Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 118 of 167
Found at i:39495686 original size:87 final size:87
Alignment explanation
Indices: 39495583--39495752 Score: 324
Period size: 87 Copynumber: 2.0 Consensus size: 87
39495573 TAAATTTAAT
39495583 TCGAGGCAATTCCTGAATTTTAATTTTGGGAGAGAGGGTTCTGGCGATATGGGCTTTT-AAAGTT
1 TCGAGGCAATTCCTGAATTTTAATTTTGGGAGAGAGGGTTCTGGCGATATGGGCTTTTCAAA-TT
39495647 GAGGTGGTAAAATAGGACACAAA
65 GAGGTGGTAAAATAGGACACAAA
39495670 TCGAGGCAATTCCTGAATTTTAATTTTGGGAGAGAGGGTTCTGGCGATATGGGCTTTTCAAATTG
1 TCGAGGCAATTCCTGAATTTTAATTTTGGGAGAGAGGGTTCTGGCGATATGGGCTTTTCAAATTG
39495735 AGGTGGTAAAATAGGACA
66 AGGTGGTAAAATAGGACA
39495753 TAAAAAGATC
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 79 0.96
88 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.31
Consensus pattern (87 bp):
TCGAGGCAATTCCTGAATTTTAATTTTGGGAGAGAGGGTTCTGGCGATATGGGCTTTTCAAATTG
AGGTGGTAAAATAGGACACAAA
Found at i:39496126 original size:17 final size:16
Alignment explanation
Indices: 39496097--39496157 Score: 63
Period size: 17 Copynumber: 3.7 Consensus size: 16
39496087 TTCTTCTTCC
39496097 TCTCTTT-TTCCTTCATT
1 TCTCTTTCTTCCTT--TT
39496114 T-TCTTTCTTCCTTTT
1 TCTCTTTCTTCCTTTT
39496129 TGCTCTTTCTTCCTTTT
1 T-CTCTTTCTTCCTTTT
*
39496146 TGCTTTTTCTTC
1 T-CTCTTTCTTC
39496158 TAGCCGAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
15 3 0.08
16 5 0.12
17 32 0.80
ACGTcount: A:0.02, C:0.28, G:0.03, T:0.67
Consensus pattern (16 bp):
TCTCTTTCTTCCTTTT
Found at i:39499739 original size:43 final size:41
Alignment explanation
Indices: 39499685--39499841 Score: 145
Period size: 43 Copynumber: 3.7 Consensus size: 41
39499675 ATATCGTACA
*
39499685 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATGTCG
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AATCACAT-TCG
* * * * *
39499728 ATGCCACTGTCCCGGATAAGGTCTTACACGAATCACAATTACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAATCAC-ATT-CG
* **
39499771 ATGCCAATATCCCAGACATGGTCTTAC-TCGAAATCGTATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACAT-G-AATCACAT-TCG
* *
39499814 ATGCCAACGTCCTAGACATGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
39499842 CGAGAACACA
Statistics
Matches: 91, Mismatches: 17, Indels: 11
0.76 0.14 0.09
Matches are distributed among these distances:
42 7 0.08
43 79 0.87
44 5 0.05
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAATCACATTCG
Found at i:39499837 original size:86 final size:86
Alignment explanation
Indices: 39499685--39499844 Score: 198
Period size: 86 Copynumber: 1.9 Consensus size: 86
39499675 ATATCGTACA
* * * * * *
39499685 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATGTCGATGCCACTGTCCCGGATAAGGT
1 ATGCCAATATCCCAGACATGGTCTTACATGAAATCACATATCGATGCCACTGTCCCAGACAAGGT
39499750 CTTACACGAATCACAATTACG
66 CTTACACGAATCACAATTACG
** * *
39499771 ATGCCAATATCCCAGACATGGTCTTAC-TCGAAATCGTATATCGATGCCAAC-GTCCTAGACATG
1 ATGCCAATATCCCAGACATGGTCTTACAT-GAAATCACATATCGATGCC-ACTGTCCCAGACAAG
39499834 GTCTTACACGA
64 GTCTTACACGA
39499845 GAACACATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
85 1 0.02
86 59 0.95
87 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.26
Consensus pattern (86 bp):
ATGCCAATATCCCAGACATGGTCTTACATGAAATCACATATCGATGCCACTGTCCCAGACAAGGT
CTTACACGAATCACAATTACG
Found at i:39500681 original size:13 final size:13
Alignment explanation
Indices: 39500663--39500693 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39500653 ATACCTAAAG
39500663 CTTTCTTTTATTT
1 CTTTCTTTTATTT
*
39500676 CTTTCTTTTGTTT
1 CTTTCTTTTATTT
39500689 CTTTC
1 CTTTC
39500694 GGTCAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.74
Consensus pattern (13 bp):
CTTTCTTTTATTT
Found at i:39528429 original size:24 final size:24
Alignment explanation
Indices: 39528385--39528467 Score: 60
Period size: 24 Copynumber: 3.5 Consensus size: 24
39528375 AATTTGCACC
*
39528385 CATAGTGCCATTTTAACCCACACA
1 CATAGTGCCATTGTAACCCACACA
* *
39528409 CATAGTGCC-TTAGTAATCCACACT
1 CATAGTGCCATT-GTAACCCACACA
* * * ** * *
39528433 CGTATTGACATTCAAATCCGCACA
1 CATAGTGCCATTGTAACCCACACA
39528457 CATAGTGCCAT
1 CATAGTGCCAT
39528468 ACAAATCTGC
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (24 bp):
CATAGTGCCATTGTAACCCACACA
Found at i:39528472 original size:24 final size:24
Alignment explanation
Indices: 39528445--39528538 Score: 136
Period size: 24 Copynumber: 3.9 Consensus size: 24
39528435 TATTGACATT
39528445 CAAATCCGCACACATAGTGCCATA
1 CAAATCCGCACACATAGTGCCATA
*
39528469 CAAATCTGCACACATAGTGCCATA
1 CAAATCCGCACACATAGTGCCATA
*
39528493 CAAA-CCTGCACACATAGTGCCATT
1 CAAATCC-GCACACATAGTGCCATA
* *
39528517 CAGATCCGCATACATAGTGCCA
1 CAAATCCGCACACATAGTGCCA
39528539 AAGTTATTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
23 1 0.02
24 60 0.95
25 2 0.03
ACGTcount: A:0.35, C:0.32, G:0.14, T:0.19
Consensus pattern (24 bp):
CAAATCCGCACACATAGTGCCATA
Found at i:39528985 original size:14 final size:14
Alignment explanation
Indices: 39528966--39528996 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39528956 ATTACTTCAA
39528966 ATAAACACACATAT
1 ATAAACACACATAT
*
39528980 ATAAACACATATAT
1 ATAAACACACATAT
39528994 ATA
1 ATA
39528997 TTTGTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAACACACATAT
Found at i:39532720 original size:43 final size:41
Alignment explanation
Indices: 39532651--39532807 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 41
39532641 ATATCGTACA
* * * *
39532651 ATGCCAACGTCCCAGACGTGGCCTTACATGTAATCACATGTCG
1 ATGCCAATGTCCCAAACATGGTCTTACATG-AATCACAT-TCG
* * * *
39532694 ATGCCACTGTCCCAAACAGGGTCTTACACGAATCACAATTATG
1 ATGCCAATGTCCCAAACATGGTCTTACATGAATCAC-ATT-CG
* * *
39532737 ATGCCAATGTTCCAGACATGGTCTTAC-TCGAAATCATATATCG
1 ATGCCAATGTCCCAAACATGGTCTTACAT-G-AATCACAT-TCG
*
39532780 ATGCCAATGTCCTAAACATGGTCTTACA
1 ATGCCAATGTCCCAAACATGGTCTTACA
39532808 CGAGAACAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
42 7 0.08
43 77 0.86
44 6 0.07
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (41 bp):
ATGCCAATGTCCCAAACATGGTCTTACATGAATCACATTCG
Found at i:39532797 original size:86 final size:86
Alignment explanation
Indices: 39532651--39532810 Score: 214
Period size: 86 Copynumber: 1.9 Consensus size: 86
39532641 ATATCGTACA
* * * *
39532651 ATGCCAACGTCCCAGACGTGGCCTTACATGTAATCACATGTCGATGCCACTGTCCCAAACAGGGT
1 ATGCCAACGTCCCAGACATGGCCTTACATGAAATCACATATCGATGCCAATGTCCCAAACAGGGT
39532716 CTTACACGAATCACAATTATG
66 CTTACACGAATCACAATTATG
* * * * * *
39532737 ATGCCAATGTTCCAGACATGGTCTTAC-TCGAAATCATATATCGATGCCAATGTCCTAAACATGG
1 ATGCCAACGTCCCAGACATGGCCTTACAT-GAAATCACATATCGATGCCAATGTCCCAAACAGGG
39532801 TCTTACACGA
65 TCTTACACGA
39532811 GAACAGATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
85 1 0.02
86 62 0.98
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (86 bp):
ATGCCAACGTCCCAGACATGGCCTTACATGAAATCACATATCGATGCCAATGTCCCAAACAGGGT
CTTACACGAATCACAATTATG
Found at i:39532821 original size:43 final size:40
Alignment explanation
Indices: 39532691--39532823 Score: 133
Period size: 43 Copynumber: 3.1 Consensus size: 40
39532681 TAATCACATG
* *
39532691 TCGATGCCACTGTCCCAAACAGGGTCTTACACGAATCACAATTA
1 TCGATGCCAATGT-CCAAACATGGTCTTACACGAA--ACAA-TA
* *
39532735 T-GATGCCAATGTTCCAGACATGGTCTTACTCGAAATCATATA
1 TCGATGCCAATG-TCCAAACATGGTCTTACACGAAA-CA-ATA
39532777 TCGATGCCAATGTCCTAAACATGGTCTTACACGAGAACAGATA
1 TCGATGCCAATGTCC-AAACATGGTCTTACACGA-AACA-ATA
39532820 TCGA
1 TCGA
39532824 AAATCCTATG
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
41 1 0.01
42 8 0.11
43 63 0.83
44 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (40 bp):
TCGATGCCAATGTCCAAACATGGTCTTACACGAAACAATA
Found at i:39534908 original size:43 final size:44
Alignment explanation
Indices: 39534842--39534998 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 44
39534832 AGCTCGTACA
*
39534842 ATGCCAATGTACCAGACGTGGTCTTACATGTAAA-CAAATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACATGTAAATCAAATATCG
* ** *
39534885 ATGCCATTGTCCCAGACAG-GGTCTTACA-CAAAATTAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAAATCAAATATCG
* * *
39534927 ATG-TAGATGTCCTAGACATGGTCTTACATGTAAATCATAAGT-T-G
1 ATGCCA-ATGTCCCAGACGTGGTCTTACATGTAAATCA-AA-TATCG
39534971 ATGCCAATGTCCCAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACGTGGTCTTACA
39534999 CGGTCACACA
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 34 0.38
44 27 0.30
45 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACGTGGTCTTACATGTAAATCAAATATCG
Found at i:39537081 original size:5 final size:5
Alignment explanation
Indices: 39537073--39537105 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
39537063 ATACTTTAAT
39537073 TATAA TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT
39537106 TTTCTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:39539366 original size:79 final size:79
Alignment explanation
Indices: 39539281--39539430 Score: 194
Period size: 79 Copynumber: 1.9 Consensus size: 79
39539271 TTAAGAATCA
* * * * ** *
39539281 AAAATAAAATAAATTCTATTAAACTATAGGAATGGAATCC-AGAAACAGAATTGTTCAATTGATT
1 AAAATAAAACAAATTCTATTAAACAACAAGAATAAAATCCTA-AAACAGAATTATTCAATTGATT
39539345 TCTATTTGGAAACAG
65 TCTATTTGGAAACAG
* * *
39539360 AAAATAAAACAAATTCTTTTGAACAACAAGAATAAAATCCTAAAATAGAATTATTCAATTGATTT
1 AAAATAAAACAAATTCTATTAAACAACAAGAATAAAATCCTAAAACAGAATTATTCAATTGATTT
39539425 CTATTT
66 CTATTT
39539431 ACAAATAGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 59 0.98
80 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.32
Consensus pattern (79 bp):
AAAATAAAACAAATTCTATTAAACAACAAGAATAAAATCCTAAAACAGAATTATTCAATTGATTT
CTATTTGGAAACAG
Found at i:39544201 original size:2 final size:2
Alignment explanation
Indices: 39544194--39544218 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39544184 TAACTAAATG
39544194 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
39544219 ATATGTGTTT
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:39546222 original size:31 final size:31
Alignment explanation
Indices: 39546186--39546248 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
