Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 56 of 89
Found at i:12727484 original size:60 final size:61
Alignment explanation
Indices: 12727373--12727490 Score: 145
Period size: 60 Copynumber: 2.0 Consensus size: 61
12727363 AATATTGGCC
* * *
12727373 TTTATTCTAAATTAGTCCCTATATTTTTTAATATTCTAGTTTTATCTCCAAAA-TATGGTT
1 TTTATTCTAAATTAGTCCCTATATTTTTTAATATTATAATTTCATCTCCAAAACTATGGTT
*
12727433 TTTATTCTAAATTAGTCTCTA-ACTTTTTTTAA-AGTTATAATTTCATC-CCAAAACTATG
1 TTTATTCTAAATTAGTCCCTATA--TTTTTTAATA-TTATAATTTCATCTCCAAAACTATG
12727491 ACCTTTCTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
59 1 0.02
60 27 0.54
61 22 0.44
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (61 bp):
TTTATTCTAAATTAGTCCCTATATTTTTTAATATTATAATTTCATCTCCAAAACTATGGTT
Found at i:12728149 original size:14 final size:14
Alignment explanation
Indices: 12728127--12728169 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
12728117 TCAATTATAT
*
12728127 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
12728141 GTTCATTTATGTTC
1 GTTCATTTATGTTC
12728155 GTTCATTTATGTTC
1 GTTCATTTATGTTC
12728169 G
1 G
12728170 AACAGAAGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:12728451 original size:14 final size:14
Alignment explanation
Indices: 12728423--12728462 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12728413 TTTTTTTTGT
12728423 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
12728436 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
12728450 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
12728463 TATTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:12728550 original size:16 final size:16
Alignment explanation
Indices: 12728529--12728559 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12728519 CAAAAAAAAT
*
12728529 TGTTCGTTTTTGTTCG
1 TGTTCGTTTATGTTCG
12728545 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
12728560 ATTTATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.03, C:0.13, G:0.23, T:0.61
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:12740557 original size:16 final size:16
Alignment explanation
Indices: 12740492--12740559 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
12740482 CATTATGTTG
*
12740492 TAAATTAAAAATATAA
1 TAAATTTAAAATATAA
* *
12740508 T--ATTTAAATTATATT
1 TAAATTTAAAATATA-A
* *
12740523 TAAACTTTTATATAT-A
1 TAAA-TTTAAAATATAA
12740539 TAAATTTAAAATATAA
1 TAAATTTAAAATATAA
12740555 TAAAT
1 TAAAT
12740560 CCAAATAATA
Statistics
Matches: 38, Mismatches: 9, Indels: 10
0.67 0.16 0.18
Matches are distributed among these distances:
14 10 0.26
15 9 0.24
16 11 0.29
17 1 0.03
18 7 0.18
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAAATATAA
Found at i:12751992 original size:16 final size:16
Alignment explanation
Indices: 12751962--12752004 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
12751952 TATTAAACCT
12751962 TTTGTT-TTTAATTTA
1 TTTGTTATTTAATTTA
*
12751977 TTTGTTATTTATTTTA
1 TTTGTTATTTAATTTA
* *
12751993 ATTATTATTTAA
1 TTTGTTATTTAA
12752005 AAAAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTGTTATTTAATTTA
Found at i:12759122 original size:31 final size:31
Alignment explanation
Indices: 12759084--12759143 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
12759074 AAACATTTTG
12759084 ATATTTCGATATAACAAATTAAGTTAAATAA
1 ATATTTCGATATAACAAATTAAGTTAAATAA
