGGCCAATTTTGTAATTAAATAAAAGTT
1 AGTCAAAGGACTAATTTATAAATCTTAAAAAACTCTCGAGCCAATTTTGTAATTAAATAAAAGTT
33258104 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
66 GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
33258169 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
131 GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
33258201 AGTCAAAGGA
1 AGTCAAAGGA
33258211 TTAAATTGAA
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 168 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (162 bp):
AGTCAAAGGACTAATTTATAAATCTTAAAAAACTCTCGAGCCAATTTTGTAATTAAATAAAAGTT
GATTTAAGGATTAAATTAAAACAAATTAAAAATGACAGGGACTAGATACATAAATAAGCCAAAAA
GTGACACGTGGCAGCCTCTGGTGCAGTCAAAC
Found at i:33259089 original size:16 final size:15
Alignment explanation
Indices: 33259069--33259107 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
33259059 CATTTATTGG
* *
33259069 TATTATTTATTATTA
1 TATTATTAATAATTA
33259084 TAATTATTAATAATTA
1 T-ATTATTAATAATTA
33259100 TATTATTA
1 TATTATTA
33259108 GTAGCAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTATTAATAATTA
Found at i:33259852 original size:17 final size:16
Alignment explanation
Indices: 33259819--33259887 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 16
33259809 ATATTTAAAC
*
33259819 ATTTAAATTCAAAATAA
1 ATTTAAATT-TAAATAA
*
33259836 ATTCAAATTTAATATAA
1 ATTTAAATTTAA-ATAA
*
33259853 ATTTAAATTCTAAATGA
1 ATTTAAATT-TAAATAA
33259870 ATTTAAATTTAAAATAA
1 ATTTAAATTT-AAATAA
33259887 A
1 A
33259888 CTAAGGTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.07
17 38 0.86
18 3 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:33259859 original size:23 final size:23
Alignment explanation
Indices: 33259833--33259882 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
33259823 AAATTCAAAA
*
33259833 TAAATTC-AAATTTAATATAAATT
1 TAAATTCTAAA-TGAATATAAATT
*
33259856 TAAATTCTAAATGAATTTAAATT
1 TAAATTCTAAATGAATATAAATT
33259879 TAAA
1 TAAA
33259883 ATAAACTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TAAATTCTAAATGAATATAAATT
Found at i:33259860 original size:34 final size:34
Alignment explanation
Indices: 33259819--33259887 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
33259809 ATATTTAAAC
*
33259819 ATTTAAATTCAAAATAAATTCAAATTTAATATAA
1 ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
* * *
33259853 ATTTAAATTCTAAATGAATTTAAATTTAAAATAA
1 ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
33259887 A
1 A
33259888 CTAAGGTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (34 bp):
ATTTAAATTCAAAATAAATTCAAATTTAAAATAA
Found at i:33261957 original size:17 final size:17
Alignment explanation
Indices: 33261926--33261977 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
33261916 ATACTAATAT
*
33261926 TTTTATATATTTTTTAAA
1 TTTTA-ATATCTTTTAAA
33261944 TTTTAATATCTTTTAAA
1 TTTTAATATCTTTTAAA
* * *
33261961 GTTTAAAATGTTTTAAA
1 TTTTAATATCTTTTAAA
33261978 AAATAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTTAATATCTTTTAAA
