Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 172 of 196
Found at i:50182659 original size:44 final size:46
Alignment explanation
Indices: 50182596--50182685 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
50182586 CCTCTATTCA
*
50182596 ATTCAACCAAACACAAGAA-TA-CTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
50182640 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
1 ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
50182686 GCCTCTATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 18 0.42
45 2 0.05
46 23 0.53
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTAC
Found at i:50182686 original size:16 final size:16
Alignment explanation
Indices: 50182665--50182701 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
50182655 AGAATTACCT
50182665 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
50182681 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
50182697 ATTAC
1 ATTAC
50182702 AGCGAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.35, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:50184508 original size:21 final size:21
Alignment explanation
Indices: 50184484--50184530 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
50184474 CAGCTTCTTG
*
50184484 GCAGTGATGACAAACTGTTCT
1 GCAGCGATGACAAACTGTTCT
50184505 GCAGCGATGACAAACTGTTCT
1 GCAGCGATGACAAACTGTTCT
50184526 GCAGC
1 GCAGC
50184531 CTTTAAGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
GCAGCGATGACAAACTGTTCT
Found at i:50191649 original size:25 final size:25
Alignment explanation
Indices: 50191570--50191649 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 25
50191560 AAGCAATTTT
*
50191570 TCAAAATCTATTCCATGGATCATTC
1 TCAAAATCTACTCCATGGATCATTC
* *** *
50191595 TCAAGA--T-C-CCAAACATC-TTT
1 TCAAAATCTACTCCATGGATCATTC
*
50191615 TCAATATCTACTCCATGGATCATTC
1 TCAAAATCTACTCCATGGATCATTC
50191640 TCAAAATCTA
1 TCAAAATCTA
50191650 TTCCCCTGTA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
20 7 0.18
21 6 0.16
22 1 0.03
23 2 0.05
24 6 0.16
25 16 0.42
ACGTcount: A:0.34, C:0.26, G:0.06, T:0.34
Consensus pattern (25 bp):
TCAAAATCTACTCCATGGATCATTC
Found at i:50196123 original size:24 final size:24
Alignment explanation
Indices: 50196091--50196136 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
50196081 TCATTCAATC
*
50196091 GAAGGGCGA-GAGAGAAGGAGAAAA
1 GAAGAGCGATGAGAG-AGGAGAAAA
*
50196115 GAAGAGCGATGGGAGAGGAGAA
1 GAAGAGCGATGAGAGAGGAGAA
50196137 GCGACACGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.46, C:0.04, G:0.48, T:0.02
Consensus pattern (24 bp):
GAAGAGCGATGAGAGAGGAGAAAA
Found at i:50203069 original size:23 final size:23
Alignment explanation
Indices: 50203043--50203094 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
50203033 TATTGAAATT
50203043 TATTTCAAATATATAATA-TTATA
1 TATTT-AAATATATAATAGTTATA
* *
50203066 TATTTAAATTTGTAATAGTTATA
1 TATTTAAATATATAATAGTTATA
50203089 T-TTTAA
1 TATTTAA
50203095 TGTTTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TATTTAAATATATAATAGTTATA
Found at i:50205563 original size:10 final size:10
Alignment explanation
Indices: 50205511--50205607 Score: 53
Period size: 11 Copynumber: 9.7 Consensus size: 10
50205501 GGGATACAAA
50205511 TTTTAGTAATT
1 TTTTA-TAATT
50205522 TTTT-TACA-T
1 TTTTATA-ATT
*
50205531 TTTTATATTGT
1 TTTTATAAT-T
*
50205542 TTTTGTAA--
1 TTTTATAATT
50205550 TTTTATAATT
1 TTTTATAATT
*
50205560 TTTTGT-A-T
1 TTTTATAATT
*
50205568 TTTTAAATATAT
1 TTTTATA-AT-T
50205580 TTTTATAATTT
1 TTTTATAA-TT
*
50205591 TTTTGTAATT
1 TTTTATAATT
50205601 TTTTATA
1 TTTTATA
50205608 GAAAACTTAA
Statistics
Matches: 65, Mismatches: 10, Indels: 23
0.66 0.10 0.23
Matches are distributed among these distances:
8 12 0.18
9 8 0.12
10 17 0.26
11 20 0.31
12 8 0.12
ACGTcount: A:0.26, C:0.01, G:0.05, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:50205569 original size:17 final size:19
Alignment explanation
Indices: 50205509--50205591 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 19
50205499 AGGGGATACA
50205509 AATTTTAGTAAT-TTTTT-T
1 AATTTTA-TAATGTTTTTGT
*
50205527 ACATTTTTATATTGTTTTTGT
1 A-A-TTTTATAATGTTTTTGT
50205548 AATTTTATAAT-TTTTTGT
1 AATTTTATAATGTTTTTGT
* * * *
50205566 ATTTTTAAATATATTTTTAT
1 AATTTTATA-ATGTTTTTGT
50205586 AATTTT
1 AATTTT
50205592 TTTGTAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.28
19 14 0.26
20 22 0.42
21 2 0.04
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (19 bp):
AATTTTATAATGTTTTTGT
Found at i:50205583 original size:38 final size:38
Alignment explanation
Indices: 50205509--50205591 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 38
50205499 AGGGGATACA
* * *
50205509 AATTTTAGTAATTTTTTTACATTTTTATATTGTTTTTGT
1 AATTTTAGTAATTTTTTTA-ATTTTTAAATTATTTTTAT
50205548 AATTTTA-TAATTTTTTGT-ATTTTTAAATATATTTTTAT
1 AATTTTAGTAATTTTTT-TAATTTTTAAAT-TATTTTTAT
50205586 AATTTT
1 AATTTT
50205592 TTTGTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
37 9 0.23
38 22 0.56
39 8 0.21
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (38 bp):
AATTTTAGTAATTTTTTTAATTTTTAAATTATTTTTAT
Found at i:50207371 original size:7 final size:7
Alignment explanation
Indices: 50207359--50207386 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
50207349 TTTTGGTACT
50207359 CTTTCCA
1 CTTTCCA
50207366 CTTTCCA
1 CTTTCCA
50207373 CTTTCCA
1 CTTTCCA
50207380 CTTTCCA
1 CTTTCCA
50207387 ATCCTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTTCCA
Found at i:50211239 original size:15 final size:16
Alignment explanation
Indices: 50211178--50211243 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 16
50211168 TTATTGAAAA
50211178 ATATTCAAT-ATAAAT
1 ATATTCAATAATAAAT
50211193 AT-TTCAATAATAAAT
1 ATATTCAATAATAAAT
* *
50211208 ATTTATTATAATTATAAAT
1 A--TATT-CAATAATAAAT
50211227 ATATT-AATAATAAAT
1 ATATTCAATAATAAAT
50211242 AT
1 AT
50211244 TTTGTAGTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.14
15 20 0.47
17 5 0.12
18 2 0.05
19 10 0.23
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATTCAATAATAAAT
Found at i:50212198 original size:19 final size:20
Alignment explanation
Indices: 50212160--50212198 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
50212150 AATTTCTGAA
*
50212160 AAATAATTTATTTTTTTTAG
1 AAATAATTTATTTATTTTAG
*
50212180 AAATGATTTA-TTATTTTAG
1 AAATAATTTATTTATTTTAG
50212199 TGTTTGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
AAATAATTTATTTATTTTAG
Found at i:50213042 original size:18 final size:18
Alignment explanation
Indices: 50213019--50213055 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
50213009 GGTTTATGCA
50213019 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
50213037 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
50213055 A
1 A
50213056 TTGATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (18 bp):
AAACCAAATATAGCATCT
Found at i:50218032 original size:5 final size:5
Alignment explanation
Indices: 50218022--50218061 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
50218012 TTCTTCGTGT
*
50218022 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
50218062 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:50218046 original size:19 final size:19
Alignment explanation
Indices: 50218022--50218058 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
50218012 TTCTTCGTGT
*
50218022 TTTTATTTTATTTTATTTA
1 TTTTATCTTATTTTATTTA
50218041 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
50218059 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTA
Found at i:50218931 original size:16 final size:18
Alignment explanation
Indices: 50218900--50218934 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
50218890 AGAAGAAAAG
50218900 AAGGAGGAAGGAAGGAGA