39546176 TCTTTTTACA
39546186 TAGGTTTTCTAGTAGGGTTTCATGTAGTAGT
1 TAGGTTTTCTAGTAGGGTTTCATGTAGTAGT
39546217 TAGGTTTTCTAGTAGGGTTTCATGTAGTAGT
1 TAGGTTTTCTAGTAGGGTTTCATGTAGTAGT
39546248 T
1 T
39546249 TTTTTCCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.06, G:0.29, T:0.46
Consensus pattern (31 bp):
TAGGTTTTCTAGTAGGGTTTCATGTAGTAGT
Found at i:39551516 original size:5 final size:5
Alignment explanation
Indices: 39551506--39551532 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39551496 GTGTTTTTTA
39551506 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
39551533 TCACATCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:39555081 original size:29 final size:30
Alignment explanation
Indices: 39555025--39555101 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
39555015 TCAATGGTCG
* * *
39555025 AAACCATCCCTTTTCTTTAATTGATAGCC-A
1 AAACTATCCCTTTTC-ATAATCGATAGCCGA
39555055 AAACTATCCCTTTTCATAATCGATAGCCGA
1 AAACTATCCCTTTTCATAATCGATAGCCGA
*
39555085 AGA-TATCCCTTTTCATA
1 AAACTATCCCTTTTCATA
39555102 TTCAATGGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (30 bp):
AAACTATCCCTTTTCATAATCGATAGCCGA
Found at i:39555196 original size:29 final size:29
Alignment explanation
Indices: 39555162--39555239 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
39555152 TTTTCGTCAA
39555162 CATCCCTTTTCATATTCGATGGTCATCAC
1 CATCCCTTTTCATATTCGATGGTCATCAC
*
39555191 CATCCCTTTTCATAGTT-GATGGTCGTCAC
1 CATCCCTTTTCATA-TTCGATGGTCATCAC
* *
39555220 CATCCCTTTTAATAATCGAT
1 CATCCCTTTTCATATTCGAT
39555240 AGCCGAAGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 41 0.93
30 2 0.05
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (29 bp):
CATCCCTTTTCATATTCGATGGTCATCAC
Found at i:39555294 original size:29 final size:29
Alignment explanation
Indices: 39555221--39555344 Score: 169
Period size: 29 Copynumber: 4.3 Consensus size: 29
39555211 GGTCGTCACC
* * *
39555221 ATCCCTTTTAATAATCGATAGCCGAAGCT
1 ATCCTTTTTCATAATTGATAGCCGAAGCT
* * * *
39555250 AT-CATTTTCATAATTGAAAGCCAAAGTT
1 ATCCTTTTTCATAATTGATAGCCGAAGCT
39555278 ATCCTTTTTCATAATTGATAGCCGAAGCT
1 ATCCTTTTTCATAATTGATAGCCGAAGCT
*
39555307 ATCCTTTTTCATAATTGATAGTCGAAGCT
1 ATCCTTTTTCATAATTGATAGCCGAAGCT
39555336 ATCCTTTTT
1 ATCCTTTTT
39555345 TATTAGTCGA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
28 22 0.27
29 61 0.73
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (29 bp):
ATCCTTTTTCATAATTGATAGCCGAAGCT
Found at i:39556493 original size:38 final size:38
Alignment explanation
Indices: 39556445--39556525 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 38
39556435 GAAAGGCCTT
*
39556445 AAGGG-CATTTTAGTTATTTGGTAAATAAAAGAATAAA
1 AAGGGACATTTTAGTCATTTGGTAAATAAAAGAATAAA
39556482 AAGGGACATTTTAGTCATTTGGTAAATAAAAGAATAAA
1 AAGGGACATTTTAGTCATTTGGTAAATAAAAGAATAAA
39556520 AAGGGA
1 AAGGGA
39556526 AAATTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 5 0.12
38 37 0.88
ACGTcount: A:0.47, C:0.04, G:0.21, T:0.28
Consensus pattern (38 bp):
AAGGGACATTTTAGTCATTTGGTAAATAAAAGAATAAA
Found at i:39558135 original size:46 final size:46
Alignment explanation
Indices: 39558085--39558174 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 46
39558075 TGAGACGAGT
*
39558085 GCTAGTGTGAGACATGTCCGGGACATGCATCAGCCT-CGAGATGTAA
1 GCTAGTGTAAGACATGTCCGGGACATGCATC-GCCTACGAGATGTAA
* *
39558131 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGT
1 GCTAGTGTAAGACATGTCCGGGACATGCATCGCCTACGAGATGT
39558175 GTCAATGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 3 0.08
46 37 0.93
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCCGGGACATGCATCGCCTACGAGATGTAA
Found at i:39565567 original size:47 final size:46
Alignment explanation
Indices: 39565499--39565622 Score: 135
Period size: 47 Copynumber: 2.7 Consensus size: 46
39565489 TGTGAGCTAG
* *
39565499 TGTAAGACATGTCCGGGACATGCATCGGCCACAT-TACGAGAGCCAA
1 TGTAAGACATGTCTGGGACATGCATCGGCCA-ATAGACGAGAGCCAA
* * ** *
39565545 TGTAAGACCATGTTTGGGACATGGCATCGG-CAATGAGACGAGTGTTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCAAT-AGACGAGAGCCAA
39565593 TGTAAGACATGTCTGGGACATGCATCGGCC
1 TGTAAGACATGTCTGGGACATGCATCGGCC
39565623 TCGAGATATA
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
46 16 0.25
47 28 0.43
48 21 0.32
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (46 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCAATAGACGAGAGCCAA
Found at i:39565710 original size:46 final size:44
Alignment explanation
Indices: 39565497--39565713 Score: 143
Period size: 46 Copynumber: 4.7 Consensus size: 44
39565487 TGTGTGAGCT
* * * * *
39565497 AGTGTAAGACATGTCCGGGACATGCATCGGCCACATTACGA-GAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAC--GA-GATGTGTC
* * * * * *
39565543 AATGTAAGACCATGTTTGGGACATGGCATCGGCAATGAGACGAGTGTT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGA--TGTGTC
*
39565591 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATATAAG-C
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGT--GTC
* * *
39565636 TAGTATAAGACATGTCTGAGACATGCATCAGCTACGAGATGTGTC
1 -AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTC
* *
39565681 AGCGTAAGACCATGTTTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
39565714 ATAGATATAC
Statistics
Matches: 133, Mismatches: 25, Indels: 26
0.72 0.14 0.14
Matches are distributed among these distances:
44 9 0.07
45 17 0.13
46 62 0.47
47 26 0.20
48 19 0.14
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGTGTC
Found at i:39571531 original size:21 final size:21
Alignment explanation
Indices: 39571507--39571571 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
39571497 ATCCCAAAGA
*
39571507 CATATCTAACTTTCGCGCTAT
1 CATATCTAACTTTCGCCCTAT
39571528 CATATCTAACTTTCGCCCTAT
1 CATATCTAACTTTCGCCCTAT
39571549 CATATCTAACTTTCGCCCTAT
1 CATATCTAACTTTCGCCCTAT
39571570 CA
1 CA
39571572 GCTTATGCAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.25, C:0.32, G:0.06, T:0.37
Consensus pattern (21 bp):
CATATCTAACTTTCGCCCTAT
Found at i:39571830 original size:28 final size:28
Alignment explanation
Indices: 39571790--39571843 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
39571780 GAGCAAAGCC
* *
39571790 TACGACCGTGTCGAATGGGATTTTCTCG
1 TACGACCATGTCGAATAGGATTTTCTCG
39571818 TACGACCATGTCGAATAGGATTTTCT
1 TACGACCATGTCGAATAGGATTTTCT
39571844 TAAAGAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (28 bp):
TACGACCATGTCGAATAGGATTTTCTCG
Found at i:39572926 original size:28 final size:29
Alignment explanation
Indices: 39572875--39572930 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
39572865 ACAGGGGTTT
39572875 TCACACGGCCTGACACACGCCCGTGTCCC
1 TCACACGGCCTGACACACGCCCGTGTCCC
39572904 TCACACGGCCAT-A-ACACGCCCGTGTCC
1 TCACACGGCC-TGACACACGCCCGTGTCC
39572931 TAGCCTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 14 0.54
29 11 0.42
30 1 0.04
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.14
Consensus pattern (29 bp):
TCACACGGCCTGACACACGCCCGTGTCCC
Found at i:39576126 original size:50 final size:48
Alignment explanation
Indices: 39575951--39576231 Score: 258
Period size: 47 Copynumber: 5.9 Consensus size: 48
39575941 CATAGTGTAT
* * *
39575951 AATGCCGATGCCATGTCCCAAACATGGTCTTACGCTGGCTCATC--CATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCTC-TCAATATC
* * * *
39575999 AA-GTCGATGCCATATCCCAGACATGGTCTTACACTGACTATCAAAATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTG-CTCTCAATATC
* *
39576047 AAGGCCGGTGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAGTATC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCAA-TATC
** * * * *
39576097 CGTGCCGATGCCATGTCCTAGACATGGTCTTACACTG-ACAC-ATCTC
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGCTCTCAATATC
* *
39576143 -ATAGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTC-GTCTC
1 AAT-GCCGATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCAATATC
*
39576189 AATGCCGATGCCA-ATCCCAGACATGGTCTTACACTGGCTCTCA
1 AATGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCTCTCA
39576232 TAATGTGGCC
Statistics
Matches: 194, Mismatches: 26, Indels: 26
0.79 0.11 0.11
Matches are distributed among these distances:
44 10 0.05
45 15 0.08
46 36 0.19
47 52 0.27
48 9 0.05
49 37 0.19
50 35 0.18
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (48 bp):
AATGCCGATGCCATGTCCCAGACATGGTCTTACACTGCTCTCAATATC
Found at i:39576130 original size:99 final size:92
Alignment explanation
Indices: 39575954--39576224 Score: 298
Period size: 96 Copynumber: 2.9 Consensus size: 92
39575944 AGTGTATAAT
* * * * *
39575954 GCCGATGCCATGTCCCAAACATGGTCTTACGCTGGCTCATC-CATCAA-GTCGATGCCATATCCC
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTATCAATGCCGATGCCATATCCC
39576017 AGACATGGTCTTACACTGACTATCAAAATCA-A
63 AGACATGGTCTTACACTGAC-A-C-AAATCATA
* ** *
39576049 GGCCGGTGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAAGTATCCGTGCCGATGCCATGTC
1 -GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTC--GTATCAATGCCGATGCCATATC
* **
39576114 CTAGACATGGTCTTACACTGACACATCTCATA
61 CCAGACATGGTCTTACACTGACACAAATCATA
*
39576146 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCA-ATCCCAGA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATATCCCAGA
39576210 CATGGTCTTACACTG
66 CATGGTCTTACACTG
39576225 GCTCTCATAA
Statistics
Matches: 152, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
91 21 0.14
92 15 0.10
94 17 0.11
95 16 0.11
96 44 0.29
97 2 0.01
98 4 0.03
99 33 0.22
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGCCGATGCCATATCCCAGA
CATGGTCTTACACTGACACAAATCATA
Found at i:39580254 original size:13 final size:13
Alignment explanation
Indices: 39580236--39580260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39580226 GCTCGACAGG
39580236 GACACGCCCGTGC
1 GACACGCCCGTGC
39580249 GACACGCCCGTG
1 GACACGCCCGTG
39580261 TGGGGTGGCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.44, G:0.32, T:0.08
Consensus pattern (13 bp):
GACACGCCCGTGC
Found at i:39588404 original size:68 final size:68
Alignment explanation
Indices: 39588254--39588411 Score: 160
Period size: 68 Copynumber: 2.3 Consensus size: 68