12759115 ATATTTCGATATAACAAATTAAGTTAAAT
1 ATATTTCGATATAACAAATTAAGTTAAAT
12759144 GAATTTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (31 bp):
ATATTTCGATATAACAAATTAAGTTAAATAA
Found at i:12760400 original size:3 final size:3
Alignment explanation
Indices: 12760392--12760461 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
12760382 TCGGACTTAC
* *
12760392 TTA TTA TTA TTA -TA TTA TTA TTA TTA TATA TAA TTA CATA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA
* *
12760437 CTA CTA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA
12760462 AATAATATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
2 4 0.07
3 45 0.79
4 8 0.14
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:12760434 original size:31 final size:31
Alignment explanation
Indices: 12760399--12760458 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12760389 TACTTATTAT
* *
12760399 TATTATATTATTATTATTATATATAATTACA
1 TATTATACTACTATTATTATATATAATTACA
*
12760430 TATTATACTACTATTATTATATATTATTA
1 TATTATACTACTATTATTATATATAATTA
12760459 TTAAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (31 bp):
TATTATACTACTATTATTATATATAATTACA
Found at i:12761549 original size:16 final size:15
Alignment explanation
Indices: 12761530--12761572 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
12761520 AGGTAAAATC
12761530 ATATATTTAGTCCTTT
1 ATAT-TTTAGTCCTTT
**
12761546 ATATTTTTAGTAGTTT
1 ATA-TTTTAGTCCTTT
12761562 ATATTTTAGTC
1 ATATTTTAGTC
12761573 TTATTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.09, T:0.58
Consensus pattern (15 bp):
ATATTTTAGTCCTTT
Found at i:12766051 original size:45 final size:45
Alignment explanation
Indices: 12765987--12766077 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
12765977 ATCATTGAAT
12765987 CAATTTCACAATCTTGTAGTTCTTTGAATATTAATGGATTAAAAA
1 CAATTTCACAATCTTGTAGTTCTTTGAATATTAATGGATTAAAAA
*
12766032 CAATTTCGCAATCTTGTAGTTCTTTGAATATTAATGGATTAAAAA
1 CAATTTCACAATCTTGTAGTTCTTTGAATATTAATGGATTAAAAA
12766077 C
1 C
12766078 TCTTTATGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (45 bp):
CAATTTCACAATCTTGTAGTTCTTTGAATATTAATGGATTAAAAA
Found at i:12768942 original size:20 final size:20
Alignment explanation
Indices: 12768917--12768967 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
12768907 ATTCTCATAA
*
12768917 ATTTGTAAAACCTTCGGGTC
1 ATTTGTAAAACCTCCGGGTC
*
12768937 ATTTGTAAAGCCTCCGGGTC
1 ATTTGTAAAACCTCCGGGTC
*
12768957 ATCTGTAAAAC
1 ATTTGTAAAAC
12768968 ATTAGGGTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (20 bp):
ATTTGTAAAACCTCCGGGTC
Found at i:12769075 original size:20 final size:20
Alignment explanation
Indices: 12769050--12769109 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
12769040 TCAAATCCTT
* *
12769050 CGGGTCATTTGTAAAGCCTC
1 CGGGTCATCTGTAAAACCTC
12769070 CGGGTCATCTGTAAAACCTC
1 CGGGTCATCTGTAAAACCTC
*
12769090 TGGGTCATCTGTAAAACCTC
1 CGGGTCATCTGTAAAACCTC
12769110 AAGGTAGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (20 bp):
CGGGTCATCTGTAAAACCTC
Found at i:12769210 original size:20 final size:20
Alignment explanation
Indices: 12769187--12769225 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12769177 ATTAAATCCT
12769187 CCGGGTAATTCGTAAAACCC
1 CCGGGTAATTCGTAAAACCC
* *
12769207 CCGGGTCATTTGTAAAACC
1 CCGGGTAATTCGTAAAACC
12769226 TCAGGGCATG