1 AAGGAGGAAGGAAGGAGA
50218918 AAGG-GGAA-GAAGGAGA
1 AAGGAGGAAGGAAGGAGA
50218934 A
1 A
50218935 GAAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AAGGAGGAAGGAAGGAGA
Found at i:50218965 original size:26 final size:28
Alignment explanation
Indices: 50218931--50218985 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
50218921 GGGAAGAAGG
*
50218931 AGAAGAAGAAAGA-AAAAAAATAGAAAA
1 AGAAGAAGAAAGAGAAAAAAATAAAAAA
50218958 AGAA-AAGAAAGAGAAAAAAATAAAAAA
1 AGAAGAAGAAAGAGAAAAAAATAAAAAA
50218985 A
1 A
50218986 TTAGAACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (28 bp):
AGAAGAAGAAAGAGAAAAAAATAAAAAA
Found at i:50219260 original size:26 final size:26
Alignment explanation
Indices: 50219224--50219282 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
50219214 AGCAGGCCAG
* *
50219224 CCAGCAGGCCCAGATTCG-GCAGCAGC
1 CCAGCAGGCCCAG-TCCGCCCAGCAGC
*
50219250 CCAGGAGGCCCAGTCCGCCCAGCAGC
1 CCAGCAGGCCCAGTCCGCCCAGCAGC
50219276 CCAGCAG
1 CCAGCAG
50219283 TGCAGCAGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.22, C:0.42, G:0.31, T:0.05
Consensus pattern (26 bp):
CCAGCAGGCCCAGTCCGCCCAGCAGC
Found at i:50219704 original size:20 final size:20
Alignment explanation
Indices: 50219679--50219716 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
50219669 AAAAATATTC
50219679 AAAAATCCTCGTGTTTTAAT
1 AAAAATCCTCGTGTTTTAAT
50219699 AAAAATCCTCGTGTTTTA
1 AAAAATCCTCGTGTTTTA
50219717 TTAGAATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
AAAAATCCTCGTGTTTTAAT
Found at i:50219875 original size:17 final size:17
Alignment explanation
Indices: 50219831--50219878 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
50219821 TAAAAAAAAA
*
50219831 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTC
**
50219848 TCACGTCTTCAAAAATTC
1 TCGTGT-TTCAAAAATTC
50219866 TCGTGTTTCAAAA
1 TCGTGTTTCAAAA
50219879 CAATAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.40
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:50219995 original size:35 final size:35
Alignment explanation
Indices: 50219955--50220028 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
50219945 TATTATTGTG
*
50219955 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
1 TTTCAAAAATTCCCGTGAATAAAAAAATTTCGTGT
** *
50219990 TTTCAAAAATTCCCGTGTTTAAAAAATTTTCGTGT
1 TTTCAAAAATTCCCGTGAATAAAAAAATTTCGTGT
50220025 TTTC
1 TTTC
50220029 GTGTTTTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (35 bp):
TTTCAAAAATTCCCGTGAATAAAAAAATTTCGTGT
Found at i:50219997 original size:17 final size:17
Alignment explanation
Indices: 50219977--50220028 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
50219967 TCGTGAATAA
50219977 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
* *
50219994 AAAAATTCCCGTG-TTTA
1 AAAAATT-TCGTGTTTTC
50220011 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
50220029 GTGTTTTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:50220130 original size:43 final size:42
Alignment explanation
Indices: 50219982--50220131 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 42
50219972 AATAAAAAAA
50219982 TTTCGTGTTTTC-AAAAATTCCCGTGTTTAAAAAATTTTCGTGT
1 TTTCGTGTTTTCAAAAAATTCCCGTGTTT--AAAATTTTCGTGT
* ** *** *
50220025 TTTCGTGTTTTCACAAAAAATTCTCGTGAATATTTTTTTGGTGT
1 TTTCGTGTTTT--CAAAAAATTCCCGTGTTTAAAATTTTCGTGT
* *
50220069 TATCGTGTTTTCAAAAAAATTCCCGTGTTTGACGAATTTTCGTGT
1 TTTCGTGTTTTC-AAAAAATTCCCGTGTTT-A-AAATTTTCGTGT
50220114 TTTCGTGTTTTCAAAAAA
1 TTTCGTGTTTTCAAAAAA
50220132 AAAAATTCGT
Statistics
Matches: 85, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
42 1 0.01
43 25 0.29
44 26 0.31
45 20 0.24
46 13 0.15
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.46
Consensus pattern (42 bp):
TTTCGTGTTTTCAAAAAATTCCCGTGTTTAAAATTTTCGTGT
Found at i:50220162 original size:18 final size:17
Alignment explanation
Indices: 50220141--50220189 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
50220131 AAAAAATTCG
50220141 TGTTTCCAAAAATTTTCA
1 TGTTTCC-AAAATTTTCA
* *
50220159 TGTTTTCAAAATTTTCG
1 TGTTTCCAAAATTTTCA
*
50220176 TGTTT-TAAAATTTT
1 TGTTTCCAAAATTTT
50220190 TTTCGTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (17 bp):
TGTTTCCAAAATTTTCA
Found at i:50220169 original size:17 final size:16
Alignment explanation
Indices: 50220149--50220239 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 16
50220139 CGTGTTTCCA
*
50220149 AAAATTTTCATGTTTT
1 AAAATTTTCGTGTTTT
50220165 CAAAATTTTCGTGTTTT
1 -AAAATTTTCGTGTTTT
50220182 AAAATTTTTTTCGTGTTATT
1 AAAA---TTTTCGTGTT-TT
* * *
50220202 AAAATTCTCATGTATTG
1 AAAATTTTCGTGT-TTT
50220219 AAAATTTTCGTGTTTT
1 AAAATTTTCGTGTTTT
50220235 CAAAA
1 -AAAA
50220240 AAATTCTGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.10
17 38 0.62
18 1 0.02
19 10 0.16
20 6 0.10
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (16 bp):
AAAATTTTCGTGTTTT
Found at i:50220194 original size:19 final size:20
Alignment explanation
Indices: 50220170--50220207 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
50220160 GTTTTCAAAA
50220170 TTTTCGTGTT-TTAAAATTT
1 TTTTCGTGTTATTAAAATTT
50220189 TTTTCGTGTTATTAAAATT
1 TTTTCGTGTTATTAAAATT
50220208 CTCATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTCGTGTTATTAAAATTT
Found at i:50220206 original size:36 final size:37
Alignment explanation
Indices: 50220153--50220226 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
50220143 TTTCCAAAAA
* * *
50220153 TTTTCATGTTTTCAAAATTTTCGTGT-TTTAAAATTT
1 TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
*
50220189 TTTTCGTGTTATT-AAAATTCTCATGTATTGAAAATTT
1 TTTTCATGTT-TTCAAAATTCTCATGTATTGAAAATTT
50220226 T
1 T
50220227 CGTGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (37 bp):
TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
Found at i:50220244 original size:20 final size:20
Alignment explanation
Indices: 50220219--50220297 Score: 110
Period size: 19 Copynumber: 4.1 Consensus size: 20
50220209 TCATGTATTG
50220219 AAAATTTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
50220239 AAAATTCT-GTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
50220258 AAAA-ATTCGTG-TTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
50220276 AAAATCTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
50220296 AA
1 AA
50220298 TTATTATTGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
18 12 0.23
19 24 0.46
20 16 0.31
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (20 bp):
AAAATTTTCGTGTTTTCAAA
Found at i:50220250 original size:19 final size:19
Alignment explanation
Indices: 50220228--50220297 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
50220218 GAAAATTTTC
50220228 GTGTTTTCAAAAAAATTCT
1 GTGTTTTCAAAAAAATTCT
50220247 GTGTTTTCAAAAAAAATTC-
1 GTGTTTTC-AAAAAAATTCT
50220266 GTG-TTTCAAAAAAA-TCTT
1 GTGTTTTCAAAAAAATTC-T
50220284 CGTGTTTTCAAAAA
1 -GTGTTTTCAAAAA
50220298 TTATTATTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.04
17 7 0.15
18 4 0.09
19 14 0.30
20 19 0.41
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (19 bp):
GTGTTTTCAAAAAAATTCT
Found at i:50220251 original size:53 final size:53
Alignment explanation
Indices: 50220149--50220251 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
50220139 CGTGTTTCCA
* * *** *
50220149 AAAATTTTCATGTTTTCAAAATTTTCGTGTTTTAAAATTTTTTTCGTGTTATT
1 AAAATTCTCATGTATTCAAAATTTTCGTGTTTTAAAAAAATTCTCGTGTTATT
*
50220202 AAAATTCTCATGTATTGAAAATTTTCGTGTTTTCAAAAAAATTCT-GTGTT
1 AAAATTCTCATGTATTCAAAATTTTCGTGTTTT-AAAAAAATTCTCGTGTT
50220252 TTCAAAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 35 0.83
54 7 0.17
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (53 bp):
AAAATTCTCATGTATTCAAAATTTTCGTGTTTTAAAAAAATTCTCGTGTTATT
Found at i:50221749 original size:18 final size:18