39588244 CTAGCCAATT
* * *
39588254 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
39588319 TTTA
65 CATA
* * *
39588323 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
39588385 CTACATA
63 C-ACATA
*
39588392 GTATCTCGTAGCTTTCTTGT
1 -TATCTCGTAGCTCTCTTGT
39588412 ACACATGATG
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
68 35 0.47
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:39594178 original size:40 final size:40
Alignment explanation
Indices: 39594101--39594437 Score: 574
Period size: 40 Copynumber: 8.5 Consensus size: 40
39594091 AAACCAAGTA
* * *
39594101 CCTTCGGGATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39594140 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39594180 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39594220 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39594260 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39594300 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39594340 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
39594380 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39594419 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39594438 TTATCATCCG
Statistics
Matches: 287, Mismatches: 7, Indels: 7
0.95 0.02 0.02
Matches are distributed among these distances:
38 1 0.00
39 49 0.17
40 237 0.83
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39604529 original size:39 final size:40
Alignment explanation
Indices: 39604475--39604651 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
39604465 AAACCAAGTA
* * * *
39604475 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
39604514 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
39604554 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
39604594 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
39604633 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39604652 TTATCATCCG
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
38 1 0.01
39 48 0.38
40 77 0.61
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39604628 original size:79 final size:80
Alignment explanation
Indices: 39604475--39604651 Score: 245
Period size: 79 Copynumber: 2.2 Consensus size: 80
39604465 AAACCAAGTA
* * * * *
39604475 CCTTCGGAATTTAG-CCGGATATAGCTACTTGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAG
1 CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
39604539 TAACTCGCACAAATG
66 TAACTAGCACAAATG
39604554 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGA-ATT
1 CCTTCGGGACTTAGCCCGGATATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-T
*
39604616 AGTCACTAGCACAAATG
64 AGTAACTAGCACAAATG
39604633 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
39604652 TTATCATCCG
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.01
79 58 0.66
80 29 0.33
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TAACTAGCACAAATG
Found at i:39612632 original size:99 final size:92
Alignment explanation
Indices: 39612505--39612725 Score: 245
Period size: 99 Copynumber: 2.3 Consensus size: 92
39612495 TCCATCAAGT
*
39612505 CGATGCCATGTCCCAGACATGGTTTTACACTGACAATCAAA-ATCG-AGGCTGATGCCATGCCCC
1 CGATGCCATGTCCCAGACATGGTCTTACACT---AA-CAAATATCGTAGGC-GATG-CATGCCCC
* *
39612568 AGACATGGTCTTAGACTAGCTCTCACATATCCG-TGC
60 AGACAT-GTCTTACACTAGCT-T-ACATAT-CGAGGC
* * *
39612604 CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATCTCGTAGTCGATGCATGTCCCAGACAT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATATCGTAGGCGATGCATGCCCCAGACAT
* *
39612669 GTCTTACACTGGCTTACATCTCGAGGC
66 GTCTTACACTAGCTTACATATCGAGGC
39612696 CGATG-CATGTCCCAGACAT-GTCTTACACTA
1 CGATGCCATGTCCCAGACATGGTCTTACACTA
39612726 GCTCTCGTCT
Statistics
Matches: 111, Mismatches: 8, Indels: 15
0.83 0.06 0.11
Matches are distributed among these distances:
90 11 0.10
91 16 0.14
92 12 0.11
93 1 0.01
94 12 0.11
95 17 0.15
96 9 0.08
97 3 0.03
99 30 0.27
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (92 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAACAAATATCGTAGGCGATGCATGCCCCAGACAT
GTCTTACACTAGCTTACATATCGAGGC
Found at i:39612700 original size:46 final size:49
Alignment explanation
Indices: 39612463--39612821 Score: 256
Period size: 46 Copynumber: 7.6 Consensus size: 49
39612453 AATGTCGAGT
* * * * * *
39612463 CCATGTCCCAGATATGGTCTTACGCTGGCTCATCCA--TC-AAGTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTC-TACATCTCGAGGCCGATG
* ** *
39612510 CCATGTCCCAGACATGGTTTTACACT-GACAATC-A-AAATCGAGGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTAG-C--TCTACATCTCGAGGCCGATG
* * * *
39612559 CCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCG-TGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCT-ACATCT-CGAGGCCGATG
* * *
39612609 CCATGTCCCAGACATGGTCTTACACTA--AC-AAATCTCGTA-GTCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCG-AGGCCGATG
*
39612655 -CATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCGAGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
* * *
39612701 -CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
* * * * *
39612747 CCATGTCCCAAACATGGTCTTACATTGGCTCT-CATAAT-GTGGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAGCTCTACAT-CTCGAGGCCGATG
*
39612795 -CATGTCCCAAACAT-GTCTTACACTAGC
1 CCATGTCCCAGACATGGTCTTACACTAGC
39612822 ACACACACAT
Statistics
Matches: 254, Mismatches: 37, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
44 10 0.04
45 17 0.07
46 76 0.30
47 54 0.21
48 26 0.10
49 34 0.13
50 35 0.14
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (49 bp):
CCATGTCCCAGACATGGTCTTACACTAGCTCTACATCTCGAGGCCGATG
Found at i:39612762 original size:138 final size:144
Alignment explanation
Indices: 39612502--39612770 Score: 354
Period size: 138 Copynumber: 1.9 Consensus size: 144
39612492 TCATCCATCA
* *
39612502 AGTCGATGCCATGTCCCAGACATGGTTTTACACTGACAATCAAAATCGAGGCTGATGCCATGCCC
1 AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCAAAATCGAGGCCGATGCCATGCCC
* ** *
39612567 CAGACATGGTCTTAGACTAGCTCTCACATATCCGTGCCGATGCCATGTCCCAGACATGGTCTTAC
66 CAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
39612632 ACTAACAAATCTCGT
130 ACTAACAAATCTCGT
* * ** *
39612647 AGTCGATG-CATGTCCCAGACAT-GTCTTACACTGGC--TTACATCTCGAGGCCGATG-CATGTC
1 AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCA-AAATCGAGGCCGATGCCATGCC
* *
39612707 CCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
65 CCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTAC
39612770 A
130 A
39612771 TTGGCTCTCA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
138 35 0.32
140 15 0.14
141 15 0.14
142 12 0.11
143 11 0.10
144 14 0.13
145 8 0.07
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (144 bp):
AGTCGATGCCATGTCCCAGACATGGTCTTACACTGACAATCAAAATCGAGGCCGATGCCATGCCC
CAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCATGTCCCAAACATGGTCTTACA
CTAACAAATCTCGT
Found at i:39612791 original size:94 final size:91
Alignment explanation
Indices: 39612555--39612822 Score: 280
Period size: 94 Copynumber: 2.9 Consensus size: 91
39612545 AATCGAGGCT
* * * *
39612555 GATGCCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCGT-GCCGATGCCATGTCCCA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATA-AT-CGTGGCCGATG-CATGTCCCA
* *
39612619 GACATGGTCTTACACTAACAAATCTCGTAGTC
63 GACAT-GTCTTACACTAGC--ATCTCGTAGCC
* *
39612651 GATG-CATGTCCCAGACAT-GTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTCCCAGA
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATCGTGGCCGATGCATGTCCCAGA
39612712 CATGTCTTACACTAGC-TCTCGTCTCAATGCC
65 CATGTCTTACACTAGCATCTCG--T--A-GCC
* * *
39612743 GATGCCATGTCCCAAACATGGTCTTACATTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCGTGGCCGATGCATGTCCCAGAC
39612807 ATGTCTTACACTAGCA
66 ATGTCTTACACTAGCA
39612823 CACACACATC
Statistics
Matches: 147, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
87 5 0.03
89 1 0.01
90 12 0.08
91 17 0.12
92 14 0.10
93 14 0.10
94 65 0.44
95 15 0.10
96 4 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (91 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATCGTGGCCGATGCATGTCCCAGAC
ATGTCTTACACTAGCATCTCGTAGCC
Found at i:39612809 original size:140 final size:140
Alignment explanation
Indices: 39612547--39612818 Score: 329
Period size: 140 Copynumber: 1.9 Consensus size: 140
39612537 ACAATCAAAA
* * **
39612547 TCGAGGCTGATGCCATGCCCCAGACATGGTCTTAGACTAGCTCTCACATATCCGTGCCGATGCCA
1 TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCT-ACATATCAATGCCGATGCCA
* * *
39612612 TGTCCCAGACATGGTCTTACACTAACAAATCTCGTAGTCGATGCATGTCCCAGACATGTCTTACA
65 TGTCCCAAACATGGTCTTACACTAACAAA-CTCGTAGCCGATGCATGTCCCAAACATGTCTTACA
39612677 CTGGCTTACATC
129 CTGGCTTACATC
* * *
39612689 TCGAGGCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT-CGTCTCAATGCCGATGCCAT
1 TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCAT
** *
39612751 GTCCCAAACATGGTCTTACATTGGCTCTCATAA-T-GTGGCCGATGCATGTCCCAAACATGTCTT
66 GTCCCAAACATGGTCTTACA----CTAACA-AACTCGTAGCCGATGCATGTCCCAAACATGTCTT
39612814 ACACT
126 ACACT
39612819 AGCACACACA
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
138 35 0.31
140 46 0.41
141 14 0.12
142 15 0.13
143 2 0.02
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (140 bp):
TCGAGGCCGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTACATATCAATGCCGATGCCAT
GTCCCAAACATGGTCTTACACTAACAAACTCGTAGCCGATGCATGTCCCAAACATGTCTTACACT
GGCTTACATC
Found at i:39613848 original size:14 final size:13
Alignment explanation
Indices: 39613825--39613856 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
39613815 GGAATATCAA
39613825 AACAATAATTAAG
1 AACAATAATTAAG
39613838 AACACATAATTAAG
1 AACA-ATAATTAAG
39613852 AACAA
1 AACAA
39613857 GTCAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.19
Consensus pattern (13 bp):
AACAATAATTAAG
Found at i:39624044 original size:50 final size:50
Alignment explanation
Indices: 39623976--39624116 Score: 147
Period size: 60 Copynumber: 2.6 Consensus size: 50
39623966 TCCATTAAGT
39623976 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGA
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGA
* * *
39624026 TGATGCCATGTCCCAGACATGTAAGGACATGGTCTTACACTAGCTCTCACATATCTGTGC
1 CGATGCCATGT-CC---C-----A-GACATGGTCTTACACTAGCTCTCACATATCCGTGA
* *
39624086 CGATTCCATGTCCTAGACATGGTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
39624117 GACACATCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
50 26 0.35
51 3 0.04
54 1 0.01
59 3 0.04
60 42 0.56
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.28
Consensus pattern (50 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGA
Found at i:39624060 original size:60 final size:60
Alignment explanation
Indices: 39623991--39624106 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
39623981 CCATGTCCCA
*
39623991 GACATGGTCTTACACTAGCTCTCACATATCCGTGATGATGCCATGTCCCAGACATGTAAG
1 GACATGGTCTTACACTAGCTCTCACATATCCGTGACGATGCCATGTCCCAGACATGTAAG
* * * *
39624051 GACATGGTCTTACACTAGCTCTCACATATCTGTGCCGATTCCATGTCCTAGACATG
1 GACATGGTCTTACACTAGCTCTCACATATCCGTGACGATGCCATGTCCCAGACATG
39624107 GTCTTACACT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (60 bp):
GACATGGTCTTACACTAGCTCTCACATATCCGTGACGATGCCATGTCCCAGACATGTAAG
Found at i:39624180 original size:46 final size:46
Alignment explanation
Indices: 39624092--39624252 Score: 211
Period size: 46 Copynumber: 3.5 Consensus size: 46
39624082 GTGCCGATTC
* * *
39624092 CATGTCCTAGACATGGTCTTACACTGAC--ACATCTC-ATAGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTTACATCTCGA-GGCCGATG
*
39624137 CATGTCCCAGACATGTCTTACACTGGCTTACATCACGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATG
* * * *
39624183 CATGTCCCTGTCATGTCTTACACTAGCTTACATCTTGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATG
39624229 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
39624253 AGCGCACAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
44 12 0.12
45 13 0.13
46 76 0.75
47 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATG
Found at i:39628326 original size:44 final size:45
Alignment explanation
Indices: 39628258--39628369 Score: 165
Period size: 46 Copynumber: 2.5 Consensus size: 45
39628248 CTAATGCCAT
39628258 GTCCCAGACATGATCTTACACTGGC-ACATCTC-ATAGCCGATGCAA
1 GTCCCAGACATG-TCTTACACTGGCTACATCTCGA-AGCCGATGCAA
* *
39628303 GTCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCAT
1 GTCCCAGACATGTCTTACACTGGC-TACATCTCGAAGCCGATGCAA
39628349 GTCCCAGACATGTCTTACACT
1 GTCCCAGACATGTCTTACACT
39628370 AGAGTACAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
44 12 0.19
45 12 0.19
46 37 0.60
47 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (45 bp):
GTCCCAGACATGTCTTACACTGGCTACATCTCGAAGCCGATGCAA
Found at i:39629094 original size:13 final size:13
Alignment explanation
Indices: 39629076--39629100 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39629066 TAAAAGTGCA
39629076 AAAATCATCAAAG
1 AAAATCATCAAAG
39629089 AAAATCATCAAA
1 AAAATCATCAAA
39629101 ATCACTTACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAATCATCAAAG
Found at i:39644215 original size:40 final size:40
Alignment explanation
Indices: 39644137--39644261 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
39644127 CCGAATGATG
* *
39644137 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGACTAAGTCCCGAAGGCATTTGTGC-GAGTGACTATA
*
39644177 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGACTAAG-TCCCGAAGGCATTTGTGCGAGTGACTATA
* * ** *
39644217 ACCGGGA-TATGTCCCGAAGGCATTTGAACGAGTGGCTATA
1 TCC-GGACTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
39644257 TCCGG
1 TCCGG
39644262 TTAAATTCCG
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
39 3 0.04
40 57 0.80
41 11 0.15
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA
Found at i:39656691 original size:23 final size:23
Alignment explanation
Indices: 39656665--39656709 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
39656655 TTCTCATTTT
39656665 TTCTCCTT-TCTTTCTCTTCTATC
1 TTCTCCTTCT-TTTCTCTTCTATC
*
39656688 TTCTCCTTCTTTTCTTTTCTAT
1 TTCTCCTTCTTTTCTCTTCTAT
39656710 TATGTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCTCCTTCTTTTCTCTTCTATC
Found at i:39656981 original size:21 final size:20
Alignment explanation
Indices: 39656948--39656988 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
39656938 AGGTGATCAT
39656948 GGGTTGGGTCGGGCCGGGCC
1 GGGTTGGGTCGGGCCGGGCC
* *
39656968 GGGTTAGGTTCGGGCTGGGCC
1 GGGTT-GGGTCGGGCCGGGCC
39656989 CAGACAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.02, C:0.22, G:0.56, T:0.20
Consensus pattern (20 bp):
GGGTTGGGTCGGGCCGGGCC
Found at i:39657179 original size:26 final size:24
Alignment explanation
Indices: 39657139--39657198 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
39657129 TTATTTCATT
* * *
39657139 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
39657163 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
39657189 AAATAAATAT
1 AAATAAATAT
39657199 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:39659642 original size:20 final size:20
Alignment explanation
Indices: 39659614--39659661 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
39659604 ATTTTAGGAT
*
39659614 TTTAT-TTTAATT-ATCTTTA
1 TTTATCTTTAATTAAT-TGTA
39659633 TTTATCTTTAATTAATTGTA
1 TTTATCTTTAATTAATTGTA
39659653 TTTATCTTT
1 TTTATCTTT
39659662 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATCTTTAATTAATTGTA
Found at i:39661627 original size:12 final size:12
Alignment explanation
Indices: 39661610--39661634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39661600 TACATTGATA
39661610 ATACAATGAGAG
1 ATACAATGAGAG
39661622 ATACAATGAGAG
1 ATACAATGAGAG
39661634 A
1 A
39661635 AACTAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
ATACAATGAGAG
Found at i:39674709 original size:36 final size:36
Alignment explanation
Indices: 39674669--39674746 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 36
39674659 TTTTTTCCCT
* * *
39674669 GAATTTTCTTTATATTTTCGGAC-TGAAACAAGACTA
1 GAATTTTATTT-TATTTTCGAACAAGAAACAAGACTA
*
39674705 GAATTTTATTTTATTTTTGAACAAAGAAACAAGACTA
1 GAATTTTATTTTATTTTCGAAC-AAGAAACAAGACTA
39674742 GAATT
1 GAATT
39674747 AAACAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 9 0.25
36 10 0.28
37 17 0.47
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (36 bp):
GAATTTTATTTTATTTTCGAACAAGAAACAAGACTA
Found at i:39674839 original size:23 final size:22
Alignment explanation
Indices: 39674788--39674840 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
39674778 AGATACTCTT
*
39674788 AAATAAATAGAAAGTAATTTAA
1 AAATAAGTAGAAAGTAATTTAA
*
39674810 AAGATAAGTAGAAA-TCAATATTTA
1 AA-ATAAGTAGAAAGT-AAT-TTAA
39674834 AAATAAG
1 AAATAAG
39674841 CAACTATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.26
Consensus pattern (22 bp):
AAATAAGTAGAAAGTAATTTAA
Found at i:39677332 original size:63 final size:63
Alignment explanation
Indices: 39677232--39677366 Score: 216
Period size: 63 Copynumber: 2.1 Consensus size: 63
39677222 TGGCTGCTGG
** * *
39677232 TATACATGGTTAACCAGCTTATGTTTTGTAATATTGTTGCTGGTATATTGTTGCTTATGTTGT
1 TATACATGGAAAACCAGCTTATGTTTTGTAATATTGTTGCTGGCATATTGTTCCTTATGTTGT
* *
39677295 TATACATGGAAAACCAGCTTATGTTTTGTAATGTTGTTGTTGGCATATTGTTCCTTATGTTGT
1 TATACATGGAAAACCAGCTTATGTTTTGTAATATTGTTGCTGGCATATTGTTCCTTATGTTGT
39677358 TATACATGG
1 TATACATGG
39677367 CTGCTAGTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.47
Consensus pattern (63 bp):
TATACATGGAAAACCAGCTTATGTTTTGTAATATTGTTGCTGGCATATTGTTCCTTATGTTGT
Found at i:39678114 original size:21 final size:21
Alignment explanation
Indices: 39678090--39678147 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
39678080 AACATCTTTT
39678090 TTGATGAGTTAGGGCA-TATTG
1 TTGATGAGTTAGGGCAGT-TTG
*
39678111 TTGATGAG-TCGGGCAGTTTG
1 TTGATGAGTTAGGGCAGTTTG
* *
39678131 TAGCTGAGTTAGGGCAG
1 TTGATGAGTTAGGGCAG
39678148 CCTCCTGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.21, C:0.09, G:0.38, T:0.33
Consensus pattern (21 bp):
TTGATGAGTTAGGGCAGTTTG
Found at i:39678131 original size:20 final size:21
Alignment explanation
Indices: 39678090--39678146 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
39678080 AACATCTTTT
39678090 TTGATGAGTTAGGGCATATTG
1 TTGATGAGTTAGGGCATATTG
*
39678111 TTGATGAG-TCGGGCAGT-TTG
1 TTGATGAGTTAGGGCA-TATTG
* *
39678131 TAGCTGAGTTAGGGCA
1 TTGATGAGTTAGGGCA
39678147 GCCTCCTGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.21, C:0.09, G:0.37, T:0.33
Consensus pattern (21 bp):
TTGATGAGTTAGGGCATATTG
Found at i:39678157 original size:21 final size:21
Alignment explanation
Indices: 39678133--39678209 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
39678123 GCAGTTTGTA
*
39678133 GCTGAGTTAGGGCAGCCTCCT
1 GCTGAGTTAGGGCAGCCTCTT
* *
39678154 GCTGAGCTAGGGTA-CTCTCTT
1 GCTGAGTTAGGGCAGC-CTCTT
* * * *
39678175 GTTGATTTAGGGTAGCCTGTT
1 GCTGAGTTAGGGCAGCCTCTT
*
39678196 GCTGAGTTGGGGCA
1 GCTGAGTTAGGGCA
39678210 ACCACTTAGT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.14, C:0.19, G:0.35, T:0.31
Consensus pattern (21 bp):
GCTGAGTTAGGGCAGCCTCTT
Found at i:39678972 original size:77 final size:77
Alignment explanation
Indices: 39678881--39679051 Score: 227
Period size: 77 Copynumber: 2.2 Consensus size: 77
39678871 AAAGTTACTG
* *
39678881 CATGCATATTAAAAAATAGTCAACAACAT-ATGACCATCCCTACCAACAATCATATACAAACAAA
1 CATGCATATTAAAAAATAGTCAACAACATGAT-ACCAGCCCTACCAACAATCATACACAAACAAA
*
39678945 TTAAAAAACACTA
65 ATAAAAAACACTA
* * * * * *
39678958 CATGCATATTAAAAAATAGTCAATAGCATGCTACCAGCCTTACCAACAATCATACACAGATAAAA
1 CATGCATATTAAAAAATAGTCAACAACATGATACCAGCCCTACCAACAATCATACACAAACAAAA
*
39679023 TAAAAAATACTA
66 TAAAAAACACTA
*
39679035 CATGCATATAAAAAAAT
1 CATGCATATTAAAAAAT
39679052 TCTCACTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 81 0.99
78 1 0.01
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.22
Consensus pattern (77 bp):
CATGCATATTAAAAAATAGTCAACAACATGATACCAGCCCTACCAACAATCATACACAAACAAAA
TAAAAAACACTA
Found at i:39681799 original size:30 final size:30
Alignment explanation
Indices: 39681763--39681830 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
39681753 ACTGTTAATC
* *
39681763 AGTGACTATTTTATCATTTTTTATAACATT-