Found at i:33263788 original size:4 final size:4
Alignment explanation
Indices: 33263781--33263807 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
33263771 GTGGACCATG
33263781 TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGT
33263808 GTATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:33276315 original size:15 final size:15
Alignment explanation
Indices: 33276295--33276324 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33276285 AATTTCATGC
33276295 TTCAATAACCATGTT
1 TTCAATAACCATGTT
*
33276310 TTCAATCACCATGTT
1 TTCAATAACCATGTT
33276325 ATCACTTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCAATAACCATGTT
Found at i:33276424 original size:26 final size:26
Alignment explanation
Indices: 33276395--33276444 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
33276385 ATATATAACA
*
33276395 TCTCAAA-ATCAATGTCCAAATGTAAG
1 TCTCAAATATCAAT-TACAAATGTAAG
*
33276421 TCTCAAATATCCATTACAAATGTA
1 TCTCAAATATCAATTACAAATGTA
33276445 TCAAATTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (26 bp):
TCTCAAATATCAATTACAAATGTAAG
Found at i:33279145 original size:368 final size:368
Alignment explanation
Indices: 33278468--33279206 Score: 1469
Period size: 368 Copynumber: 2.0 Consensus size: 368
33278458 GATCAAGATA
33278468 TTTGAAGAACTCGGATGAGTTTTTCTCAACTTTGAAAATCTTTCTAAAGAATTTTGAGAGAATTT
1 TTTGAAGAACTCGGATGAGTTTTTCTCAACTTTGAAAATCTTTCTAAAGAATTTTGAGAGAATTT
33278533 GGAGAGAATAAAAGATGAGATCTAATTTTTGATATGAGGACTTCGAAAATGAAAAAAAAGAGAGA
66 GGAGAGAATAAAAGATGAGATCTAATTTTTGATATGAGGACTTCGAAAATGAAAAAAAAGAGAGA
33278598 AAATGCTTAAAAATCGAGTGAAAATTGTGTGTGAAGTGAGGAGATTACAGCATTTTTGAGCTGAA
131 AAATGCTTAAAAATCGAGTGAAAATTGTGTGTGAAGTGAGGAGATTACAGCATTTTTGAGCTGAA
*
33278663 GAATCCCCACCTGATTTTAAAAAATTGGGGAAATTGCTGTAAGGACACTCTCACAATTCTCTTGT
196 GAATCCCCACCTGATTTTAAAAAATTGGGGAAATTGCCGTAAGGACACTCTCACAATTCTCTTGT
33278728 TTTACAAAATAACCCTTTCCCTTCGAAATTCTAAAAATATGAGTAATTTGCCATAGAACCACTCA
261 TTTACAAAATAACCCTTTCCCTTCGAAATTCTAAAAATATGAGTAATTTGCCATAGAACCACTCA
33278793 AACATTTCCATTGTTTTGTAAAATGGTCCTATGCAATTAATAT
326 AACATTTCCATTGTTTTGTAAAATGGTCCTATGCAATTAATAT
33278836 TTTGAAGAACTCGGATGAGTTTTTCTCAACTTTGAAAATCTTTCTAAAGAATTTTGAGAGAATTT
1 TTTGAAGAACTCGGATGAGTTTTTCTCAACTTTGAAAATCTTTCTAAAGAATTTTGAGAGAATTT
33278901 GGAGAGAATAAAAGATGAGATCTAATTTTTGATATGAGGACTTCGAAAATGAAAAAAAAGAGAGA
66 GGAGAGAATAAAAGATGAGATCTAATTTTTGATATGAGGACTTCGAAAATGAAAAAAAAGAGAGA
33278966 AAATGCTTAAAAATCGAGTGAAAATTGTGTGTGAAGTGAGGAGATTACAGCATTTTTGAGCTGAA
131 AAATGCTTAAAAATCGAGTGAAAATTGTGTGTGAAGTGAGGAGATTACAGCATTTTTGAGCTGAA
33279031 GAATCCCCACCTGATTTTAAAAAATTGGGGAAATTGCCGTAAGGACACTCTCACAATTCTCTTGT
196 GAATCCCCACCTGATTTTAAAAAATTGGGGAAATTGCCGTAAGGACACTCTCACAATTCTCTTGT
33279096 TTTACAAAATAACCCTTTCCCTTCGAAATTCTAAAAATATGAGTAATTTGCCATAGAACCACTCA
261 TTTACAAAATAACCCTTTCCCTTCGAAATTCTAAAAATATGAGTAATTTGCCATAGAACCACTCA
33279161 AACATTTCCATTGTTTTGTAAAATGGTCCTATGCAATTAATAT
326 AACATTTCCATTGTTTTGTAAAATGGTCCTATGCAATTAATAT
33279204 TTT
1 TTT