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:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
CCGGGTAATTCGTAAAACCC
Found at i:12769223 original size:138 final size:139
Alignment explanation
Indices: 12768916--12769227 Score: 473
Period size: 139 Copynumber: 2.3 Consensus size: 139
12768906 AATTCTCATA
* * * *
12768916 AATTTGTAAAACCTTCGGGTCATTTGTAAAGCCTCCGGGTCATCTGTAAAACATTAGGGTAGGAT
1 AATTTGTAAAACCTCCGGGTCATTTGTAAAACCTCCGGGTCATCTGTAAAACATCAAGGTAGGAT
*
12768981 GTTTTCGCATGAAAACGAGATAGCGATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAAT
66 GTTTTCGCATGAAAACGAGATAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAAT
*
12769046 CCTTCGGGT
131 CCTCCGGGT
* * * * *
12769055 CATTTGTAAAGCCTCCGGGTCATCTGTAAAACCTCTGGGTCATCTGTAAAACCTCAAGGTAGGAT
1 AATTTGTAAAACCTCCGGGTCATTTGTAAAACCTCCGGGTCATCTGTAAAACATCAAGGTAGGAT
* * *
12769120 GTTTTCGCATGAAAATGAGATAGCAATTTTC-AAGTTTTTCATTTAATGTTCTAGAAAATTAAAT
66 GTTTTCGCATGAAAACGAGATAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAAT
12769184 CCTCCGGGT
131 CCTCCGGGT
* *
12769193 AATTCGTAAAACCCCCGGGTCATTTGTAAAACCTC
1 AATTTGTAAAACCTCCGGGTCATTTGTAAAACCTC
12769228 AGGGCATGAT
Statistics
Matches: 154, Mismatches: 19, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
138 69 0.45
139 85 0.55
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (139 bp):
AATTTGTAAAACCTCCGGGTCATTTGTAAAACCTCCGGGTCATCTGTAAAACATCAAGGTAGGAT
GTTTTCGCATGAAAACGAGATAGCAATTTTCAAAGTTTCTCATTTAATGTTCTAGAAAATCAAAT
CCTCCGGGT
Found at i:12769381 original size:3 final size:3
Alignment explanation
Indices: 12769373--12769463 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
12769363 CGGTCTTACA
* *
12769373 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT AAT T-T CA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * *
12769417 TAT TA- TAC TAC TAT TAT TAT ATAT TAT TAT TAA TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
12769462 TA
1 TA
12769464 AATAATATTA
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
2 4 0.05
3 66 0.87
4 6 0.08
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:12770653 original size:16 final size:16
Alignment explanation
Indices: 12770629--12770673 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
12770619 AAGGTAAATC
*
12770629 ATATATTTAGTCCTTT
1 ATATTTTTAGTCCTTT
**
12770645 ATATTTTTAGTAGTTT
1 ATATTTTTAGTCCTTT
12770661 ATA-TTTTAGTCCT
1 ATATTTTTAGTCCT
12770674 ATTCATAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (16 bp):
ATATTTTTAGTCCTTT
Found at i:12774707 original size:27 final size:27
Alignment explanation
Indices: 12774669--12774720 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12774659 TTATACTATT
*
12774669 TTTCAAATTACAATTTTATTTAATATA
1 TTTCAAATTACAATATTATTTAATATA
12774696 TTTCAACA-TACAATATTATTTAATA
1 TTTCAA-ATTACAATATTATTTAATA
12774721 AATCAATACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTCAAATTACAATATTATTTAATATA
Found at i:12776002 original size:12 final size:12
Alignment explanation
Indices: 12775985--12776009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12775975 AATTATAAAT
12775985 TTAAATTTTTTA
1 TTAAATTTTTTA
12775997 TTAAATTTTTTA
1 TTAAATTTTTTA
12776009 T
1 T
12776010 AATATATAGC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:12781535 original size:50 final size:50
Alignment explanation