1 AGTGACTATTTTATCATTTTTCA-AAAATTG
*
39681793 AGTGACTATTTTGTCATTTTTCAAAAATTG
1 AGTGACTATTTTATCATTTTTCAAAAATTG
39681823 AGTGACTA
1 AGTGACTA
39681831 AAATAAAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 5 0.15
30 29 0.85
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (30 bp):
AGTGACTATTTTATCATTTTTCAAAAATTG
Found at i:39681956 original size:6 final size:6
Alignment explanation
Indices: 39681945--39681970 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39681935 AATTGTTGAT
39681945 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
39681971 GTGATGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:39682651 original size:17 final size:18
Alignment explanation
Indices: 39682629--39682668 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39682619 ATAATTTAAC
*
39682629 ATTTCT-ATGTAAAAGCA
1 ATTTCTAATGTAAAAGAA
*
39682646 ATTTCTAATTTAAAAGAA
1 ATTTCTAATGTAAAAGAA
39682664 ATTTC
1 ATTTC
39682669 AAAATTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (18 bp):
ATTTCTAATGTAAAAGAA
Found at i:39687901 original size:22 final size:22
Alignment explanation
Indices: 39687849--39687901 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
39687839 TGGACAAGCT
*
39687849 ACCACATAATTGTCGATAAACG
1 ACCACATAATTGTCAATAAACG
*
39687871 ACCATATAATTG-CAAATAAACTG
1 ACCACATAATTGTC-AATAAAC-G
39687894 -CCACATAA
1 ACCACATAA
39687902 CTTCCACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.45, C:0.23, G:0.09, T:0.23
Consensus pattern (22 bp):
ACCACATAATTGTCAATAAACG
Found at i:39689358 original size:17 final size:20
Alignment explanation
Indices: 39689323--39689358 Score: 51
Period size: 17 Copynumber: 1.9 Consensus size: 20
39689313 GGAAAGTGAA
39689323 ATAATAAAAGATGATAAATG
1 ATAATAAAAGATGATAAATG
39689343 ATAA-AAAA-ATGA-AAAT
1 ATAATAAAAGATGATAAAT
39689359 ATCATCAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 4 0.25
20 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (20 bp):
ATAATAAAAGATGATAAATG
Found at i:39692919 original size:134 final size:135
Alignment explanation
Indices: 39692678--39692952 Score: 439
Period size: 134 Copynumber: 2.0 Consensus size: 135
39692668 TTCTTTTTTC
*
39692678 GAAGTTGAGAGAAAATGGAGGTGAAAGAAATGAAAAAAAAAGGGAATATGGGACAATGAAGGAGG
1 GAAGTTGAGAGAAAATAGAGGTGAAAGAAATGAAAAAAAAAGGGAATATGGGACAATGAAGGAGG
** *
39692743 TAGAGATGACAATAGGAGTAGTAAGCTTGGTTAACTATGACCAGGTTCATTGAATCACAAA-AAA
66 TAGAGACAACAATAGGAGTAGTAAGCTTGGTTAACTATGACCAAGTTCATTGAATCA-AAACAAA
39692807 AGACAA-
130 AGA-AAT
39692813 GAAGTTGAGAGAAAATAGAGGTGAAAGAAATGAAAAAAAAA-GGAATATGGGACAATGAAGGAGG
1 GAAGTTGAGAGAAAATAGAGGTGAAAGAAATGAAAAAAAAAGGGAATATGGGACAATGAAGGAGG
* * * *
39692877 TAGAGACAACAATGGGAGTGGTAAGCTTGGTTAATTGTGACCAAGTTCATTGAATCAAAACAAAA
66 TAGAGACAACAATAGGAGTAGTAAGCTTGGTTAACTATGACCAAGTTCATTGAATCAAAACAAAA
39692942 GAAAT
131 GAAAT
39692947 GAAGTT
1 GAAGTT
39692953 TTGGCAAGGG
Statistics
Matches: 130, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
133 5 0.04
134 85 0.65
135 40 0.31
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.19
Consensus pattern (135 bp):
GAAGTTGAGAGAAAATAGAGGTGAAAGAAATGAAAAAAAAAGGGAATATGGGACAATGAAGGAGG
TAGAGACAACAATAGGAGTAGTAAGCTTGGTTAACTATGACCAAGTTCATTGAATCAAAACAAAA
GAAAT
Found at i:39693732 original size:14 final size:14
Alignment explanation
Indices: 39693713--39693742 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39693703 TTTTAGATAC
*
39693713 ATATCTTTTTTAAA
1 ATATCTTTTCTAAA
39693727 ATATCTTTTCTAAA
1 ATATCTTTTCTAAA
39693741 AT
1 AT
39693743 GAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATCTTTTCTAAA
Found at i:39694887 original size:17 final size:17
Alignment explanation
Indices: 39694854--39694887 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39694844 GTTTCTTCCC
* *
39694854 TAAAATCCTTTATTCCT
1 TAAAATCCCTTAATCCT
39694871 TAAAATCCCTTAATCCT
1 TAAAATCCCTTAATCCT
39694888 CCAAAAAATT
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:0.32, C:0.26, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAATCCCTTAATCCT
Found at i:39697023 original size:25 final size:25
Alignment explanation
Indices: 39696995--39697155 Score: 159
Period size: 25 Copynumber: 6.4 Consensus size: 25
39696985 CCATAATGAA
* * *
39696995 TTTCCAGATAATTAGCCATAAAGGC
1 TTTCCAAAGAATTAGCCACAAAGGC
* *
39697020 TTTCCAAATAA-TACGCCACAAGGGC
1 TTTCCAAAGAATTA-GCCACAAAGGC
* *
39697045 TTTCCAAAGAATTTGCCACAAAGGT
1 TTTCCAAAGAATTAGCCACAAAGGC
39697070 TTTCCAAATG-A-TACGCCACAAAGGC
1 TTTCCAAA-GAATTA-GCCACAAAGGC
* *
39697095 TTTCTAGAGAATTCA-CCACAAAGGC
1 TTTCCAAAGAATT-AGCCACAAAGGC
* *
39697120 TTTCCAGAGAATTCGCCACAAAGGC
1 TTTCCAAAGAATTAGCCACAAAGGC
39697145 TTTCCAAAGAA
1 TTTCCAAAGAA
39697156 GTCTCGAGTT
Statistics
Matches: 114, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
24 4 0.04
25 106 0.93
26 3 0.03
27 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (25 bp):
TTTCCAAAGAATTAGCCACAAAGGC
Found at i:39697068 original size:50 final size:50
Alignment explanation
Indices: 39696995--39697155 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
39696985 CCATAATGAA
* * * *
39696995 TTTCCAGATAATTAGCCATAAAGGCTTTCCAAATAATACGCCACAAGGGC
1 TTTCCAAAGAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAGGC
* * *
39697045 TTTCCAAAGAATTTGCCACAAAGGTTTTCCAAATGATACGCCACAAAGGC
1 TTTCCAAAGAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAGGC
* * * * *
39697095 TTTCTAGAGAATTCA-CCACAAAGGCTTTCCAGAGAATTCGCCACAAAGGC
1 TTTCCAAAGAATT-AGCCACAAAGGCTTTCCAAATAATACGCCACAAAGGC
39697145 TTTCCAAAGAA
1 TTTCCAAAGAA
39697156 GTCTCGAGTT
Statistics
Matches: 93, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (50 bp):
TTTCCAAAGAATTAGCCACAAAGGCTTTCCAAATAATACGCCACAAAGGC
Found at i:39706416 original size:23 final size:23
Alignment explanation
Indices: 39706386--39706436 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
39706376 TACTATTTCA
39706386 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
39706409 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
39706432 TATTT
1 TATTT
39706437 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:39707230 original size:47 final size:45
Alignment explanation
Indices: 39707124--39707246 Score: 151
Period size: 47 Copynumber: 2.7 Consensus size: 45
39707114 TTTAGATAAT
* * * *
39707124 GATGCCATAGCCCAGCTATGGTCTTACACGAGTCACATATCTCACA
1 GATGCCATACCCCAGATATGGTCTTATAC-AGTCACATATATCACA
39707170 -ATGCCATACCCCAGATATGGTCTTATACAGT-AGCATATATCACA
1 GATGCCATACCCCAGATATGGTCTTATACAGTCA-CATATATCACA
*
39707214 CCGATGCCATATCCCAGATATGGTCTTATACAG
1 --GATGCCATACCCCAGATATGGTCTTATACAG
39707247 AAATCACTTG
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
43 1 0.01
44 13 0.19
45 25 0.37
47 29 0.43
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (45 bp):
GATGCCATACCCCAGATATGGTCTTATACAGTCACATATATCACA
Found at i:39707298 original size:31 final size:31
Alignment explanation
Indices: 39707263--39707442 Score: 290
Period size: 31 Copynumber: 5.8 Consensus size: 31
39707253 CTTGTCACTT
*
39707263 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
39707294 GTAGCC-AGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
* *
39707325 GTAGCCGGAGCTACCACTTTTCACTGATCGG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
39707356 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
39707387 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
39707418 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
39707443 TGTTATTTGT
Statistics
Matches: 138, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
30 1 0.01
31 137 0.99
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:39707523 original size:50 final size:50
Alignment explanation
Indices: 39707418--39707594 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
39707408 CACTGATCAG
* * * *
39707418 GTAGCCGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
39707469 GTAGCCGAAGCTATCACTTCTCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
39707519 GTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
39707569 GTTGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
39707595 GTTGCCATGG
Statistics
Matches: 116, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 92 0.79
51 24 0.21
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:39709691 original size:33 final size:33
Alignment explanation
Indices: 39709649--39709718 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
39709639 AAAAATAAAG
39709649 TCAGCTTGATTGAGATAATCAAACCTAAATTGA
1 TCAGCTTGATTGAGATAATCAAACCTAAATTGA
**
39709682 TCAGCTTGATTGAGATGGTCAAACCTAAATTGA
1 TCAGCTTGATTGAGATAATCAAACCTAAATTGA
39709715 TCAG
1 TCAG
39709719 TCGTTTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.30
Consensus pattern (33 bp):
TCAGCTTGATTGAGATAATCAAACCTAAATTGA
Found at i:39713545 original size:21 final size:21
Alignment explanation
Indices: 39713517--39713561 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
39713507 CGAGAATAAT
* *
39713517 AAAATAAATG-TAAACCACAG
1 AAAATAAAGGTTAAACAACAG
39713537 AAAACTAAAGGTTAAACAACAG
1 AAAA-TAAAGGTTAAACAACAG
39713559 AAA
1 AAA
39713562 TTTGAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (21 bp):
AAAATAAAGGTTAAACAACAG
Found at i:39718920 original size:40 final size:40
Alignment explanation
Indices: 39718865--39718942 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
39718855 ACCCACTATG
* **
39718865 TGGGGATAAAATCGACCCACCTATCCCTGTACACCATATA
1 TGGGGATAAAATCGACCCACCTAACCCTACACACCATATA
* *
39718905 TGGGGATATAATCGACCCATCTAACCCTACACACCATA
1 TGGGGATAAAATCGACCCACCTAACCCTACACACCATA
39718943 AAATACCGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCTAACCCTACACACCATATA
Found at i:39719448 original size:61 final size:61
Alignment explanation
Indices: 39719378--39719498 Score: 145
Period size: 61 Copynumber: 2.0 Consensus size: 61
39719368 TCTCACACGC
* * * * * * *
39719378 CCGTGTGATTCACTCGTGCCTGA-ACTTGTGCCTCACACACGTCCTAAAAGCCATCACATGT
1 CCGTATGATTCACCCGTGCATGAGACCT-TGCCTCACACACATCCTAAAAGACACCACATGT
* *
39719439 CCGTATGATTCACCCGTGCATGAGCCCTTGCCTCGCACACATCCTAAAAGACACCACATG