33279207 AAATTCTCTC
Statistics
Matches: 370, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
368 370 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (368 bp):
TTTGAAGAACTCGGATGAGTTTTTCTCAACTTTGAAAATCTTTCTAAAGAATTTTGAGAGAATTT
GGAGAGAATAAAAGATGAGATCTAATTTTTGATATGAGGACTTCGAAAATGAAAAAAAAGAGAGA
AAATGCTTAAAAATCGAGTGAAAATTGTGTGTGAAGTGAGGAGATTACAGCATTTTTGAGCTGAA
GAATCCCCACCTGATTTTAAAAAATTGGGGAAATTGCCGTAAGGACACTCTCACAATTCTCTTGT
TTTACAAAATAACCCTTTCCCTTCGAAATTCTAAAAATATGAGTAATTTGCCATAGAACCACTCA
AACATTTCCATTGTTTTGTAAAATGGTCCTATGCAATTAATAT
Found at i:33279278 original size:27 final size:27
Alignment explanation
Indices: 33279248--33279302 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
33279238 GTTTTTTCAA
33279248 TTCTAATTTGACCCAAAATATTTATTT
1 TTCTAATTTGACCCAAAATATTTATTT
33279275 TTCTAATTTGACCCAAAATATTTATTT
1 TTCTAATTTGACCCAAAATATTTATTT
33279302 T
1 T
33279303 ACTCAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.04, T:0.49
Consensus pattern (27 bp):
TTCTAATTTGACCCAAAATATTTATTT
Found at i:33288548 original size:15 final size:16
Alignment explanation
Indices: 33288506--33288542 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
33288496 CGTACATAGG
*
33288506 AATTTAAATTAGTTTT
1 AATTTAACTTAGTTTT
33288522 AATTTAACTTAG-TTT
1 AATTTAACTTAGTTTT
33288537 AATTTA
1 AATTTA
33288543 GTTTAGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (16 bp):
AATTTAACTTAGTTTT
Found at i:33312784 original size:18 final size:18
Alignment explanation
Indices: 33312763--33312815 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
33312753 ACATTCGAAC
*
33312763 ATGTGGTTGCATCTGATT
1 ATGTGATTGCATCTGATT
**
33312781 ATGTGATTGCATCTGGGT
1 ATGTGATTGCATCTGATT
33312799 ATGTGATTGCATCTGAT
1 ATGTGATTGCATCTGAT
33312816 CAGGCTTCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (18 bp):
ATGTGATTGCATCTGATT
Found at i:33318961 original size:42 final size:42
Alignment explanation
Indices: 33318906--33319093 Score: 198
Period size: 42 Copynumber: 4.5 Consensus size: 42
33318896 TATGCTCTAT
* * *
33318906 CGAGTCATAAGTCTTCCTTTAATCATATTCTCATTCTCATCC
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
* * * * *
33318948 CGAGACATGAGTCTTCCTTTAGTGATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
* * *
33318990 CGAGACATGGGTCTTCCTTTAATCATATTTTCATGCTCATTC
1 CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
** * * * *
33319032 CGAGTTACGAGTCTTCCATTT-ATACAAATTCTCATGCTAAACC
1 CGAGACATGAGTCTTCC-TTTAAT-CATATTCTCATGCTCATCC
33319075 CGAGACATGAGTCTTCCTT
1 CGAGACATGAGTCTTCCTT
33319094 CTCATACATC
Statistics
Matches: 118, Mismatches: 26, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
42 87 0.74
43 31 0.26
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (42 bp):
CGAGACATGAGTCTTCCTTTAATCATATTCTCATGCTCATCC
Found at i:33334378 original size:15 final size:15
Alignment explanation
Indices: 33334360--33334398 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33334350 AGTGGCAGTG
*