Indices: 12781441--12781535 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
12781431 GTTTCGTCCG
* * * *
12781441 AGCTGACGCCACGTCATGAAAGGCGCAGATGGCCATCTGCGCCTTATTCT
1 AGCTGACGCCACGTAATGAAAGGCACAGATAGCCATCCGCGCCTTATTCT
* *
12781491 AGCTGGCGCCACGTAATGACAA-GCACAGATAGCCATCCGTGCCTT
1 AGCTGACGCCACGTAATGA-AAGGCACAGATAGCCATCCGCGCCTT
12781536 TTTAGGGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
50 36 0.95
51 2 0.05
ACGTcount: A:0.24, C:0.31, G:0.25, T:0.20
Consensus pattern (50 bp):
AGCTGACGCCACGTAATGAAAGGCACAGATAGCCATCCGCGCCTTATTCT
Found at i:12781771 original size:21 final size:19
Alignment explanation
Indices: 12781732--12781771 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
12781722 GTAAAATTAT
12781732 TTTTATTATATTATATTTA
1 TTTTATTATATTATATTTA
*
12781751 TTTTATATATGATTATTTTTA
1 TTTTAT-TAT-ATTATATTTA
12781772 AAAAAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (19 bp):
TTTTATTATATTATATTTA
Found at i:12785061 original size:13 final size:12
Alignment explanation
Indices: 12785033--12785093 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
12785023 ACAATTAAGT
*
12785033 AATAAAAAAATT
1 AATAAAAAAATA
12785045 AATAAACAAAATA
1 AATAAA-AAAATA
12785058 AATAATAATTAAATA
1 AATAA-AA--AAATA
* * *
12785073 ATTAAATAATTA
1 AATAAAAAAATA
12785085 AATAAAAAA
1 AATAAAAAA
12785094 TTTACAATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
12 17 0.44
13 11 0.28
14 2 0.05
15 9 0.23
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAAAAAAATA
Found at i:12785074 original size:8 final size:8
Alignment explanation
Indices: 12785061--12785089 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
12785051 CAAAATAAAT
12785061 AATAATTA
1 AATAATTA
12785069 AATAATTA
1 AATAATTA
12785077 AATAATTA
1 AATAATTA
12785085 AATAA
1 AATAA
12785090 AAAATTTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AATAATTA
Found at i:12785236 original size:3 final size:3
Alignment explanation
Indices: 12785228--12785308 Score: 110
Period size: 3 Copynumber: 27.0 Consensus size: 3
12785218 AACTCCTCAC
*
12785228 TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA TCA TCA TCA -CAA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC-A TCA
* * *
12785273 TCA TCA CCA CCA TCA TTA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
12785309 GGAGCAGATA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
2 1 0.01
3 68 0.97
4 1 0.01
ACGTcount: A:0.35, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
TCA
Found at i:12787509 original size:24 final size:24
Alignment explanation
Indices: 12787477--12787538 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
12787467 AATGTTTGTG
12787477 TTTAAATGAAGAGGAGATGAGATA
1 TTTAAATGAAGAGGAGATGAGATA
12787501 TTTAAATGAAGAGGAGATGAGATA
1 TTTAAATGAAGAGGAGATGAGATA
* *
12787525 TTTATAGGAAGAGG
1 TTTAAATGAAGAGG
12787539 GGAGGTGGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (24 bp):
TTTAAATGAAGAGGAGATGAGATA
Found at i:12787805 original size:129 final size:129
Alignment explanation
Indices: 12787573--12787835 Score: 483
Period size: 129 Copynumber: 2.0 Consensus size: 129
12787563 TAAATGTGGG
12787573 AGGTGTGAACGGTTGGAGTATTAATGGAAGGCGCGAATGGTTATCCACGCCTTACTGGCACGTGT
1 AGGTGTGAACGGTTGGAGTATTAATGGAAGGCGCGAATGGTTATCCACGCCTTACTGGCACGTGT
12787638 CAGAAACATCAGAAAGGCGCGGATGACGATCCGCTCCTGTCCTTATGTGTCGCCAGTTCAGATA