Alignment explanation
Indices: 50221709--50221746 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50221699 ATAGTAAATT
50221709 TAAA-ATTTATATTAATA
1 TAAATATTTATATTAATA
*
50221726 TTAATATTTATATTAA-A
1 TAAATATTTATATTAATA
50221743 TAAA
1 TAAA
50221747 ATAAAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATTTATATTAATA
Found at i:50222838 original size:6 final size:6
Alignment explanation
Indices: 50222822--50222872 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
50222812 TTTTTTTTTT
**
50222822 TTAATA TTTAATA TTAATA -TAATCA TTTTTA CTTAATA TTAATA TTAATA
1 TTAATA -TTAATA TTAATA TTAAT-A TTAATA -TTAATA TTAATA TTAATA
50222872 T
1 T
50222873 ACAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.11
6 21 0.57
7 12 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:50222971 original size:50 final size:50
Alignment explanation
Indices: 50222877--50222977 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
50222867 TAATATACAA
* * * *
50222877 TTTAAATTTATTATCAGTGTTTGAAAATATCTATCTATTTTTTATCTATT
1 TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATTATTTATATATT
* * *
50222927 TTTAAATCTATTATTATGTTTTTGAAAATATTTATATA-TATTTATATATT
1 TTTAAATCTATTATCA-GTGTTTGAAAATATCTATATATTATTTATATATT
50222977 T
1 T
50222978 ATTTGATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 25 0.58
51 18 0.42
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (50 bp):
TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATTATTTATATATT
Found at i:50234976 original size:16 final size:18
Alignment explanation
Indices: 50234943--50234993 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
50234933 ATTCTCTTTC
50234943 ATCCTCTTTCTCAACAAA
1 ATCCTCTTTCTCAACAAA
*
50234961 ATCCT-TTTCTC-CCAAA
1 ATCCTCTTTCTCAACAAA
**
50234977 ATTTATCTTTCTCAACA
1 A-TCCTCTTTCTCAACA
50234994 GTATTCTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (18 bp):
ATCCTCTTTCTCAACAAA
Found at i:50264553 original size:28 final size:29
Alignment explanation
Indices: 50264517--50264571 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
50264507 ATTTTAATTT
50264517 TTTTAAAAATTACTTTTTATA-ATTTTTAA
1 TTTTAAAAA-TACTTTTTATATATTTTTAA
*
50264546 TTTT-AAAATATTTTTTATATATTTTT
1 TTTTAAAAATACTTTTTATATATTTTT
50264572 TTAATTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 10 0.42
29 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTTAAAAATACTTTTTATATATTTTTAA
Found at i:50264566 original size:29 final size:29
Alignment explanation
Indices: 50264517--50264579 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
50264507 ATTTTAATTT
50264517 TTTTAAAAATTACTTTTTATA-ATTTTTAA
1 TTTTAAAAATTA-TTTTTATATATTTTTAA
*
50264546 TTTTAAAATATT-TTTTATATATTTTTTTAA
1 TTTTAAAA-ATTATTTT-TATATATTTTTAA
50264576 TTTT
1 TTTT
50264580 TGAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.13
29 12 0.40
30 14 0.47
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAAAATTATTTTTATATATTTTTAA
Found at i:50267997 original size:29 final size:30
Alignment explanation
Indices: 50267942--50268003 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
50267932 GTTATATATA
*
50267942 AACTTTGATTTAATGTGTAATGTCATACATG
1 AACTTTGATTT-ATGTGTAATGTCATAAATG
* *
50267973 AACTTTGATTT-TGTGTGATTTCATAAATG
1 AACTTTGATTTATGTGTAATGTCATAAATG
50268002 AA
1 AA
50268004 ATTTTGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (30 bp):
AACTTTGATTTATGTGTAATGTCATAAATG
Found at i:50269164 original size:28 final size:28
Alignment explanation
Indices: 50269133--50269194 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
50269123 AAAGCCGTTT
50269133 TTTTTCAA-AATTTATCGAAATGGGCCGA
1 TTTTTCAATAATTTATCGAAATGGGCC-A
* *
50269161 TTTTTTAATTATTTATCGAAATGGGCCA
1 TTTTTCAATAATTTATCGAAATGGGCCA
50269189 TTTTTC
1 TTTTTC
50269195 GGGAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (28 bp):
TTTTTCAATAATTTATCGAAATGGGCCA
Found at i:50291206 original size:19 final size:20
Alignment explanation
Indices: 50291179--50291220 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
50291169 ATTAGAAATG
* *
50291179 AAATAATCATAAA-CTTTTA
1 AAATAATCACAAATCTATTA
*
50291198 AAATTATCACAAATCTATTA
1 AAATAATCACAAATCTATTA
50291218 AAA
1 AAA
50291221 ACAAATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATCACAAATCTATTA
Found at i:50291335 original size:14 final size:14
Alignment explanation
Indices: 50291316--50291343 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50291306 GAAAAAGAAA
50291316 GGATTCCACTGTTT
1 GGATTCCACTGTTT
50291330 GGATTCCACTGTTT
1 GGATTCCACTGTTT
50291344 TTCCACCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
GGATTCCACTGTTT
Found at i:50303440 original size:17 final size:17
Alignment explanation
Indices: 50303427--50303468 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
50303417 TTTAAATATG
50303427 AAAAATTTGAAAATCATA
1 AAAAATTT-AAAATCATA
50303445 AAAAATTTAAAA-C-TA
1 AAAAATTTAAAATCATA
50303460 ATAAAATTT
1 A-AAAATTT
50303469 GTAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 8 0.35
17 4 0.17
18 8 0.35
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAAATTTAAAATCATA
Found at i:50303450 original size:18 final size:16
Alignment explanation
Indices: 50303427--50303474 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
50303417 TTTAAATATG
50303427 AAAAATTTGAAAATCATA
1 AAAAATTTGAAAA-C-TA
50303445 AAAAATTT-AAAACTA
1 AAAAATTTGAAAACTA
50303460 ATAAAATTTGTAAAA
1 A-AAAATTTG-AAAA
50303475 ATTATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 3 0.11
16 8 0.30
17 4 0.15
18 12 0.44
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (16 bp):
AAAAATTTGAAAACTA
Found at i:50303591 original size:18 final size:19
Alignment explanation
Indices: 50303556--50303592 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
50303546 ACAAAAATTA
*
50303556 TAAAAATTATTATAATTTT
1 TAAAAAATATTATAATTTT
50303575 TAAAAAATA-TATAATTTT
1 TAAAAAATATTATAATTTT
50303593 AGATTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAAAATATTATAATTTT
Found at i:50303819 original size:9 final size:9
Alignment explanation
Indices: 50303786--50303839 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
50303776 TTTTTTACTC
50303786 ATTTTTATA
1 ATTTTTATA
*
50303795 ATGTTTTACA
1 AT-TTTTATA
*
50303805 AGTTTTATA
1 ATTTTTATA
*
50303814 ATTTTTTTACA
1 A--TTTTTATA
50303825 ATTTTTATA
1 ATTTTTATA
50303834 ATTTTT
1 ATTTTT
50303840 TTTATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 22 0.61
10 7 0.19
11 7 0.19
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:50303840 original size:20 final size:20
Alignment explanation
Indices: 50303776--50303841 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
50303766 TTTTAAATGA
*
50303776 TTTTTTACTCATTTTTATAA-
1 TTTTTTAC-AATTTTTATAAT
* *
50303796 TGTTTTACAAGTTTTATAAT
1 TTTTTTACAATTTTTATAAT
50303816 TTTTTTACAATTTTTATAAT
1 TTTTTTACAATTTTTATAAT
50303836 TTTTTT
1 TTTTTT
50303842 TATATTTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.22
20 31 0.77
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTTTTACAATTTTTATAAT
Found at i:50303848 original size:20 final size:21
Alignment explanation
Indices: 50303776--50303851 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 21
50303766 TTTTAAATGA
50303776 TTTTTTACTCATTTTTATAA--
1 TTTTTTACT-ATTTTTATAATT
* * *
50303796 TGTTTTACAAGTTTTATAA-T
1 TTTTTTACTATTTTTATAATT
*
50303816 TTTTTTACAATTTTTATAATT
1 TTTTTTACTATTTTTATAATT
50303837 TTTTTTA-TATTTTTA
1 TTTTTTACTATTTTTA
50303852 AATAATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.19
20 31 0.65
21 8 0.17
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTTTACTATTTTTATAATT
Found at i:50303852 original size:125 final size:126
Alignment explanation