33334360 TTCTCAGTAGATTCT
1 TTCTCAGCAGATTCT
**
33334375 TTCTCAGCATCTTCT
1 TTCTCAGCAGATTCT
33334390 TTCTCAGCA
1 TTCTCAGCA
33334399 TTTTCTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.18, C:0.28, G:0.10, T:0.44
Consensus pattern (15 bp):
TTCTCAGCAGATTCT
Found at i:33334399 original size:15 final size:15
Alignment explanation
Indices: 33334371--33334405 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
33334361 TCTCAGTAGA
33334371 TTCTTTCTCAGCATC
1 TTCTTTCTCAGCATC
*
33334386 TTCTTTCTCAGCATT
1 TTCTTTCTCAGCATC
33334401 TTCTT
1 TTCTT
33334406 CCTCGTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.11, C:0.29, G:0.06, T:0.54
Consensus pattern (15 bp):
TTCTTTCTCAGCATC
Found at i:33356545 original size:3 final size:3
Alignment explanation
Indices: 33356495--33356529 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
33356485 ACCAATTGCA
*
33356495 CAT CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
33356530 ATTCATGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (3 bp):
CAT
Found at i:33356577 original size:45 final size:45
Alignment explanation
Indices: 33356525--33356614 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
33356515 TCACCATCAT
*
33356525 CATCAATTCATGTCATCATCAATTAAAATATATATAACCTATACC
1 CATCAATTCATGTCATCATCAATTAAAATACATATAACCTATACC
33356570 CATCAATTCATGTCATCATCAATTAAAATACATATAACCTATACC
1 CATCAATTCATGTCATCATCAATTAAAATACATATAACCTATACC
33356615 ACACAATGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.32
Consensus pattern (45 bp):
CATCAATTCATGTCATCATCAATTAAAATACATATAACCTATACC
Found at i:33366126 original size:32 final size:32
Alignment explanation
Indices: 33366090--33366154 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
33366080 TAGAGCTTAG
33366090 AGCTAGCTATCATTAGTTTATTGATGAGAACA
1 AGCTAGCTATCATTAGTTTATTGATGAGAACA
33366122 AGCTAGCTATCATTAGTTTATTGATGAGAACA
1 AGCTAGCTATCATTAGTTTATTGATGAGAACA
33366154 A
1 A
33366155 ACATTGAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.34
Consensus pattern (32 bp):
AGCTAGCTATCATTAGTTTATTGATGAGAACA
Found at i:33372360 original size:30 final size:31
Alignment explanation
Indices: 33372303--33372369 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
33372293 TTTAAGGGTT
33372303 GGTGACCGAAAAAGAAAAATTCAAATAGTTG
1 GGTGACCGAAAAAGAAAAATTCAAATAGTTG
* *
33372334 GGTGACC-AAAAAG-AAATTTCCTAATAGTTG
1 GGTGACCGAAAAAGAAAAATT-CAAATAGTTG
33372364 GGTGAC
1 GGTGAC
33372370 TACCAGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 5 0.15
30 21 0.64
31 7 0.21
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (31 bp):
GGTGACCGAAAAAGAAAAATTCAAATAGTTG
Found at i:33378027 original size:18 final size:16
Alignment explanation
Indices: 33378004--33378038 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
33377994 TATTAATTTT
33378004 ATTTTAATATAAATATAA
1 ATTTTAAT-T-AATATAA
33378022 ATTTTAATTAATATAA
1 ATTTTAATTAATATAA
33378038 A
1 A
33378039 ATCTCAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 1 0.06