66 CAGAAACATCAGAAAGGCGCGGATGACGATCCGCTCCTGTCCTTATGTGTCGCCAGTTCAGATA
* *
12787702 AGGTGTGAACGGTTGGGGTATTAATGGAAGGCGTGAATGGTTATCCACGCCTTACTGG-ACTGTG
1 AGGTGTGAACGGTTGGAGTATTAATGGAAGGCGCGAATGGTTATCCACGCCTTACTGGCAC-GTG
*
12787766 TCAGAAACATCAGAAAGGCGCGGATGACGATCCGTTCCTGTCCTTATGTGTCGCCAGTTCAGATA
65 TCAGAAACATCAGAAAGGCGCGGATGACGATCCGCTCCTGTCCTTATGTGTCGCCAGTTCAGATA
12787831 AGGTG
1 AGGTG
12787836 CGAATGACCA
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
128 2 0.02
129 128 0.98
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.25
Consensus pattern (129 bp):
AGGTGTGAACGGTTGGAGTATTAATGGAAGGCGCGAATGGTTATCCACGCCTTACTGGCACGTGT
CAGAAACATCAGAAAGGCGCGGATGACGATCCGCTCCTGTCCTTATGTGTCGCCAGTTCAGATA
Found at i:12794965 original size:16 final size:15
Alignment explanation
Indices: 12794920--12795005 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 15
12794910 ATGTAAAGAC
**
12794920 TAAAATT-AAATAAA
1 TAAAATTAAAATGCA
12794934 TAAAA-TAAAATGCA
1 TAAAATTAAAATGCA
*
12794948 TAAATTTAAAAGTGCA
1 TAAAATTAAAA-TGCA
*
12794964 TAAAATT-AAAT-AA
1 TAAAATTAAAATGCA
12794977 TAGAAA-TAAAATGCAA
1 TA-AAATTAAAATGC-A
*
12794993 TAAAAATAAAATG
1 TAAAATTAAAATG
12795006 TTAATATCGA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
13 5 0.09
14 22 0.38
15 11 0.19
16 20 0.34
ACGTcount: A:0.64, C:0.03, G:0.07, T:0.26
Consensus pattern (15 bp):
TAAAATTAAAATGCA
Found at i:12795461 original size:104 final size:109
Alignment explanation
Indices: 12795211--12795496 Score: 370
Period size: 104 Copynumber: 2.7 Consensus size: 109
12795201 CTGTTAGAAA
* * ** *
12795211 AGTTAGCAGAGTCCGGACCATAATAATGTCAATCATACCCCGGATCGGGTAACCACAAGGTCAAA
1 AGTTAGTAGAGTCC-AACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAA
*
12795276 TTGAATAATTCAAACACATTAATAAAATGAAATAAAAAAGTTAGTG
65 TTGAATAATTCAAACAAATTAATAAAATG-AATAAAAAAGTTAGTG
* *
12795322 -GTTAGTAGAGTCCGAACCATAATAATGTGGGTCATACCCCGGATCGAGTCACCACAAGGTCAAA
1 AGTTAGTAGAGTCC-AACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAA
12795386 -T-AATAATTCAAACAAATTAAT-AAA-G-ATAAAAAAGTTAG-G
65 TTGAATAATTCAAACAAATTAATAAAATGAATAAAAAAGTTAGTG
* * * *
12795425 AGTTAGTAGAGTCCATACCATAATAATATGGATCATACCCCGAATTGGGTCACCACAAGGTCGAA
1 AGTTAGTAGAGTCCA-ACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAA
*
12795490 TCGAATA
65 TTGAATA
12795497 TTAGAAACAA
Statistics
Matches: 156, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
103 2 0.01
104 69 0.44
106 5 0.03
107 3 0.02
108 19 0.12
109 1 0.01
110 57 0.37
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (109 bp):
AGTTAGTAGAGTCCAACCATAATAATGTGGATCATACCCCGGATCGGGTCACCACAAGGTCAAAT
TGAATAATTCAAACAAATTAATAAAATGAATAAAAAAGTTAGTG
Found at i:12795561 original size:29 final size:29
Alignment explanation
Indices: 12795538--12795593 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12795528 ATGGTTAGAG
12795538 TGCAATAAAATAAAAGTTAGTGGTTAATA
1 TGCAATAAAATAAAAGTTAGTGGTTAATA
* * *
12795567 TTCAATGAAATAAAAGTTAGTAGTTAA
1 TGCAATAAAATAAAAGTTAGTGGTTAA
12795594 CTTGGAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.32
Consensus pattern (29 bp):
TGCAATAAAATAAAAGTTAGTGGTTAATA
Found at i:12797012 original size:139 final size:139
Alignment explanation
Indices: 12796757--12797022 Score: 336
Period size: 139 Copynumber: 1.9 Consensus size: 139
12796747 GAGGAAGTCT
* * * * * *