Indices: 50303692--50303938 Score: 365
Period size: 125 Copynumber: 2.0 Consensus size: 126
50303682 TTTTCATATA
*
50303692 TTTTTTAAAATTTTTAGAACTTTTTAATATTTTTAAATAGTATATATTTATACATTTTTTAAATA
1 TTTTTTAAAATTTTTAGAACTTTTTAATATTTTTAAATAATATATATTTATACATTTTTTAAATA
*
50303757 AATTCTAAA-TTTTAAAT-G-ATTTTTTACTCATTTTTATAATGTTTTACAAGTTTTATAAT
66 AATTCTAAATTTTTAAATGGTATTTTTTACTAATTTTTATAAT-TTTTACAAGTTTTATAAT
* * * *
50303816 TTTTTTACAATTTTTATAATTTTTTTTATATTTTTAAATAATATATATTTATACATTTTTTAAAT
1 TTTTTTAAAATTTTTAGAA-CTTTTTAATATTTTTAAATAATATATATTTATACATTTTTTAAAT
* *
50303881 AAATTTTAAATTTTTAAATGGTCTTTTTTTTACTAATTTTTATAATTTTTACAAGTTT
65 AAATTCTAAATTTTTAAATGG--TATTTTTTACTAATTTTTATAATTTTTACAAGTTT
50303939 CTTTTTACAT
Statistics
Matches: 109, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
124 17 0.16
125 51 0.47
126 8 0.07
127 1 0.01
129 12 0.11
130 20 0.18
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.58
Consensus pattern (126 bp):
TTTTTTAAAATTTTTAGAACTTTTTAATATTTTTAAATAATATATATTTATACATTTTTTAAATA
AATTCTAAATTTTTAAATGGTATTTTTTACTAATTTTTATAATTTTTACAAGTTTTATAAT
Found at i:50303983 original size:20 final size:20
Alignment explanation
Indices: 50303917--50303983 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
50303907 TTTTTACTAA
* *
50303917 TTTTTATAATTTTTACAAGTTT
1 TTTTTACAA-TTTTA-AAATTT
*
50303939 CTTTTTAC-ATTTTAAAATATA
1 -TTTTTACAATTTTAAAAT-TT
50303960 TTTTTACAATTTTAAAATTT
1 TTTTTACAATTTTAAAATTT
50303980 TTTT
1 TTTT
50303984 AATGATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 15 0.39
21 16 0.42
22 1 0.03
23 6 0.16
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (20 bp):
TTTTTACAATTTTAAAATTT
Found at i:50303992 original size:20 final size:21
Alignment explanation
Indices: 50303940--50303984 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
50303930 TACAAGTTTC
50303940 TTTTTAC-ATTTTAAAATATA
1 TTTTTACAATTTTAAAATATA
50303960 TTTTTACAATTTTAAAAT-T-
1 TTTTTACAATTTTAAAATATA
50303979 TTTTTA
1 TTTTTA
50303985 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTTACAATTTTAAAATATA
Found at i:50304410 original size:18 final size:18
Alignment explanation
Indices: 50304387--50304421 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
50304377 AAATACAATA
50304387 ATATTTTAATTTTAAAAC
1 ATATTTTAATTTTAAAAC
*
50304405 ATATTTTATTTTTAAAA
1 ATATTTTAATTTTAAAA
50304422 TATAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTTTAATTTTAAAAC
Found at i:50324328 original size:19 final size:18
Alignment explanation
Indices: 50324301--50324340 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
50324291 TATTATCAAA
* *
50324301 AAAATAAATCCAATTACT
1 AAAATAAATCAAAATACT
50324319 AAAATGAAATCAAAATACT
1 AAAAT-AAATCAAAATACT
50324338 AAA
1 AAA
50324341 CCGAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATCAAAATACT
Found at i:50328758 original size:34 final size:35
Alignment explanation
Indices: 50328714--50328780 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
50328704 CAGTAAAAAG
* *
50328714 TTTTCCGTAAAATGATTT-TTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
50328748 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
50328781 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:50331344 original size:25 final size:25
Alignment explanation
Indices: 50331305--50331356 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
50331295 AAAATGTCTG
50331305 CTGCTTAGAAGAGAATGGAAAATGT
1 CTGCTTAGAAGAGAATGGAAAATGT
50331330 CTGCTTAG-AGAAGAATGGAAAATGT
1 CTGCTTAGAAG-AGAATGGAAAATGT
50331355 CT
1 CT
50331357 TACCAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.38, C:0.10, G:0.27, T:0.25
Consensus pattern (25 bp):
CTGCTTAGAAGAGAATGGAAAATGT
Found at i:50332260 original size:30 final size:30
Alignment explanation
Indices: 50332224--50332324 Score: 104
Period size: 28 Copynumber: 3.4 Consensus size: 30
50332214 ATATTTTTAT
50332224 TTTTTTAATTTTAAAATACTTTTTTTAAAAT--
1 TTTTTTAATTTT-AAAT--TTTTTTTAAAATAC
*
50332255 TTTTTAAATTTTAAATTTTTTTTAAAATAC
1 TTTTTTAATTTTAAATTTTTTTTAAAATAC
* *
50332285 TTTTTTAATTTT---TTTAATTTTAAAATAT
1 TTTTTTAATTTTAAATTT-TTTTTAAAATAC
50332313 TTTTTTAATTTT
1 TTTTTTAATTTT
50332325 TGTTTTAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
27 3 0.05
28 34 0.54
30 15 0.24
31 11 0.17
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTTTAATTTTAAATTTTTTTTAAAATAC
Found at i:50332265 original size:31 final size:28
Alignment explanation
Indices: 50332222--50332296 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 28
50332212 AAATATTTTT
50332222 ATTTTTTTAATTTTAAAATACTTTTTTTAAA
1 ATTTTTTTAATTTT-AAAT--TTTTTTTAAA
*
50332253 ATTTTTTAAATTTTAAATTTTTTTTAAA
1 ATTTTTTTAATTTTAAATTTTTTTTAAA
50332281 ATACTTTTTTAATTTT
1 AT--TTTTTTAATTTT
50332297 TTTAATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 12 0.30
30 15 0.38
31 13 0.32
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTTTTTAATTTTAAATTTTTTTTAAA
Found at i:50332289 original size:40 final size:42
Alignment explanation
Indices: 50332232--50332320 Score: 130
Period size: 41 Copynumber: 2.1 Consensus size: 42
50332222 ATTTTTTTAA
50332232 TTTTAAAATACTTTTTTTAAAATTTTTTAAATTTT-AAAT-TTT
1 TTTTAAAATAC-TTTTTT-AAATTTTTTAAATTTTAAAATATTT
*
50332274 TTTTAAAATACTTTTTT-AATTTTTTTAATTTTAAAATATTT
1 TTTTAAAATACTTTTTTAAATTTTTTAAATTTTAAAATATTT
50332315 TTTTAA
1 TTTTAA
50332321 TTTTTGTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
39 14 0.32
40 4 0.09
41 15 0.34
42 11 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (42 bp):
TTTTAAAATACTTTTTTAAATTTTTTAAATTTTAAAATATTT
Found at i:50332305 original size:28 final size:31
Alignment explanation
Indices: 50332273--50332343 Score: 103
Period size: 28 Copynumber: 2.4 Consensus size: 31
50332263 TTTTAAATTT
50332273 TTTTTAAAATACTTTTTTAA-TTT-TTTTAA
1 TTTTTAAAATACTTTTTTAATTTTGTTTTAA
*
50332302 -TTTTAAAATATTTTTTTAATTTTTGTTTTAA
1 TTTTTAAAATACTTTTTTAA-TTTTGTTTTAA
50332333 TTTTTAAAATA
1 TTTTTAAAATA
50332344 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 18 0.49
30 3 0.08
31 6 0.16
32 10 0.27
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTTTAAAATACTTTTTTAATTTTGTTTTAA
Found at i:50332337 original size:39 final size:38
Alignment explanation
Indices: 50332232--50332342 Score: 107
Period size: 39 Copynumber: 2.8 Consensus size: 38
50332222 ATTTTTTTAA
*
50332232 TTTTAAAATACTTTTTTTAAAATTTTTTAAATTTTAAATTT
1 TTTTTAAATAC-TTTTTT--AATTTTTTAAATTTTAAATTT
*
50332273 TTTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATATT
1 TTTTT-AAATACTTTTTTAATTTTTTAAATTTT-AAAT-TT
** *
50332314 TTTTT-AATTTTTGTTTTAATTTTTAAAAT
1 TTTTTAAATACTT-TTTTAATTTTTTAAAT
50332343 AAATTTTTGG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
39 19 0.32
40 18 0.30
41 17 0.28
42 6 0.10
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (38 bp):
TTTTTAAATACTTTTTTAATTTTTTAAATTTTAAATTT
Found at i:50337874 original size:40 final size:40
Alignment explanation
Indices: 50337819--50337897 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
50337809 ACTACGAGTA
50337819 AGAAAAGAAATTATGAGAGATAACAATTAAAGAAGTACCT
1 AGAAAAGAAATTATGAGAGATAACAATTAAAGAAGTACCT
50337859 AGAAAAGAAATTATGAGAGATAACAATTAAAGAAGTACC
1 AGAAAAGAAATTATGAGAGATAACAATTAAAGAAGTACC
50337898 AACAATTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.56, C:0.08, G:0.18, T:0.19
Consensus pattern (40 bp):
AGAAAAGAAATTATGAGAGATAACAATTAAAGAAGTACCT
Found at i:50337948 original size:20 final size:22
Alignment explanation
Indices: 50337914--50337961 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
50337904 TTCTTGGTAC
*
50337914 CCAAAAATATTA-TTTTTTATT
1 CCAAAAATATAATTTTTTTATT
*
50337935 TCAAAAAT-TAATTTTTTTATT
1 CCAAAAATATAATTTTTTTATT
50337956 CCAAAA
1 CCAAAA