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTTTAATTAATATAA
Found at i:33379928 original size:91 final size:91
Alignment explanation
Indices: 33379773--33379948 Score: 352
Period size: 91 Copynumber: 1.9 Consensus size: 91
33379763 ATTACTTTTT
33379773 TAGTAGGTCAGTTTCTCTCTCGCTCCTAAATTCATTCGTTGAACTTCATCTGTGAGATTTAATAT
1 TAGTAGGTCAGTTTCTCTCTCGCTCCTAAATTCATTCGTTGAACTTCATCTGTGAGATTTAATAT
33379838 CTTTAAACACATTGATTGTAGAATTC
66 CTTTAAACACATTGATTGTAGAATTC
33379864 TAGTAGGTCAGTTTCTCTCTCGCTCCTAAATTCATTCGTTGAACTTCATCTGTGAGATTTAATAT
1 TAGTAGGTCAGTTTCTCTCTCGCTCCTAAATTCATTCGTTGAACTTCATCTGTGAGATTTAATAT
33379929 CTTTAAACACATTGATTGTA
66 CTTTAAACACATTGATTGTA
33379949 AAAGGAGCTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (91 bp):
TAGTAGGTCAGTTTCTCTCTCGCTCCTAAATTCATTCGTTGAACTTCATCTGTGAGATTTAATAT
CTTTAAACACATTGATTGTAGAATTC
Found at i:33381695 original size:19 final size:20
Alignment explanation
Indices: 33381673--33381715 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
33381663 TAAATAAAAT
* *
33381673 AATAAGTAGTAAAAT-TTTA
1 AATAAGTAATAAAATATATA
33381692 AAT-AGTAATAAAATATATA
1 AATAAGTAATAAAATATATA
33381711 AATAA
1 AATAA
33381716 TTTATCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.50
19 9 0.45
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (20 bp):
AATAAGTAATAAAATATATA
Found at i:33398135 original size:17 final size:16
Alignment explanation
Indices: 33398100--33398132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33398090 TATGGAAACA
33398100 TCATAATTTTTTGTAT
1 TCATAATTTTTTGTAT
33398116 TCATAATTTTTTGTAT
1 TCATAATTTTTTGTAT
33398132 T
1 T
33398133 TCAAGACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (16 bp):
TCATAATTTTTTGTAT
Found at i:33409803 original size:17 final size:17
Alignment explanation
Indices: 33409751--33409805 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
33409741 TGGACTTTTT
33409751 AATTT-AAATAAATTTA
1 AATTTAAAATAAATTTA
** *
33409767 AACCTAGAATAAATTTA
1 AATTTAAAATAAATTTA
33409784 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
33409801 AATTT
1 AATTT
33409806 TGTTGGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 3 0.09
17 29 0.91
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:33410451 original size:209 final size:209
Alignment explanation
Indices: 33410075--33410763 Score: 877
Period size: 209 Copynumber: 3.3 Consensus size: 209
33410065 TCTAATGGTT
* * * * **
33410075 TGGTGTCATTGATTTGATCTACTTCTCAGTGTCTCATCAGGAAGATGATCGCATCACTTGTTTTG
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
** * * * * * ** *
33410140 ATCCACTTCTATGTGTCTCATCAGGAAGATGGATTTGTTTTACTTCTCT-GTATCTTATCAGGAA
66 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCT-TAGTATCTCATCAGGAA
* * * *
33410204 GGTAACAGCTTTATTGCTTTGACCTG-TTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGAT
130 GCTAACCGCTTTATTGCTTCGACCTGCTTT-TCAGTATCTCATTAGGAAGCTGGGGTTCGAAGAT
*
33410268 TCGCTCACTTTGAGCC
194 TTGCTCACTTTGAGCC
* * * *