1 CCGTATGATTCACCCGTGCATGAGACCTTGCCTCACACACATCCTAAAAGACACCACATG
39719499 CCCCAGGCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
61 48 0.96
62 2 0.04
ACGTcount: A:0.25, C:0.35, G:0.17, T:0.23
Consensus pattern (61 bp):
CCGTATGATTCACCCGTGCATGAGACCTTGCCTCACACACATCCTAAAAGACACCACATGT
Found at i:39722092 original size:14 final size:14
Alignment explanation
Indices: 39722073--39722101 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39722063 AACTACGTCG
39722073 TTTTGATAAATATT
1 TTTTGATAAATATT
39722087 TTTTGATAAATATT
1 TTTTGATAAATATT
39722101 T
1 T
39722102 ACCTTTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTTGATAAATATT
Found at i:39723344 original size:4 final size:4
Alignment explanation
Indices: 39723335--39723387 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
39723325 ACAAATAGAT
* * * *
39723335 ATTA ATTA ATTA ATTA ATTA AGTTA ACTAA ATTA ATTT TTTA ATTA AATA
1 ATTA ATTA ATTA ATTA ATTA A-TTA A-TTA ATTA ATTA ATTA ATTA ATTA
39723385 ATT
1 ATT
39723388 TTCTCAATCT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
4 32 0.82
5 7 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (4 bp):
ATTA
Found at i:39723388 original size:16 final size:17
Alignment explanation
Indices: 39723357--39723389 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39723347 ATTAATTAAG
39723357 TTAACTAAATTAATTTT
1 TTAACTAAATTAATTTT
*
39723374 TTAATTAAA-TAATTTT
1 TTAACTAAATTAATTTT
39723390 CTCAATCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAACTAAATTAATTTT
Found at i:39726247 original size:27 final size:26
Alignment explanation
Indices: 39726230--39726299 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 26
39726220 ATATTAAGTC
39726230 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATAT-ATCAACT
*
39726257 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATAT-ATC-AACT
*
39726285 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
39726300 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (26 bp):
CGCACACTCAGTGCTATATATCAACT
Found at i:39726293 original size:28 final size:28
Alignment explanation
Indices: 39726230--39726327 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
39726220 ATATTAAGTC
*
39726230 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
39726257 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
39726285 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
39726314 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39726328 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:39738432 original size:153 final size:153
Alignment explanation
Indices: 39738154--39738459 Score: 612
Period size: 153 Copynumber: 2.0 Consensus size: 153
39738144 GTGTAACCAT
39738154 TGATATTTAGGATAAATTCAACAGGTAAAAATCTTGATATGAAAAGATATGGATAAGAAATGAGT
1 TGATATTTAGGATAAATTCAACAGGTAAAAATCTTGATATGAAAAGATATGGATAAGAAATGAGT
39738219 TATTACACGTATCCAGTTGAAATACAAGTAAACGATGATACATGACATATGATATATGAAAACAT
66 TATTACACGTATCCAGTTGAAATACAAGTAAACGATGATACATGACATATGATATATGAAAACAT
39738284 GAGATGATGATATTTGTACATGG
131 GAGATGATGATATTTGTACATGG
39738307 TGATATTTAGGATAAATTCAACAGGTAAAAATCTTGATATGAAAAGATATGGATAAGAAATGAGT
1 TGATATTTAGGATAAATTCAACAGGTAAAAATCTTGATATGAAAAGATATGGATAAGAAATGAGT
39738372 TATTACACGTATCCAGTTGAAATACAAGTAAACGATGATACATGACATATGATATATGAAAACAT
66 TATTACACGTATCCAGTTGAAATACAAGTAAACGATGATACATGACATATGATATATGAAAACAT
39738437 GAGATGATGATATTTGTACATGG
131 GAGATGATGATATTTGTACATGG
39738460 ACTTTATTTG
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.29
Consensus pattern (153 bp):
TGATATTTAGGATAAATTCAACAGGTAAAAATCTTGATATGAAAAGATATGGATAAGAAATGAGT
TATTACACGTATCCAGTTGAAATACAAGTAAACGATGATACATGACATATGATATATGAAAACAT
GAGATGATGATATTTGTACATGG
Found at i:39740795 original size:22 final size:22
Alignment explanation
Indices: 39740748--39740803 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
39740738 GAATAGTGCC
* *
39740748 ACACGTCCGTGTGGCTAGTGTA
1 ACACGCCCGTGTGGATAGTGTA
*
39740770 ACACGCCCGTGTGGAT-GATGTG
1 ACACGCCCGTGTGGATAG-TGTA
39740792 ACACGCCCGTGT
1 ACACGCCCGTGT
39740804 CATCACCCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (22 bp):
ACACGCCCGTGTGGATAGTGTA
Found at i:39741771 original size:6 final size:6
Alignment explanation
Indices: 39741761--39741798 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
39741751 CACCGTAAAG
*
39741761 GTAACA ATAACA GTAACA GTAACA GTAACA GTAACA GT
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTAACA GT
39741799 CAGGTATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:39742673 original size:23 final size:23
Alignment explanation
Indices: 39742629--39742673 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
39742619 TCAAAACCCT
* *
39742629 ATTTTTCCTTTCTTTTTCTTTCC
1 ATTTTTCCTTTCTTTCTATTTCC
39742652 ATTTTT-CTTTCCTTTCTATTTC
1 ATTTTTCCTTT-CTTTCTATTTC
39742674 TTTTTCATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTTTTCCTTTCTTTCTATTTCC
Found at i:39742679 original size:17 final size:17
Alignment explanation
Indices: 39742632--39742679 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
39742622 AAACCCTATT
39742632 TTTCC-TTTCTTTTT-C
1 TTTCCATTTCTTTTTCC
39742647 TTTCCATTT-TTCTTTCC
1 TTTCCATTTCTT-TTTCC
*
39742664 TTTCTATTTCTTTTTC
1 TTTCCATTTCTTTTTC
39742680 ATCCTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 6 0.21
17 13 0.46
18 2 0.07
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCCATTTCTTTTTCC
Found at i:39743390 original size:7 final size:7
Alignment explanation
Indices: 39743378--39743406 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
39743368 ATAATAATAT
39743378 AATTTTA
1 AATTTTA
39743385 AATTTTA
1 AATTTTA
39743392 AATTTT-
1 AATTTTA
39743398 AATTTTA
1 AATTTTA
39743405 AA
1 AA
39743407 ATGCGACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATTTTA
Found at i:39743408 original size:14 final size:14
Alignment explanation
Indices: 39743378--39743406 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39743368 ATAATAATAT
39743378 AATTTTAAATTTTA
1 AATTTTAAATTTTA
39743392 AATTTT-AATTTTA
1 AATTTTAAATTTTA
39743405 AA
1 AA
39743407 ATGCGACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTTAAATTTTA
Found at i:39751723 original size:21 final size:22
Alignment explanation
Indices: 39751699--39751744 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
39751689 GACTGCCTTC
* *
39751699 GATGTCGCGACATA-GCCTGAA
1 GATGTCGCAACATACCCCTGAA
39751720 GATGTCGCAACATACCCCTGAA
1 GATGTCGCAACATACCCCTGAA
39751742 GAT
1 GAT
39751745 AAGCATACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (22 bp):
GATGTCGCAACATACCCCTGAA
Found at i:39754279 original size:21 final size:21
Alignment explanation
Indices: 39754252--39754292 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39754242 CGCCACCACC
*
39754252 TTTTTTTATAATATTTTTTTTG
1 TTTTTTTA-AATATTATTTTTG
39754274 TTTTTTTAAATATTATTTT
1 TTTTTTTAAATATTATTTT
39754293 ATTAGTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTTAAATATTATTTTTG
Found at i:39754374 original size:25 final size:25
Alignment explanation
Indices: 39754341--39754397 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
39754331 TATTTTTCTA
*
39754341 GTAC-AATACATGACTCGTGTATAT
1 GTACGAATACATGACCCGTGTATAT
39754365 GTACGAATACATGACCCGTGTATAT
1 GTACGAATACATGACCCGTGTATAT
39754390 GTACGAAT
1 GTACGAAT
39754398 GTGGTATGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (25 bp):
GTACGAATACATGACCCGTGTATAT
Found at i:39757779 original size:75 final size:73
Alignment explanation
Indices: 39757639--39757828 Score: 224
Period size: 75 Copynumber: 2.6 Consensus size: 73
39757629 TTATGTAAAT
* ** * *
39757639 AATACAAAGTTTATTATTTAAATTTCAAAAAAAATCCTAAAAATTAATAACTAAAGTGGCAAAAA
1 AATACAAAG-TTA-TATTTAAATTAC-AAAAAACCCCT-AAAATTAATAACTAAAATGGAAAAAA
39757704 AGTCATTACATA
62 AGTCATTACATA
* *
39757716 AATACAAAGTTGACTATTTAAATTGCAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAAAT
1 AATACAAAGTT-A-TATTTAAATTACAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAAAG
39757781 TCATTACATA
64 TCATTACATA
* *
39757791 AATATAAAG-T-TATTTAAATTAC-AAAACCCCCTAAAATT
1 AATACAAAGTTATATTTAAATTACAAAAAACCCCTAAAATT
39757829 GATGGTTTGA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
70 15 0.15
71 11 0.11
74 1 0.01
75 43 0.42
76 11 0.11
77 21 0.21
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.29
Consensus pattern (73 bp):
AATACAAAGTTATATTTAAATTACAAAAAACCCCTAAAATTAATAACTAAAATGGAAAAAAAGTC
ATTACATA
Found at i:39758070 original size:46 final size:46
Alignment explanation
Indices: 39757996--39758092 Score: 137
Period size: 46 Copynumber: 2.1 Consensus size: 46
39757986 GCCAAAAGTA
*
39757996 GTGGAGTACAGTAGTGGATACAGGCCGGGAGGAGTGGAGTAC-GATG
1 GTGGAGTACAGGAGTGGATACAGGCCGGGAGGAGTGGAGTACTGA-G
39758042 GTGGAGTACAGCGA-TGGATAC-GGACCGGGAGGAGTGGAGTACTGAG
1 GTGGAGTACAG-GAGTGGATACAGG-CCGGGAGGAGTGGAGTACTGAG
39758088 GTGGA
1 GTGGA
39758093 TATAAGTCGG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
45 2 0.04
46 42 0.89
47 3 0.06
ACGTcount: A:0.26, C:0.11, G:0.46, T:0.16
Consensus pattern (46 bp):
GTGGAGTACAGGAGTGGATACAGGCCGGGAGGAGTGGAGTACTGAG
Found at i:39760421 original size:104 final size:104
Alignment explanation
Indices: 39760143--39760708 Score: 604
Period size: 104 Copynumber: 5.5 Consensus size: 104
39760133 ATAAATAAAA
* * * * * *
39760143 ATAAAATTACATTATATATAAATTACATTA--AAAAAATCACAAAACACTAAATTAAATACTAAA
1 ATAAAATTA-TTTTTATAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC
* *
39760206 AATTTATTTAACCTAATCATAAATTACTAAAAAAATAACT
65 AATTTATATAACCTAATCATAAATTACTAACAAAATAACT
**
39760246 ATAAAATTATTTTT-TTTAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACA
1 ATAAAATTATTTTTATAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACA
39760310 ATTTATATAACCTAATCATAAATTACTAACAAAATAACT
66 ATTTATATAACCTAATCATAAATTACTAACAAAATAACT
* * * * *
39760349 AT-AAATT-TTTTTAAAAAAAATTTAAATTACTAAAGAATCACAAAACACTAAATTAAATACTAA
1 ATAAAATTATTTTT-ATAAAAA-TTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAA
* *
39760412 CAATTTATATAACATAATCATAAATTACTAACAAAATAACG
64 CAATTTATATAACCTAATCATAAATTACTAACAAAATAACT
* * *