50337962 CCTATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (22 bp):
CCAAAAATATAATTTTTTTATT
Found at i:50337970 original size:21 final size:21
Alignment explanation
Indices: 50337914--50337970 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
50337904 TTCTTGGTAC
50337914 CCAAAAA-TATTATTTTTTATT
1 CCAAAAACTATT-TTTTTTATT
* * *
50337935 TCAAAAATTAATTTTTTTATT
1 CCAAAAACTATTTTTTTTATT
*
50337956 CCAAAACCTATTTTT
1 CCAAAAACTATTTTT
50337971 AAAAGCATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (21 bp):
CCAAAAACTATTTTTTTTATT
Found at i:50344354 original size:41 final size:40
Alignment explanation
Indices: 50344286--50344373 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 40
50344276 GGTGCCAATT
50344286 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
1 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
** * *
50344326 TACTTCGGATTTATTCGATGAGATACTGGGTGTCAATTTAC
1 TACTTCGG-TTTAACCGATGAGACACTGGGTATCAATTTAC
50344367 TACTTCG
1 TACTTCG
50344374 AATTATCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 8 0.19
41 35 0.81
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (40 bp):
TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
Found at i:50345437 original size:17 final size:17
Alignment explanation
Indices: 50345408--50345451 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
50345398 GAATTTGGAA
50345408 GAATTTT-TGAATTAGT
1 GAATTTTGTGAATTAGT
*
50345424 GAATTTTGTGAATTATT
1 GAATTTTGTGAATTAGT
50345441 GAATTTTGTGA
1 GAATTTTGTGA
50345452 TTTAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (17 bp):
GAATTTTGTGAATTAGT
Found at i:50346319 original size:46 final size:46
Alignment explanation
Indices: 50346202--50346431 Score: 363
Period size: 46 Copynumber: 5.0 Consensus size: 46
50346192 CATGGCAAAG
* * * *
50346202 TGTGAAATGTAGGTATGATATTTCAGTGAAGAAAACCATAATGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
50346248 TGTG-AAAGTATGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
50346293 TGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
50346339 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
50346385 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
50346431 T
1 T
50346432 ATAGCAATGT
Statistics
Matches: 170, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 40 0.24
46 130 0.76
ACGTcount: A:0.36, C:0.08, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:50352856 original size:21 final size:20
Alignment explanation
Indices: 50352826--50352864 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
50352816 AAAACGAAAT
50352826 AAAAAGGAAAGAAAGAAAAG
1 AAAAAGGAAAGAAAGAAAAG
50352846 AAAAAGAGAAAGAAAGAAA
1 AAAAAG-GAAAGAAAGAAA
50352865 GAAGAAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAAGGAAAGAAAGAAAAG
Found at i:50352857 original size:17 final size:17
Alignment explanation
Indices: 50352835--50352869 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
50352825 TAAAAAGGAA
50352835 AGAAAGAAAAGAAA-AAG
1 AGAAAG-AAAGAAAGAAG
50352852 AGAAAGAAAGAAAGAAG
1 AGAAAGAAAGAAAGAAG
50352869 A
1 A
50352870 AACGCAAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAGAAAGAAG
Found at i:50353791 original size:37 final size:40
Alignment explanation
Indices: 50353749--50353879 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 40
50353739 GTCGATTAGG
50353749 CACTAGGTGTCAA-TT-TACTTCGG-TTTAACCGATGAGA
1 CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
* **
50353786 CACTAGGTATCAATTTACTACTTCGGATTTATTCGATGAGA
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
* * * * * * *
50353827 CACTCGGTGTTATTTTAGTACTTC-GAATTATCCAATGAGG
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
*
50353867 CACTGGGTGTCAA
1 CACTAGGTGTCAA
50353880 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
37 12 0.16
38 2 0.03
40 30 0.40
41 31 0.41
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
Found at i:50353830 original size:41 final size:37
Alignment explanation
Indices: 50353740--50353830 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 37
50353730 CGACTTCGAG
* * *
50353740 TCGATTAGGCACTAGGTGTCAATTTACTTCGGTTTAA
1 TCGATGAGACACTAGGTATCAATTTACTTCGGTTTAA
* *
50353777 CCGATGAGACACTAGGTATCAATTTACTACTTCGGATTTAT
1 TCGATGAGACACTAGGTATCAA-TT--TACTTCGG-TTTAA
50353818 TCGATGAGACACT
1 TCGATGAGACACT
50353831 CGGTGTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 18 0.41
38 2 0.05
40 8 0.18
41 16 0.36
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (37 bp):
TCGATGAGACACTAGGTATCAATTTACTTCGGTTTAA
Found at i:50363610 original size:20 final size:21
Alignment explanation
Indices: 50363576--50363614 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
50363566 TTTATTTTAT
*
50363576 TTAATTTTCATTTTTTTTAAA
1 TTAATTTTCAGTTTTTTTAAA
50363597 TTAATTTT-AGTTTTTTTA
1 TTAATTTTCAGTTTTTTTA
50363615 TTTTATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (21 bp):
TTAATTTTCAGTTTTTTTAAA
Found at i:50365660 original size:17 final size:18
Alignment explanation
Indices: 50365640--50365678 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
50365630 TGTTTTTTTT
50365640 TCTTTTTC-ATTTTAATA
1 TCTTTTTCTATTTTAATA
50365657 TC-TTTTCTATTTTAATA
1 TCTTTTTCTATTTTAATA
50365674 -CTTTT
1 TCTTTT
50365679 CATATCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTTCTATTTTAATA
Found at i:50365662 original size:16 final size:15
Alignment explanation
Indices: 50365643--50365681 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
50365633 TTTTTTTTCT
50365643 TTTTCATTTTAATATC
1 TTTTCATTTTAATA-C
50365659 TTTTCTATTTTAATAC
1 TTTTC-ATTTTAATAC
50365675 TTTTCAT
1 TTTTCAT
50365682 ATCCATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTAATAC
Found at i:50368211 original size:5 final size:5
Alignment explanation
Indices: 50368203--50368227 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
50368193 TTTTCTTTTT
50368203 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
50368228 ACACATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:50370877 original size:21 final size:22
Alignment explanation
Indices: 50370853--50370911 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
50370843 GCAAAAGATT
*
50370853 ATAAAAGCTGAACAGAAA-CTC
1 ATAAGAGCTGAACAGAAAGCTC
*
50370874 ATAAGAGTTGAACA-AAAGCTC
1 ATAAGAGCTGAACAGAAAGCTC
* *
50370895 GTAAGAGCTTAACAGAA
1 ATAAGAGCTGAACAGAA
50370912 GCTTGAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 3 0.10
21 26 0.84
22 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (22 bp):
ATAAGAGCTGAACAGAAAGCTC
Found at i:50370913 original size:21 final size:21
Alignment explanation
Indices: 50370858--50370924 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
50370848 AGATTATAAA
* * *
50370858 AGCTGAACAGAAACTCATAAG
1 AGCTTAACAGAAGCTCGTAAG
*
50370879 AG-TTGAACAAAAGCTCGTAAG
1 AGCTT-AACAGAAGCTCGTAAG
* *
50370900 AGCTTAACAGAAGCTTGAAAG
1 AGCTTAACAGAAGCTCGTAAG
50370921 AGCT
1 AGCT
50370925 AAAGAAAAAG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.92
22 2 0.05
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.18
Consensus pattern (21 bp):
AGCTTAACAGAAGCTCGTAAG
Found at i:50372404 original size:31 final size:33
Alignment explanation
Indices: 50372342--50372404 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
50372332 ATAACAATAT
*
50372342 AGTGACTTAAATAAAAAAATATTTGAATAGTTC
1 AGTGACTTAAATAAAAAAATATTCGAATAGTTC
* *
50372375 AGTGACTTAAAT-GAAAACT-TTCGAATAGTT
1 AGTGACTTAAATAAAAAAATATTCGAATAGTT
50372405 TAATGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 10 0.37
32 5 0.19
33 12 0.44
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (33 bp):
AGTGACTTAAATAAAAAAATATTCGAATAGTTC
Found at i:50373530 original size:25 final size:25
Alignment explanation