33410284 TGGCTTCATTGATTTGGTCTTCTTTTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTCA
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
*
33410349 ATCTGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAG
66 ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAG
* * *
33410414 CTAACCGCTTTATTGCTTCGACGTGCTTTTTAGTATCTCATTAGGAAGCTGGGGTTTGAAGATTT
131 CTAACCGCTTTATTGCTTCGACCTGCTTTTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTT
* * *
33410479 GCTTACATTGAGCT
196 GCTCACTTTGAGCC
* * *
33410493 TTGTTTCATTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTCA
1 TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
* *
33410558 AT-TCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAA
66 ATCT-GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAA
** * * *
33410622 GCTAACCATTTTATTGCTTCGACTTGCTTCTCAGTATCTCATTAGGAAGCTGGAGTTCGAAGATT
130 GCTAACCGCTTTATTGCTTCGACCTGCTTTTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATT
33410687 TGCTCACTTTGAGCC
195 TGCTCACTTTGAGCC
* * * *
33410702 TGATTTCATCGAGTTGGTATACTTCTCTA-TATCTCATCAGGAAGATGACCAGC-TCAC-TGTTT
1 TGGTTTCATTGATTTGGTCTACTTCTC-AGTATCTCATCAGGAAGATGACC-GCATCACTTGTTT
33410764 TGGGTAGTCG
Statistics
Matches: 418, Mismatches: 57, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
208 7 0.02
209 405 0.97
210 6 0.01
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (209 bp):
TGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCA
ATCTGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAG
CTAACCGCTTTATTGCTTCGACCTGCTTTTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTT
GCTCACTTTGAGCC
Found at i:33413415 original size:16 final size:17
Alignment explanation
Indices: 33413384--33413421 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
33413374 ATTAAGTTGG
*
33413384 ATTAAGAATGAAAGAATA
1 ATTAAGAA-GAAAGAAAA
33413402 ATTAAGAA-AAAGAAAA
1 ATTAAGAAGAAAGAAAA
33413418 ATTA
1 ATTA
33413422 TCATATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (17 bp):
ATTAAGAAGAAAGAAAA
Found at i:33417946 original size:29 final size:29
Alignment explanation
Indices: 33417914--33417981 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
33417904 AGGCAGAACG
* *
33417914 GTAATTTTTGAATGTTCAGGGGTAAAAAC
1 GTAATTTTTGAAAGTTCAAGGGTAAAAAC
* * *
33417943 GTAAATTTTGGAAAGTTCAAGGTTAAAAAT
1 GT-AATTTTTGAAAGTTCAAGGGTAAAAAC
33417973 GTAATTTTT
1 GTAATTTTT
33417982 AGACATACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGAAAGTTCAAGGGTAAAAAC
Found at i:33418028 original size:29 final size:28
Alignment explanation
Indices: 33417992--33418137 Score: 102
Period size: 30 Copynumber: 5.0 Consensus size: 28
33417982 AGACATACGA
*
33417992 GGGTAAAATGGTAATTTTGAAAATTTTG
1 GGGTAAAATGGTAATTTTGGAAATTTTG
* *
33418020 GGGTCAAAAATGG-AATATTTGGACATTTAG
1 GGGT--AAAATGGTAAT-TTTGGAAATTTTG
*
33418050 GGGTAAAATGGTAATTTTTGGATATTTTG
1 GGGTAAAATGGTAA-TTTTGGAAATTTTG
* * *
33418079 AGGTCAAAAATTGG-AATTTTCGGATA-TCTG
1 GGGT--AAAA-TGGTAATTTT-GGAAATTTTG
*