39760453 ATAAAATTATTTTTTTTAAAAATTACATTACTAAAAAAATCACAAAACTCAAAACTAAACACTAA
1 ATAAAATTA-TTTTTATAAAAATTACATTACT-AAAAAATCACAAAACACTAAACTAAACACTAA
*
39760518 CAA-TT-TATAACGTAATCCCATAAATTACTAACAAAATAAATAACT
64 CAATTTATATAACCTAAT--CATAAATTACTAAC---A-AAATAACT
* **** * * *
39760563 ATAACATT-TAAAAAAAAAGAAATTACATTACTAAAAAATAAC-AAA-AC-AGA--AAACACTAA
1 ATAAAATTAT-TTTTATAA-AAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAA
*
39760622 CAA-TT-TATAACCTAATCATAAACTACTAACAAAATAACT
64 CAATTTATATAACCTAATCATAAATTACTAACAAAATAACT
* * * *
39760661 ATAAAATTATTTTTTTTAAAATTATATTACTAAAAACTCACAAAACAC
1 ATAAAATTATTTTTATAAAAATTACATTACTAAAAAATCACAAAACAC
39760709 AACAATTTAT
Statistics
Matches: 393, Mismatches: 50, Indels: 44
0.81 0.10 0.09
Matches are distributed among these distances:
97 20 0.05
98 19 0.05
99 4 0.01
101 18 0.05
102 21 0.05
103 82 0.21
104 113 0.29
105 16 0.04
106 51 0.13
107 6 0.02
108 4 0.01
109 12 0.03
110 27 0.07
ACGTcount: A:0.55, C:0.14, G:0.01, T:0.30
Consensus pattern (104 bp):
ATAAAATTATTTTTATAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACA
ATTTATATAACCTAATCATAAATTACTAACAAAATAACT
Found at i:39760550 original size:210 final size:211
Alignment explanation
Indices: 39760173--39760710 Score: 735
Period size: 207 Copynumber: 2.6 Consensus size: 211
39760163 AATTACATTA
* * *
39760173 AAAAAATCACAAAACACTAAATTAAATACTAAAAATTTATTTAACCTAATCATAAATTACTAAAA
1 AAAAAATCACAAAACACTAAATTAAATACTAACAATTTATATAACCTAATCATAAATTACTAACA
*
39760238 AAATAACTATAAAATTATTTTTTTT-AAATTACATTACTAAAAAATCACAAAACACTAAACTAAA
66 AAATAACTATAAAATTATTTTTTTTAAAATTACATTACTAAAAAATCACAAAACACAAAACTAAA
***
39760302 CACTAACAATTTATATAACCTAATCATAAATTACTAAC-A-AAATAACTATAA-ATTTTTTTAAA
131 CACTAACAATTTATATAACCTAATCATAAATTACTAACAATAAATAACTATAACA-TTTAAAAAA
*
39760364 AAA-AATTTAAATTACT
195 AAAGAAATTAAATTACT
* *
39760380 AAAGAATCACAAAACACTAAATTAAATACTAACAATTTATATAACATAATCATAAATTACTAACA
1 AAAAAATCACAAAACACTAAATTAAATACTAACAATTTATATAACCTAATCATAAATTACTAACA
* *
39760445 AAATAACGATAAAATTATTTTTTTTAAAAATTACATTACTAAAAAAATCACAAAACTCAAAACTA
66 AAATAACTATAAAATTATTTTTTTT-AAAATTACATTACT-AAAAAATCACAAAACACAAAACTA
*
39760510 AACACTAACAA-TT-TATAACGTAATCCCATAAATTACTAACAAAATAAATAACTATAACATTTA
129 AACACTAACAATTTATATAACCTAAT--CATAAATTACTAAC--AATAAATAACTATAACATTTA
*
39760573 AAAAAAAAGAAATTACATTACT
190 AAAAAAAAGAAATTAAATTACT
* * * *
39760595 AAAAAATAAC-AAA-AC-AGA--AAACACTAACAA-TT-TATAACCTAATCATAAACTACTAACA
1 AAAAAATCACAAAACACTAAATTAAATACTAACAATTTATATAACCTAATCATAAATTACTAACA
* *
39760653 AAATAACTATAAAATTATTTTTTTTAAAATTATATTACTAAAAACTCACAAAACACAA
66 AAATAACTATAAAATTATTTTTTTTAAAATTACATTACTAAAAAATCACAAAACACAA
39760711 CAATTTATAA
Statistics
Matches: 296, Mismatches: 24, Indels: 23
0.86 0.07 0.07
Matches are distributed among these distances:
206 17 0.06
207 97 0.33
208 58 0.20
209 17 0.06
210 58 0.20
212 2 0.01
213 3 0.01
214 24 0.08
215 20 0.07
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (211 bp):
AAAAAATCACAAAACACTAAATTAAATACTAACAATTTATATAACCTAATCATAAATTACTAACA
AAATAACTATAAAATTATTTTTTTTAAAATTACATTACTAAAAAATCACAAAACACAAAACTAAA
CACTAACAATTTATATAACCTAATCATAAATTACTAACAATAAATAACTATAACATTTAAAAAAA
AAGAAATTAAATTACT
Found at i:39764267 original size:12 final size:12
Alignment explanation
Indices: 39764250--39764286 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
39764240 AACCATATTT
39764250 AACTAACTAACA
1 AACTAACTAACA
39764262 AACTAACTAACCA
1 AACTAACTAA-CA
39764275 AACT-ACTAACA
1 AACTAACTAACA
39764286 A
1 A
39764287 TTTAACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 15 0.62
13 6 0.25
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (12 bp):
AACTAACTAACA
Found at i:39771295 original size:20 final size:20
Alignment explanation
Indices: 39771270--39771311 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39771260 TGTCGATACA
* *
39771270 TTTTTAAGTATCAATACTTT
1 TTTTTAAGGAACAATACTTT
*
39771290 TTTTTAAGGAACAGTACTTT
1 TTTTTAAGGAACAATACTTT
39771310 TT
1 TT
39771312 AAAGGTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (20 bp):
TTTTTAAGGAACAATACTTT
Found at i:39778275 original size:22 final size:20
Alignment explanation
Indices: 39778249--39778289 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
39778239 TAGACATTAT
39778249 AAAGGAAGAAAAAAGAAAAATA
1 AAAGGAA-AAAAAA-AAAAATA
*
39778271 AAAGGAAAATAAAAAAAAT
1 AAAGGAAAAAAAAAAAAAT
39778290 TTAAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAGGAAAAAAAAAAAAATA
Found at i:39779611 original size:13 final size:13
Alignment explanation
Indices: 39779593--39779624 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
39779583 TTTTTAGTAC
39779593 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
39779606 AAAAAGAAAAAGG
1 AAAAAGAAAAAAG
39779619 AAAAAG
1 AAAAAG
39779625 GGCAAGGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:39781186 original size:20 final size:20
Alignment explanation
Indices: 39781154--39781199 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
39781144 TCCTTTCGTA
*
39781154 TTTTTCGTGTCTACAT-TT-T
1 TTTTTTGTGTCTA-ATCTTCT
39781173 TTTTTTGTGTTCTAATCTTCT
1 TTTTTTGTG-TCTAATCTTCT
39781194 TTTTTT
1 TTTTTT
39781200 CTTTTTGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 6 0.26
21 7 0.30
ACGTcount: A:0.09, C:0.13, G:0.09, T:0.70
Consensus pattern (20 bp):
TTTTTTGTGTCTAATCTTCT
Found at i:39786977 original size:31 final size:31
Alignment explanation
Indices: 39786939--39787000 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39786929 CTTCAAAGCC
39786939 GTCGTTGGGTTTGGCTCCTTTAAGCTGCTAA
1 GTCGTTGGGTTTGGCTCCTTTAAGCTGCTAA
39786970 GTCGTTGGGTTTGGCTCCTTTAAGCTGCTAA
1 GTCGTTGGGTTTGGCTCCTTTAAGCTGCTAA
39787001 CTCCAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.13, C:0.19, G:0.29, T:0.39
Consensus pattern (31 bp):
GTCGTTGGGTTTGGCTCCTTTAAGCTGCTAA
Found at i:39788839 original size:30 final size:27
Alignment explanation
Indices: 39788801--39788856 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
39788791 TTCATGATGA
*
39788801 TCATAACAACAACAAATCTTATACAAT
1 TCATAATAACAACAAATCTTATACAAT
39788828 TCATAATAACAACAAATCTTATACAAT
1 TCATAATAACAACAAATCTTATACAAT
39788855 TC
1 TC
39788857 CTTAACCCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (27 bp):
TCATAATAACAACAAATCTTATACAAT
Found at i:39789427 original size:43 final size:43
Alignment explanation
Indices: 39789366--39789521 Score: 206
Period size: 43 Copynumber: 3.6 Consensus size: 43
39789356 TTTTTTTAAG
* * * *
39789366 AAGCGCCGCTAAAGATCATGTTCTATAGCGGCATTAT-TAGTAA
1 AAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTT-TGTAGGAA
* *
39789409 AAGCGCCGTTAAAGATCATGATCTTTAGCAGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTAGGAA
* *
39789452 AAACGCCGCTAAAAATCATGTTCTTTAGCAGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTAGGAA
* *
39789495 AAGCACCACTAAAGATCATGTTCTTTA
1 AAGCGCCGCTAAAGATCATGTTCTTTA
39789522 AACCAGTACC
Statistics
Matches: 98, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 1 0.01
43 97 0.99
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
AAGCGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTGTAGGAA
Found at i:39790332 original size:28 final size:29
Alignment explanation
Indices: 39790278--39790332 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
39790268 ACAGAGGTTT
39790278 TCACACGGCCAAGCACACGTCCGTGTCCC
1 TCACACGGCCAAGCACACGTCCGTGTCCC
*
39790307 TCACACGGCCTAGACACAC-T-CGTGTC
1 TCACACGGCCAAG-CACACGTCCGTGTC
39790333 ATCGCTCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 13 0.54
30 5 0.21
ACGTcount: A:0.22, C:0.42, G:0.20, T:0.16
Consensus pattern (29 bp):
TCACACGGCCAAGCACACGTCCGTGTCCC
Found at i:39796708 original size:244 final size:244
Alignment explanation
Indices: 39796277--39796762 Score: 837
Period size: 244 Copynumber: 2.0 Consensus size: 244
39796267 TAGGTTCTAT
** * *
39796277 AGACATATCCATACTAGACACCAAGTTTATACAAATTTACGAATGGATTAACCCTGGATCAATTA
1 AGACATATCCATACTAGACACCAAGTCCATACAAATGTACGAATGGATTAACCCTAGATCAATTA
*
39796342 AGGCAATGACACAAGTATTACAAATATAAAATGTACCCTGATGACATCGGGAGTAGTGGCTTCCT
66 AGGCAATGACACAAGTATTACAAATATAAAATGTACCCTGATGACATCGGGAGTAGTGGCTTCAT
* * *
39796407 CTCGAGCGCTTATTGCATAAGTTCTTGCCGGGGCTCGAGCCTCTGGTTTTGCAGTAGCATCCTTA
131 CTCGAGCGCGTATTGCATAAGTTCTTGCCCGGGCTCGAGCCTCTGGTTTTACAGTAGCATCCTTA
*
39796472 GCAACAGTTCGACTGCCACTTGCACTTCTGGGATGTCTCGGGGGTCTGC
196 GCAACAGTTCAACTGCCACTTGCACTTCTGGGATGTCTCGGGGGTCTGC
* *
39796521 AGACATATCCATACTAGACACCAAGTCCATACAAATGTATGAATGGATTGACCCTAGATCAATTA
1 AGACATATCCATACTAGACACCAAGTCCATACAAATGTACGAATGGATTAACCCTAGATCAATTA
* *
39796586 AGGCAATGACACGAGTATTACAGATATAAAATGTACCCTGATGACATCGGGAGTAGTGGCTTCAT
66 AGGCAATGACACAAGTATTACAAATATAAAATGTACCCTGATGACATCGGGAGTAGTGGCTTCAT
*
39796651 CTCGAGCGCGTATTGCATAAGTTCTTTCCCGGGCTCGAGCCTCTGGTTTTACAGTAGCATCCTTA
131 CTCGAGCGCGTATTGCATAAGTTCTTGCCCGGGCTCGAGCCTCTGGTTTTACAGTAGCATCCTTA
*
39796716 GCAACAGTTCAACTGCCACTTGCATTTCTGGGATGTCTCGGGGGTCT
196 GCAACAGTTCAACTGCCACTTGCACTTCTGGGATGTCTCGGGGGTCT
39796763 ACCTCGAGAA
Statistics
Matches: 227, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
244 227 1.00
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (244 bp):
AGACATATCCATACTAGACACCAAGTCCATACAAATGTACGAATGGATTAACCCTAGATCAATTA
AGGCAATGACACAAGTATTACAAATATAAAATGTACCCTGATGACATCGGGAGTAGTGGCTTCAT
CTCGAGCGCGTATTGCATAAGTTCTTGCCCGGGCTCGAGCCTCTGGTTTTACAGTAGCATCCTTA
GCAACAGTTCAACTGCCACTTGCACTTCTGGGATGTCTCGGGGGTCTGC
Found at i:39807883 original size:33 final size:33
Alignment explanation
Indices: 39807788--39807946 Score: 137
Period size: 33 Copynumber: 4.8 Consensus size: 33
39807778 CGATAAACTT
* * *
39807788 TATT-TGTGTTTACTTTCCCAGTGGACTATCTC
1 TATTATGTGTTTACTGTCCTAGCGGACTATCTC
* * * * *
39807820 TGTTATGTGTTTAATGTCAC-AGTAGG-CTATTTT
1 TATTATGTGTTTACTGTC-CTAG-CGGACTATCTC
*
39807853 TATTATGTGTTTACTGTCCTAGCGGACTATTTC
1 TATTATGTGTTTACTGTCCTAGCGGACTATCTC
* * *
39807886 TATTTTGTGTTTACTGTCTCT-GCAGATTATCTC
1 TATTATGTGTTTACTGTC-CTAGCGGACTATCTC
* *
39807919 TATTATGTGCTTACTGTCCTAGTGGACT
1 TATTATGTGTTTACTGTCCTAGCGGACT
39807947 TTCAATGTTC
Statistics