Indices: 50373502--50373584 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
50373492 ATTTTATAAA
50373502 ATAATTATAAGAGCTTCATTGAAAT
1 ATAATTATAAGAGCTTCATTGAAAT
* *** * * * *
50373527 ATAATAATGAATTTCATAATTTTATAAA
1 ATAATTAT-AAGAGCTTCA-TTGA-AAT
50373555 ATAATTATAAGAGCTTCATTGAAAT
1 ATAATTATAAGAGCTTCATTGAAAT
50373580 ATAAT
1 ATAAT
50373585 AATGAATTTC
Statistics
Matches: 39, Mismatches: 16, Indels: 6
0.64 0.26 0.10
Matches are distributed among these distances:
25 14 0.36
26 8 0.21
27 8 0.21
28 9 0.23
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (25 bp):
ATAATTATAAGAGCTTCATTGAAAT
Found at i:50373571 original size:53 final size:53
Alignment explanation
Indices: 50373491--50373597 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
50373481 TTATGAGTTA
50373491 AATTTTATAAAATAATTATAAGAGCTTCATTGAAATATAATAATGAATTTCAT
1 AATTTTATAAAATAATTATAAGAGCTTCATTGAAATATAATAATGAATTTCAT
50373544 AATTTTATAAAATAATTATAAGAGCTTCATTGAAATATAATAATGAATTTCAT
1 AATTTTATAAAATAATTATAAGAGCTTCATTGAAATATAATAATGAATTTCAT
50373597 A
1 A
50373598 GCGGTTATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (53 bp):
AATTTTATAAAATAATTATAAGAGCTTCATTGAAATATAATAATGAATTTCAT
Found at i:50373585 original size:28 final size:28
Alignment explanation
Indices: 50373501--50373587 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
50373491 AATTTTATAA
50373501 AATAATTATAAGAGCTTCATTGAAATAT
1 AATAATTATAAGAGCTTCATTGAAATAT
* *** * * ** *
50373529 AATAA-T-GAATTTCATAATT-TTATAA
1 AATAATTATAAGAGCTTCATTGAAATAT
50373554 AATAATTATAAGAGCTTCATTGAAATAT
1 AATAATTATAAGAGCTTCATTGAAATAT
50373582 AATAAT
1 AATAAT
50373588 GAATTTCATA
Statistics
Matches: 38, Mismatches: 18, Indels: 6
0.61 0.29 0.10
Matches are distributed among these distances:
25 8 0.21
26 8 0.21
27 8 0.21
28 14 0.37
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (28 bp):
AATAATTATAAGAGCTTCATTGAAATAT
Found at i:50374693 original size:20 final size:19
Alignment explanation
Indices: 50374646--50374694 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
50374636 CATGTTTTTA
*
50374646 AAATGATTTGATTTATACC
1 AAATTATTTGATTTATACC
* *
50374665 AAATGTATTTGAGTTTATTCT
1 AAAT-TATTTGA-TTTATACC
50374686 AAATTATTT
1 AAATTATTT
50374695 TAAAGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 10 0.40
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (19 bp):
AAATTATTTGATTTATACC
Found at i:50376571 original size:21 final size:21
Alignment explanation
Indices: 50376525--50376582 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
50376515 CTAGAAGGGT
* *
50376525 AAAGTGTCAATACTTGATCTT
1 AAAGTATCAATACTTGATCTA
*
50376546 GAAGTATCAATACTT-ACTCTA
1 AAAGTATCAATACTTGA-TCTA
**
50376567 AAAGTATTTATACTTG
1 AAAGTATCAATACTTG
50376583 CCTTAAAGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
AAAGTATCAATACTTGATCTA
Found at i:50387975 original size:167 final size:167
Alignment explanation
Indices: 50387692--50388027 Score: 636
Period size: 167 Copynumber: 2.0 Consensus size: 167
50387682 ATGACATTAA
*
50387692 CAACCTCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
*
50387757 CATCCAATATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
66 CATCCAAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
50387822 ATGATCCACCCACCATTATGATCTCGCACTAATCCTT
131 ATGATCCACCCACCATTATGATCTCGCACTAATCCTT
50387859 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
* *
50387924 CATCCAAGATGCCCCAAAGCTCAACTTTCGTCACCGTGCAATTTCCTAAGTATCTGCAGAACCCA
66 CATCCAAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
50387989 ATGATCCACCCACCATTATGATCTCGCACTAATCCTT
131 ATGATCCACCCACCATTATGATCTCGCACTAATCCTT
50388026 CA
1 CA
50388028 GCAGCAGTGA
Statistics
Matches: 165, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 165 1.00
ACGTcount: A:0.32, C:0.31, G:0.11, T:0.26
Consensus pattern (167 bp):
CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
CATCCAAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
ATGATCCACCCACCATTATGATCTCGCACTAATCCTT
Found at i:50389630 original size:31 final size:31
Alignment explanation
Indices: 50389571--50389630 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
50389561 AGTCACAAAT
* * ***
50389571 GTTTTCGATCATTTCTATTTTGGTCACTCAC
1 GTTTTAGATCATTTCTAGTTTAACCACTCAC
50389602 GTTTTAGATCATTTCTAGTTTAACCACTC
1 GTTTTAGATCATTTCTAGTTTAACCACTC
50389631 TCCTTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (31 bp):
GTTTTAGATCATTTCTAGTTTAACCACTCAC
Found at i:50390277 original size:17 final size:16
Alignment explanation
Indices: 50390238--50390277 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
50390228 GTAATATTTT
50390238 TAATTTTTTATATACA
1 TAATTTTTTATATACA
*
50390254 TAGATTTTTTATAATTCA
1 TA-ATTTTTTAT-ATACA
50390272 TAATTT
1 TAATTT
50390278 CTTTTGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 13 0.62
18 6 0.29
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (16 bp):
TAATTTTTTATATACA
Found at i:50390340 original size:22 final size:22
Alignment explanation
Indices: 50390298--50390341 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
50390288 TTAAATTTCT
* * *
50390298 TTTATATATTTTATTATAAATA
1 TTTAAATATTTTATAAAAAATA
50390320 TTTAAATATTTTATAAAAAATA
1 TTTAAATATTTTATAAAAAATA
50390342 GAGTATGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAATATTTTATAAAAAATA
Found at i:50391225 original size:13 final size:13
Alignment explanation
Indices: 50391196--50391235 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
50391186 ATTTTTTATA
*
50391196 TAAAATAAATAAAT
1 TAAAAAAAAT-AAT
*
50391210 TAACAAAAATAAT
1 TAAAAAAAATAAT
50391223 TAAAAAAAATAAT
1 TAAAAAAAATAAT
50391236 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAAAAAATAAT
Found at i:50395306 original size:39 final size:39
Alignment explanation
Indices: 50395255--50395335 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
50395245 AGTTTGATGA
* * *
50395255 AATAATGCAAATACATAGTTGAGCGAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
*
50395294 AATAATGTAAATACATAGATAAGCAAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
50395333 AAT
1 AAT
50395336 TAAATTAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (39 bp):
AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
Found at i:50401479 original size:19 final size:19
Alignment explanation
Indices: 50401455--50401492 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
50401445 GTCAAATCTA
50401455 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
50401474 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
50401493 ATTGTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTATATTTAATT
Found at i:50410812 original size:11 final size:11
Alignment explanation
Indices: 50410785--50410827 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
50410775 TGACCTTTCC
50410785 AAGGTATGGG-
1 AAGGTATGGGA
*
50410795 TAGGTATGGGA
1 AAGGTATGGGA
*
50410806 AAGGTATGGGC
1 AAGGTATGGGA
50410817 AAGGTATGGGA
1 AAGGTATGGGA
50410828 TATATTCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:50410824 original size:22 final size:21
Alignment explanation
Indices: 50410785--50410827 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
50410775 TGACCTTTCC
*
50410785 AAGGTATGGGTAGGTATGGGA
1 AAGGTATGGGAAGGTATGGGA
50410806 AAGGTATGGGCAAGGTATGGGA
1 AAGGTATGGG-AAGGTATGGGA
50410828 TATATTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (21 bp):
AAGGTATGGGAAGGTATGGGA
Found at i:50414892 original size:18 final size:18
Alignment explanation
Indices: 50414869--50414943 Score: 105
Period size: 18 Copynumber: 4.2 Consensus size: 18
50414859 CCCAACTACT
* *
50414869 GTATACGTGAACAGTACC
1 GTATACGTAAATAGTACC
*
50414887 GTATACGTGAATAGTACC
1 GTATACGTAAATAGTACC
* *