33418109 AGGG-AAAATGGTAACTTTTGGAAAGTTTG
1 -GGGTAAAATGGTAA-TTTTGGAAATTTTG
33418138 AGGACAAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
27 3 0.03
28 21 0.22
29 26 0.27
30 29 0.31
31 13 0.14
32 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAATTTTG
Found at i:33418045 original size:58 final size:59
Alignment explanation
Indices: 33417933--33418176 Score: 219
Period size: 59 Copynumber: 4.2 Consensus size: 59
33417923 GAATGTTCAG
** * * ** * * *
33417933 GGGTAAAAACGTAAATTTTGGAAAGTTCAAGGTTAAAAATGTAATTTTTAGACATACGA
1 GGGTAAAATGGTAACTTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATACGA
* * *
33417992 GGGTAAAATGGTAA-TTTTGAAAATTTTGGGGTCAAAAATGGAATATTTGGACATTTA-G-
1 GGGTAAAATGGTAACTTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACA--TACGA
* * * *
33418050 GGGTAAAATGGTAATTTTTGGATATTTTGAGGTCAAAAATTGGAATTTTCGGATAT-CTGA
1 GGGTAAAATGGTAACTTTTGGAAATTTTGAGGTCAAAAA-TGGAATTTTTGGACATAC-GA
* * * * * *
33418110 GGG-AAAATGGTAACTTTTGGAAAGTTTGAGGACAAAAAGGGGATTTTTGGACATTCGG
1 GGGTAAAATGGTAACTTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATACGA
33418168 GGGTAAAAT
1 GGGTAAAAT
33418177 ACTAATTGTT
Statistics
Matches: 150, Mismatches: 26, Indels: 18
0.77 0.13 0.09
Matches are distributed among these distances:
58 61 0.41
59 72 0.48
60 17 0.11
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAACTTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATACGA
Found at i:33418097 original size:31 final size:30
Alignment explanation
Indices: 33417996--33418105 Score: 109
Period size: 30 Copynumber: 3.7 Consensus size: 30
33417986 ATACGAGGGT
* *
33417996 AAAATGGTAA-TTTTGAAAATTTTGGGGTCA
1 AAAATGG-AATTTTTGGATATTTTGGGGTCA
* * *
33418026 AAAATGGAATATTTGGACATTTAGGGGT--
1 AAAATGGAATTTTTGGATATTTTGGGGTCA
*
33418054 AAAATGGTAATTTTTGGATATTTTGAGGTCA
1 AAAATGG-AATTTTTGGATATTTTGGGGTCA
*
33418085 AAAATTGGAATTTTCGGATAT
1 AAAA-TGGAATTTTTGGATAT
33418106 CTGAGGGAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.11
29 19 0.29
30 21 0.32
31 16 0.24
32 3 0.05
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTGGATATTTTGGGGTCA
Found at i:33418175 original size:29 final size:30
Alignment explanation
Indices: 33418143--33418274 Score: 94
Period size: 29 Copynumber: 4.5 Consensus size: 30
33418133 GTTTGAGGAC
*
33418143 AAAAAGGGGATTTTTGGACA-TTCGGGGGT
1 AAAAAGGGAATTTTTGGACAGTTCGGGGGT
** * * *
33418172 AAAATA-CTAATTGTTGGACA-TCCGAGGGT
1 AAAA-AGGGAATTTTTGGACAGTTCGGGGGT
* * * *
33418201 AAAATGGTAATTTTTGGAAAGTTC-GAGGT
1 AAAAAGGGAATTTTTGGACAGTTCGGGGGT
33418230 CAAAAAGGGAATTTTTGGA-AGTTCGGGGGT
1 -AAAAAGGGAATTTTTGGACAGTTCGGGGGT
* * *
33418260 GAAAATGTAATTTTT
1 AAAAAGGGAATTTTT
33418275 TAGAAATTTG
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
29 56 0.71
30 23 0.29
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.31
Consensus pattern (30 bp):
AAAAAGGGAATTTTTGGACAGTTCGGGGGT
Found at i:33418189 original size:59 final size:58
Alignment explanation
Indices: 33417946--33418176 Score: 225