Matches: 101, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
32 8 0.08
33 88 0.87
34 5 0.05
ACGTcount: A:0.18, C:0.17, G:0.18, T:0.47
Consensus pattern (33 bp):
TATTATGTGTTTACTGTCCTAGCGGACTATCTC
Found at i:39807898 original size:66 final size:66
Alignment explanation
Indices: 39807785--39807946 Score: 182
Period size: 66 Copynumber: 2.5 Consensus size: 66
39807775 TCCCGATAAA
* * * * *
39807785 CTTTATT-TGTGTTTACTTTCCCAGTGGACTATCTCTGTTATGTGTTTAATGTCACAGTAGGCTA
1 CTTTATTATGTGTTTACTGTCCTAGTGGACTATCTCTATTATGTGTTTAATGTCACAGCAGACTA
39807849 T
66 T
* * * * * * * *
39807850 TTTTATTATGTGTTTACTGTCCTAGCGGACTATTTCTATTTTGTGTTTACTGTCTCTGCAGATTA
1 CTTTATTATGTGTTTACTGTCCTAGTGGACTATCTCTATTATGTGTTTAATGTCACAGCAGACTA
39807915 T
66 T
* *
39807916 CTCTATTATGTGCTTACTGTCCTAGTGGACT
1 CTTTATTATGTGTTTACTGTCCTAGTGGACT
39807947 TTCAATGTTC
Statistics
Matches: 79, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
65 6 0.08
66 73 0.92
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (66 bp):
CTTTATTATGTGTTTACTGTCCTAGTGGACTATCTCTATTATGTGTTTAATGTCACAGCAGACTA
T
Found at i:39810079 original size:40 final size:40
Alignment explanation
Indices: 39810015--39810093 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
39810005 ATACGGTACC
* *
39810015 ACTTGGTGTGTAGGGTTGGATGGGTTGATTCTATCCCCAT
1 ACTTGGTGTGTAGAGCTGGATGGGTTGATTCTATCCCCAT
* * *
39810055 ACTTGGTGTGTAGAGCTGGGTGGGTTTATTTTATCCCCA
1 ACTTGGTGTGTAGAGCTGGATGGGTTGATTCTATCCCCA
39810094 CCTGGTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (40 bp):
ACTTGGTGTGTAGAGCTGGATGGGTTGATTCTATCCCCAT
Found at i:39814039 original size:88 final size:88
Alignment explanation
Indices: 39813939--39814114 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
39813929 GCTCTTTTAC
39813939 AACATTAGAAAAAAATCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTATG
1 AACATTAGAAAAAAATCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTATG
39814004 TTTTGAGGGTTCTTTGTTTTCAG
66 TTTTGAGGGTTCTTTGTTTTCAG
39814027 AACATTAGAAAAAAATCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTATG
1 AACATTAGAAAAAAATCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTATG
39814092 TTTTGAGGGTTCTTTGTTTTCAG
66 TTTTGAGGGTTCTTTGTTTTCAG
39814115 GTTTTCAGGG
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (88 bp):
AACATTAGAAAAAAATCCATTAGAGATTAGAACTCATAACACATTTAGAGAATTTTGTGTTTATG
TTTTGAGGGTTCTTTGTTTTCAG
Found at i:39815008 original size:21 final size:21
Alignment explanation
Indices: 39814974--39815013 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39814964 ATTAATTATT
39814974 TAATTATAAAAAATTAAATGA
1 TAATTATAAAAAATTAAATGA
39814995 TAATT-TAAAGAAATTAAAT
1 TAATTATAAA-AAATTAAAT
39815014 TAAATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
TAATTATAAAAAATTAAATGA
Found at i:39821958 original size:43 final size:43
Alignment explanation
Indices: 39821820--39822355 Score: 532
Period size: 43 Copynumber: 12.4 Consensus size: 43
39821810 TACTTTGGTA
** ** *
39821820 TATCCGATGATGCACTGCATGTGCCAGTATATTTGCTTTAGTA
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * * * * * **
39821863 TATCCAACGATGCATTATGTATGCAAGTATATTTGCTTCAGCA
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * *
39821906 TAGCTGATGATGCACTGTGTGTGCCAGTATATTTTCTTTGGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * *
39821949 TATCCGATGATGCATTGTGTGTGCCAATATAGTAGCTTCGGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * *
39821992 TCATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGATT
1 T-ATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * *
39822036 TATCCGATGATCCACTGTGTGTGCCAGTATAGTAGCTTCGGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * *
39822079 TCATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGATT
1 T-ATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * *
39822123 TATCCGATGATCCACTGTGTGTGCCAGTATAGTAGCTTCGGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * *
39822166 TCATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTT
1 T-ATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * * * *
39822210 TATCCGATGATGCACTGTGTGTGCTAATATAGTAGTTTCAGTT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* ** * *
39822253 TCATCCAATGATGCACTGTGTGTGTTAGTATATTTGCTTCAGTA
1 T-ATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
* * * * **
39822297 TATCTGATGATGCACTATTTGTGCCAGTATATTTTCTTCAATT
1 TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
39822340 TATCCGATGATGCACT
1 TATCCGATGATGCACT
39822356 TACGTGCCGG
Statistics
Matches: 397, Mismatches: 92, Indels: 8
0.80 0.19 0.02
Matches are distributed among these distances:
43 253 0.64
44 144 0.36
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (43 bp):
TATCCGATGATGCACTGTGTGTGCCAGTATATTTGCTTCGGTT
Found at i:39822025 original size:87 final size:87
Alignment explanation
Indices: 39821821--39822355 Score: 626
Period size: 87 Copynumber: 6.2 Consensus size: 87
39821811 ACTTTGGTAT
** * * * * * * * * *
39821821 ATCCGATGATGCACTGCATGTGCCAGTATATTTGCTTTAGTATATCCAACGATGCATTATGTATG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
* * **
39821886 -CAAGTATATTTGCTTCAGCAT-
66 CCAA-TATAGTAGCTTCAGTTTC
* * * *
39821907 AGCTGATGATGCACTGTGTGTGCCAGTATATTTTCTTTGGTTTATCCGATGATGCATTGTGTGTG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
*
39821972 CCAATATAGTAGCTTCGGTTTC
66 CCAATATAGTAGCTTCAGTTTC
* *
39821994 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGATTTATCCGATGATCCACTGTGTGTG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
* *
39822059 CCAGTATAGTAGCTTCGGTTTC
66 CCAATATAGTAGCTTCAGTTTC
* *
39822081 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGATTTATCCGATGATCCACTGTGTGTG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
* *
39822146 CCAGTATAGTAGCTTCGGTTTC
66 CCAATATAGTAGCTTCAGTTTC
39822168 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
* *
39822233 CTAATATAGTAGTTTCAGTTTC
66 CCAATATAGTAGCTTCAGTTTC
* *** * ** * * * *
39822255 ATCCAATGATGCACTGTGTGTGTTAGTATATTTGCTTCAGTATATCTGATGATGCACTATTTGTG
1 ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
* * ** *
39822320 CCAGTATATTTTCTTCAATTT-
66 CCAATATAGTAGCTTCAGTTTC
39822341 ATCCGATGATGCACT
1 ATCCGATGATGCACT
39822356 TACGTGCCGG
Statistics
Matches: 399, Mismatches: 48, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
86 80 0.20
87 319 0.80
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (87 bp):
ATCCGATGATGCACTGTGTGTACCAGTATATTTTCTTTGGTTTATCCGATGATGCACTGTGTGTG
CCAATATAGTAGCTTCAGTTTC
Found at i:39823079 original size:19 final size:19
Alignment explanation
Indices: 39823055--39823107 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
39823045 TAACTAGAAT
* *
39823055 CAGAATCAGAATTAGGTGA
1 CAGAATCAGAATCAGGTAA
*
39823074 CAGAATCAGTATCAGGTAA
1 CAGAATCAGAATCAGGTAA
*
39823093 CAGAATCAAAATCAG
1 CAGAATCAGAATCAG
39823108 AATCAGTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (19 bp):
CAGAATCAGAATCAGGTAA
Found at i:39823109 original size:31 final size:32
Alignment explanation
Indices: 39823074--39823142 Score: 122
Period size: 31 Copynumber: 2.2 Consensus size: 32
39823064 AATTAGGTGA
*
39823074 CAGAATCAGTATCAGGTAACAGAAT-CAAAAT
1 CAGAATCAGTATCAGGTAACAGAATAAAAAAT
39823105 CAGAATCAGTATCAGGTAACAGAATAAAAAAT
1 CAGAATCAGTATCAGGTAACAGAATAAAAAAT
39823137 CAGAAT
1 CAGAAT
39823143 GGTGGTTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 25 0.69
32 11 0.31
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (32 bp):
CAGAATCAGTATCAGGTAACAGAATAAAAAAT
Found at i:39823639 original size:16 final size:16
Alignment explanation
Indices: 39823620--39823654 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39823610 AATAATGAGT
39823620 AAAT-AAAATAACAATG
1 AAATAAAAATAA-AATG
39823636 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
39823652 AAA
1 AAA
39823655 ACAAGTAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:39825393 original size:27 final size:27
Alignment explanation
Indices: 39825355--39825410 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
39825345 TGAACTCAAG
39825355 TATGGATATTTTTACATCTAGTATCGA
1 TATGGATATTTTTACATCTAGTATCGA
39825382 TATGGATATTTTTACATCTAGTATCGA
1 TATGGATATTTTTACATCTAGTATCGA
39825409 TA
1 TA
39825411 CCTGACCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (27 bp):
TATGGATATTTTTACATCTAGTATCGA
Found at i:39831713 original size:26 final size:26
Alignment explanation
Indices: 39831682--39831789 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
39831672 TGAAATGCCC
*
39831682 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
39831708 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
39831734 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
39831760 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
39831786 ATCA
1 ATCA
39831790 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:39836112 original size:17 final size:17
Alignment explanation
Indices: 39836090--39836122 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
39836080 GCGACAATGT
39836090 GAAAAAAATAAAATAAA
1 GAAAAAAATAAAATAAA
39836107 GAAAAAAATAAAATAA
1 GAAAAAAATAAAATAA
39836123 CACACAAATT
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:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
GAAAAAAATAAAATAAA
Found at i:39840339 original size:5 final size:5
Alignment explanation
Indices: 39840329--39840368 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
39840319 ATTTGTGAAA
*
39840329 AAAAT AAAAT AAAAT AAAAT -AAAG AAAA- AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
39840369 CACACAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 7 0.22
5 25 0.78
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:39840344 original size:10 final size:10
Alignment explanation
Indices: 39840329--39840368 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
39840319 ATTTGTGAAA
39840329 AAAATAAAAT
1 AAAATAAAAT
39840339 AAAATAAAAT
1 AAAATAAAAT
*
39840349 -AAAGAAAA-
1 AAAATAAAAT
39840357 AAAATAAAAT
1 AAAATAAAAT
39840367 AA
1 AA
39840369 CACACAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (10 bp):
AAAATAAAAT
Done.