50414905 GTATACATAAATAGTGCC
1 GTATACGTAAATAGTACC
50414923 GTATACGTAAATAGTACC
1 GTATACGTAAATAGTACC
50414941 GTA
1 GTA
50414944 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (18 bp):
GTATACGTAAATAGTACC
Found at i:50420228 original size:17 final size:17
Alignment explanation
Indices: 50420198--50420231 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50420188 TTTGTCACCC
*
50420198 ACCATATGGGTCTCATT
1 ACCATATGGATCTCATT
*
50420215 ACCATTTGGATCTCATT
1 ACCATATGGATCTCATT
50420232 GGTTTTTGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (17 bp):
ACCATATGGATCTCATT
Found at i:50422087 original size:20 final size:19
Alignment explanation
Indices: 50422064--50422107 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
50422054 ATATGCTTTC
*
50422064 AAAATTAAATTTTGATATGA
1 AAAATCAAATTTTGATAT-A
* *
50422084 AAAATCAATTTTTGGTATA
1 AAAATCAAATTTTGATATA
50422103 AAAAT
1 AAAAT
50422108 ACCATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
AAAATCAAATTTTGATATA
Found at i:50422429 original size:23 final size:24
Alignment explanation
Indices: 50422403--50422451 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
50422393 TTGTCCTCCT
* *
50422403 AACA-AAATTTCATAGTATGTCAA
1 AACATAAATTTCAAAGTATATCAA
*
50422426 AACATAAATTTGAAAGTATATCAA
1 AACATAAATTTCAAAGTATATCAA
50422450 AA
1 AA
50422452 ATCAAGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (24 bp):
AACATAAATTTCAAAGTATATCAA
Found at i:50431382 original size:56 final size:56
Alignment explanation
Indices: 50431296--50431427 Score: 228
Period size: 56 Copynumber: 2.4 Consensus size: 56
50431286 GGAGCAAGGC
* *
50431296 AAATTAAAGATACAAGGTAGTGAATCTGATATCTCAGCTCATTTTCAGAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
* *
50431352 AAATTAAAGATATAAGTTAGTGAATCTGATATCTCAGCTCATTTTTACAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
50431408 AAATTAAAGATATAAGGTAG
1 AAATTAAAGATATAAGGTAG
50431428 CTCTCTTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (56 bp):
AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
Found at i:50433337 original size:14 final size:15
Alignment explanation
Indices: 50433302--50433336 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
50433292 AAAAAAACAG
50433302 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
*
50433317 AAAAAAGAAGAAGCAA
1 AAAAAAGAAAAAG-AA
50433333 AAAA
1 AAAA
50433337 GCGCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:50433347 original size:11 final size:12
Alignment explanation
Indices: 50433331--50433360 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50433321 AAGAAGAAGC
*
50433331 AAAAAAGCGCAA
1 AAAAAACCGCAA
50433343 AAAAAACCGCAA
1 AAAAAACCGCAA
50433355 AAAAAA
1 AAAAAA
50433361 AGTTGCCTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.17, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAACCGCAA
Found at i:50439323 original size:23 final size:23
Alignment explanation
Indices: 50439233--50439324 Score: 89
Period size: 23 Copynumber: 3.9 Consensus size: 23
50439223 GAGCCATGAT
*
50439233 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
*
50439259 CGGTAAGCTC-TATCGAGTTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
*
50439282 CGGTAAGCTCCGTA-GAGCTGAAA
1 CGGTAAGCT-CATACGAGCTGAAA
*
50439305 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACGAGCTG
50439325 TGGTGAGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.05
23 34 0.60
24 2 0.04
25 8 0.14
26 10 0.18
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:50439609 original size:29 final size:29
Alignment explanation
Indices: 50439576--50439634 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
50439566 CTATATAATG
50439576 TATATAGTATTTGTAACATTTCATTTGCA
1 TATATAGTATTTGTAACATTTCATTTGCA
50439605 TATATAGTATTTGTAACATTTCATTTGCA
1 TATATAGTATTTGTAACATTTCATTTGCA
50439634 T
1 T
50439635 TCATGTAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
TATATAGTATTTGTAACATTTCATTTGCA
Found at i:50446207 original size:41 final size:41
Alignment explanation
Indices: 50446173--50446286 Score: 183
Period size: 41 Copynumber: 2.8 Consensus size: 41
50446163 ACCGGCAATT
*
50446173 AGCCTGCTAGACTTAAAGTCTGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
* *
50446214 AGCCTGCTAGACATAAAGTCTGAAATATTTTACTGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
* *
50446255 AACCTGCTAGACATAAAGTCTGAATTATTTCA
1 AGCCTGCTAGACATAAAGTCTGAAATATTTCA
50446287 TTGGCAATAG
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
Found at i:50448481 original size:19 final size:19
Alignment explanation
Indices: 50448436--50448475 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
50448426 AGTTCATGTT
* *
50448436 TTCATTTCACATTTTCATA
1 TTCAATTCACATTTTCAAA
50448455 TTCAATTCACATTTTCAAA
1 TTCAATTCACATTTTCAAA
50448474 TT
1 TT
50448476 ATATTCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTCACATTTTCAAA
Found at i:50448762 original size:39 final size:39
Alignment explanation
Indices: 50448669--50448850 Score: 184
Period size: 39 Copynumber: 4.4 Consensus size: 39
50448659 AGCAGTAACA
* * *
50448669 GTAACAGTAATAGTATTCAACACACAAAGTGTCGAATCTG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TG
* *
50448709 TAATAGTACGGTAACAGTATTCGACACACAAAGTGCCGAATTG
1 --GTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
* *
50448752 GTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG
1 GTAACAGTAAC----A--GTATTCGACACACAAAGTGCCGAATTG
* *
50448797 ATAACAGTAACAGTATTCGACACACAAAGTGCCGAATTA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
50448836 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
50448851 GTCGGCATAT
Statistics
Matches: 118, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
39 45 0.38
41 3 0.03
42 2 0.02
43 3 0.03
44 30 0.25
45 35 0.30
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.21
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
Found at i:50448840 original size:84 final size:87
Alignment explanation
Indices: 50448662--50448850 Score: 269
Period size: 84 Copynumber: 2.2 Consensus size: 87
50448652 TTACGGTAGC
* * *
50448662 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGTCGAATCTGTAATAGTACGGTAACAGT
1 AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTG-AATAG-ACAGTAACAGT
50448727 ATTCGACACACAAAGTGCCGAATT
64 ATTCGACACACAAAGTGCCGAATT
* * *
50448751 GGTAACAGTAACGGTAACCGTATTCGAA-ACACAAAGTGCCGAATC-G-ATA-ACAGTAACAGTA
1 AGTAACAGTAACAGTAACAGTATTC-AACACACAAAGTGCCGAATCTGAATAGACAGTAACAGTA
50448812 TTCGACACACAAAGTGCCGAATT
65 TTCGACACACAAAGTGCCGAATT
50448835 AGTAACAGTAACAGTA
1 AGTAACAGTAACAGTA
50448851 GTCGGCATAT
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
84 48 0.53
86 3 0.03
88 1 0.01
89 37 0.41
90 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (87 bp):
AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTGAATAGACAGTAACAGTAT
TCGACACACAAAGTGCCGAATT
Found at i:50448847 original size:45 final size:45
Alignment explanation
Indices: 50448662--50448850 Score: 223
Period size: 45 Copynumber: 4.4 Consensus size: 45
50448652 TTACGGTAGC
* * *
50448662 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGTCGAATCT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-T
* *
50448708 -GTAATAGT-ACGGTAACAGTATTCGACACACAAAGTGCCGAATT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
* * * *
50448751 GGTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAA-T
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
*
50448795 CG----A-TAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
50448835 AGTAACAGTAACAGTA
1 AGTAACAGTAACAGTA
50448851 GTCGGCATAT
Statistics
Matches: 122, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
39 32 0.26
40 3 0.02
43 1 0.01
44 40 0.33
45 46 0.38