Period size: 58 Copynumber: 3.9 Consensus size: 58
33417936 TAAAAACGTA
* ** * * * *
33417946 AATTTTGGAAAGTTCAAGGTTAAAAATGTAATTTTTAGACATACGAGGGTAAAATGGT
1 AATTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGT
* * * *
33418004 AATTTTGAAAATTTTGGGGTCAAAAATGGAATATTTGGACATT-TAGGGGTAAAATGGT
1 AATTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATTCGA-GGGTAAAATGGT
* * *
33418062 AATTTTTGGATATTTTGAGGTCAAAAATTGGAATTTTCGGATA-TCTGAGGG-AAAATGGT
1 AA-TTTTGGAAATTTTGAGGTCAAAAA-TGGAATTTTTGGACATTC-GAGGGTAAAATGGT
* * * * *
33418121 AACTTTTGGAAAGTTTGAGGACAAAAAGGGGATTTTTGGACATTCGGGGGTAAAAT
1 AA-TTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAAT
33418177 ACTAATTGTT
Statistics
Matches: 139, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
57 1 0.01
58 62 0.45
59 60 0.43
60 15 0.11
61 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.33
Consensus pattern (58 bp):
AATTTTGGAAATTTTGAGGTCAAAAATGGAATTTTTGGACATTCGAGGGTAAAATGGT
Found at i:33418243 original size:30 final size:29
Alignment explanation
Indices: 33417916--33418254 Score: 84
Period size: 29 Copynumber: 11.6 Consensus size: 29
33417906 GCAGAACGGT
* * * *
33417916 AATTTTT-GAATGTTCAGGGGTAAAAACGT
1 AATTTTTGGAAAGTTC-GAGGTAAAAAGGG
* * * *
33417945 AAATTTTGGAAAGTTCAAGGTTAAAAATGT
1 AATTTTTGGAAAGTTCGAGG-TAAAAAGGG
* * * * *
33417975 AATTTTTAGACA-TACGAGGGTAAAATGGT
1 AATTTTTGGAAAGTTCGA-GGTAAAAAGGG
* * * * *
33418004 AA-TTTTGAAAATTTTGGGGTCAAAAATGG
1 AATTTTTGGAAAGTTCGAGGT-AAAAAGGG
* * * * * * *
33418033 AATATTTGGACATTTAGGGGTAAAATGGT
1 AATTTTTGGAAAGTTCGAGGTAAAAAGGG
* * * *
33418062 AATTTTTGGATATTTTGAGGTCAAAAATTGG
1 AATTTTTGGAAAGTTCGAGGT-AAAAA-GGG
* * * * *
33418093 AATTTTCGGATA--TCTGAGGGAAAATGGT
1 AATTTTTGGAAAGTTC-GAGGTAAAAAGGG
* * *
33418121 AACTTTTGGAAAGTTTGAGGACAAAAAGGG
1 AATTTTTGGAAAGTTCGAGG-TAAAAAGGG
* * * **
33418151 GATTTTTGGACA-TTCGGGGGTAAAATA-CT
1 AATTTTTGGAAAGTTC-GAGGTAAAA-AGGG
* * * * *
33418180 AATTGTTGGACA-TCCGAGGGTAAAATGGT
1 AATTTTTGGAAAGTTCGA-GGTAAAAAGGG
33418209 AATTTTTGGAAAGTTCGAGGTCAAAAAGGG
1 AATTTTTGGAAAGTTCGAGGT-AAAAAGGG
33418239 AATTTTTGG-AAGTTCG
1 AATTTTTGGAAAGTTCG
33418255 GGGGTGAAAA
Statistics
Matches: 225, Mismatches: 67, Indels: 36
0.69 0.20 0.11
Matches are distributed among these distances:
28 20 0.09
29 106 0.47
30 87 0.39
31 12 0.05
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAAGTTCGAGGTAAAAAGGG
Found at i:33418341 original size:30 final size:30
Alignment explanation
Indices: 33418305--33418390 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
33418295 TGGATTTTGT
33418305 AAAGTTC-AGGGGTCAAAATATGATTTTTAA
1 AAAGTTCGA-GGGTCAAAATATGATTTTTAA
* * * *
33418335 AAAGTTCGAGGGTTAAAACATAATTTTTGA
1 AAAGTTCGAGGGTCAAAATATGATTTTTAA
* * *
33418365 GAATTTCGAGAGTCAAAATATGATTT
1 AAAGTTCGAGGGTCAAAATATGATTT
33418391 CTGGACAGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
30 44 0.98
31 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
AAAGTTCGAGGGTCAAAATATGATTTTTAA
Done.