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (45 bp):
AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
Found at i:50457568 original size:22 final size:22
Alignment explanation
Indices: 50457543--50457606 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
50457533 TCTCCAATTA
50457543 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
50457565 TTAGCACATTTGTGCTCTATGT
1 TTAGCACATTAGTGCTCTCTGT
* *
50457587 ATAGCACTTTAGTGCTCTCT
1 TTAGCACATTAGTGCTCTCT
50457607 ATTCAATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:50464649 original size:36 final size:36
Alignment explanation
Indices: 50464602--50464674 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
50464592 TTTTTATGGA
50464602 TAAACTATAAAAACGGTCATCCAACTATGCCATTCG
1 TAAACTATAAAAACGGTCATCCAACTATGCCATTCG
* *
50464638 TAAACTATAAAAACGGTCATCCAGCTATGCCTTTCG
1 TAAACTATAAAAACGGTCATCCAACTATGCCATTCG
50464674 T
1 T
50464675 TCTATTTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (36 bp):
TAAACTATAAAAACGGTCATCCAACTATGCCATTCG
Found at i:50466018 original size:61 final size:61
Alignment explanation
Indices: 50465891--50466017 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
50465881 TATATTTAAA
*** *
50465891 ATTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGGGCAAAATTTATTGAT
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
* ** *
50465952 ATTTTTAGAATTAGAACTAAAACAATAAATTTTGTAAACATTGAGGGTTAAATTTGTTGA-
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
50466012 ATTTTT
1 ATTTTT
50466018 TTTATATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 6 0.10
61 52 0.90
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (61 bp):
ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
Found at i:50469192 original size:7 final size:6
Alignment explanation
Indices: 50469173--50469208 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
50469163 TGCAGTGAAT
*
50469173 ATAAATA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
50469209 GGTATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:50471431 original size:2 final size:2
Alignment explanation
Indices: 50471424--50471457 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50471414 GACAAATCTC
50471424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50471458 CAAAACATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50480367 original size:17 final size:17
Alignment explanation
Indices: 50480340--50480373 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
50480330 CGATTCAAAG
50480340 TAAATAAATTATTAAAAA
1 TAAATAAATTA-TAAAAA
50480358 TAAA-AAATTATAAAAA
1 TAAATAAATTATAAAAA
50480374 CCAAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Found at i:50485560 original size:16 final size:16
Alignment explanation
Indices: 50485512--50485560 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
50485502 TCAAGAATAC
50485512 TTATATTTAGAACAA-
1 TTATATTTAGAACAAT
* * *
50485527 CTATTATTTGGAAAAAT
1 TTA-TATTTAGAACAAT
50485544 TTATATTTAGAACAAT
1 TTATATTTAGAACAAT
50485560 T
1 T
50485561 GTGTTTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
TTATATTTAGAACAAT
Found at i:50488068 original size:4 final size:4
Alignment explanation
Indices: 50488061--50488164 Score: 190
Period size: 4 Copynumber: 25.5 Consensus size: 4
50488051 CATAACATTA
50488061 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
50488109 TATG TATG TATG TATG TAAATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG T--ATG TATG TATG TATG TATG TATG TATG TATG
50488159 TATG TA
1 TATG TA
50488165 AAGGTGTCAT
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 94 0.96
6 4 0.04
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:50488314 original size:17 final size:17
Alignment explanation
Indices: 50488292--50488324 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
50488282 GCCCATCTCC
50488292 GAAGCTTGGCAAATATG
1 GAAGCTTGGCAAATATG
50488309 GAAGCTTGGCAAATAT
1 GAAGCTTGGCAAATAT
50488325 AATCTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (17 bp):
GAAGCTTGGCAAATATG
Found at i:50504255 original size:2 final size:2
Alignment explanation
Indices: 50504248--50504277 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
50504238 ACCTTTATAA
50504248 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
50504278 TTCTGTGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:50512334 original size:16 final size:17
Alignment explanation
Indices: 50512308--50512344 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
50512298 GTTTTTTCCG
*
50512308 GGAGAAGTGGGAAAGGA
1 GGAGAAGTGGGAAAGCA
50512325 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGCA
50512341 GGAG
1 GGAG
50512345 TTGAAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.38, C:0.03, G:0.54, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGCA
Found at i:50517458 original size:24 final size:24
Alignment explanation
Indices: 50517431--50517482 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
50517421 TTTCTAGAAG
* **
50517431 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
50517455 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
50517479 ATTT
1 ATTT
50517483 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:50534663 original size:33 final size:33
Alignment explanation
Indices: 50534620--50534687 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
50534610 CAAAGTTACC
* *
50534620 TTCACGAGCAACGACATCATCTTAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
50534653 TTCACAAGCAACGACATCATCTCAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
50534686 TT
1 TT
50534688 GCTAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (33 bp):
TTCACAAGCAACGACATCATCTCAGTGGAAACA
Found at i:50540047 original size:22 final size:22
Alignment explanation
Indices: 50540008--50540080 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 22
50539998 GCAACCCAAT
*
50540008 TTTTATTTTTATTATTATTTATT-
1 TTTTA-TTTTACT-TTATTTATTA
*
50540031 TTTTTTCTTTACTTTATTTATTA
1 TTTTAT-TTTACTTTATTTATTA
*
50540054 TTTTATTTTATTTTATTTTACTTA
1 TTTTATTTTACTTTA-TTTA-TTA
50540078 TTT
1 TTT
50540081 GGATATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 18 0.43
23 18 0.43
24 6 0.14
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATTTTACTTTATTTATTA
Found at i:50540059 original size:5 final size:5
Alignment explanation
Indices: 50540008--50540073 Score: 57
Period size: 5 Copynumber: 13.0 Consensus size: 5
50539998 GCAACCCAAT
* *
50540008 TTTTA TTTTTA TTATTA -TTTA TTTT- TTTT- CTTTA CTTTA TTTATTA
1 TTTTA -TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA -TT-TTA
50540054 TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA
50540074 CTTATTTGGA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
4 10 0.19
5 29 0.55
6 11 0.21
7 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:50540063 original size:17 final size:16
Alignment explanation
Indices: 50540008--50540073 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
50539998 GCAACCCAAT
50540008 TTTTATTTTTATTATTA
1 TTTTATTTTTATT-TTA
*
50540025 -TTTATTTTTTTTCTTTA
1 TTTTA-TTTTTAT-TTTA
*
50540042 CTTTATTTATTATTTTA
1 TTTTATTT-TTATTTTA
50540059 TTTTA-TTTTATTTTA
1 TTTTATTTTTATTTTA
50540074 CTTATTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 8 0.19
16 6 0.14
17 20 0.48
18 8 0.19
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTTATTTTA
Found at i:50541118 original size:20 final size:20
Alignment explanation
Indices: 50541093--50541131 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
50541083 CCTAAAGCAT
*
50541093 AAAAAAATGAGAAAAAAAAC
1 AAAAAAAAGAGAAAAAAAAC
*
50541113 AAAAAAAAGATAAAAAAAA
1 AAAAAAAAGAGAAAAAAAA
50541132 ATAATTTGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAAC
Done.