12796757 GGATAATTTGAAGATAATACGGTTCCTTCGCGTTGAGGAAGTATGGTTATCTTAGGATGACACTG
1 GGATAATTTGAAGATAACACGATTCCTTCGCGATGAGGAAGTATGATTATCTGAGGATGACACTA
* *
12796822 CTTATTCGAGTTGAGGAGAAATGGTCGGTGGATGACATTGTTCTTTCGTGATGAGGACGTCTAGC
66 CTTATTCGAGTTGAGGAGAAATGGTCGGTAGATGACATTATTCTTTCGTGATGAGGACGTCTAGC
12796887 CTTCTTTAG
131 CTTCTTTAG
* * * * * *
12796896 GGATAATTTGGAGATAACACGATTCTTTCGTGATGAGGAAGTCTGATTGTCTGAGGATGGCACTA
1 GGATAATTTGAAGATAACACGATTCCTTCGCGATGAGGAAGTATGATTATCTGAGGATGACACTA
* * ** * *
12796961 CTTATTTGTGTTGAGGAGATCTGGTCGGTATATGATATTATTCCTTT-GTGATGAGGACGTCT
66 CTTATTCGAGTTGAGGAGAAATGGTCGGTAGATGACATTATT-CTTTCGTGATGAGGACGTCT
12797023 TGTAACATCC
Statistics
Matches: 106, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
139 102 0.96
140 4 0.04
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.35
Consensus pattern (139 bp):
GGATAATTTGAAGATAACACGATTCCTTCGCGATGAGGAAGTATGATTATCTGAGGATGACACTA
CTTATTCGAGTTGAGGAGAAATGGTCGGTAGATGACATTATTCTTTCGTGATGAGGACGTCTAGC
CTTCTTTAG
Found at i:12797964 original size:59 final size:59
Alignment explanation
Indices: 12797844--12797965 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 59
12797834 CAATCCCGAG
* ** * * *
12797844 TATGACACATAAGGTCATGCCCACCATCTGTACTATGTATCCTTAAGTACAGTCTCGAA
1 TATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
** * ** *
12797903 TATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCAAA
1 TATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
12797962 TATG
1 TATG
12797966 CAGCCTGTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (59 bp):
TATGACACATAAGGTCATGCCCACCATATACACTAGGTATCCTTAAGTACAGTCCCAAA
Found at i:12805607 original size:59 final size:59
Alignment explanation
Indices: 12805508--12805629 Score: 172
Period size: 59 Copynumber: 2.1 Consensus size: 59
12805498 AAATCCTGAG
* ** *
12805508 TATGACACATAAGGTCGTGCCCACCATCTGTACTATGTATCCTTAAGTATAGTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
* * * *
12805567 TATGACACATAAGGTTGTGCCCACCATATACACTAGGTATCCTTTAGTGTATTCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
12805626 TATG
1 TATG
12805630 CAGCCTGCTG
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTATAGTCCCGAA
Found at i:12807780 original size:139 final size:138
Alignment explanation
Indices: 12807520--12807970 Score: 521
Period size: 139 Copynumber: 3.3 Consensus size: 138
12807510 GGGGTATTAC
* * * *
12807520 ACGTCTAGCCATCTTTAGGGATAATTTAGAGACAACACAGTTCATTCGCGTTGAGGAAGTCTGAT
1 ACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGGTTCATTCGTGATGAGGAAGTCTGAT
* * * * ** * * * * * *
12807585 TTTCTAAGGATGATACTACTGATTTGCATTGAGAAGATATGATCGGTGGACAACATTATTCCTTC
66 TGTCTGAGGATGAAACTGCTCCTTCGCGTTGAGTAGATCTGGTC-GTGGATAACATTATTCCTTC
12807650 GTGATGAGG
130 GTGATGAGG
*
12807659 ACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGGTTCCTTCGTGATGAGGAAGTCTGAT
1 ACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGGTTCATTCGTGATGAGGAAGTCTGAT
* * *
12807724 TGTCTGAGGATGACACTGCTCCTTCGCGTTGAGTAGATCTGGTCGTTGGATTACATTTTTCCTTC
66 TGTCTGAGGATGAAACTGCTCCTTCGCGTTGAGTAGATCTGGTCG-TGGATAACATTATTCCTTC
12807789 GTGATGAGG
130 GTGATGAGG
* ** * * * *
12807798 ACATCTAATCGTCTTTAGAGATAATTTGGAGACAACACGGTTCTTTTGTGATGAGGAAGTCTGAT
1 ACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGGTTCATTCGTGATGAGGAAGTCTGAT
* * * *
12807863 TGTCTGAGGATGAAACTGTTCCTTCGCGTTAAGGT-GATCTAGTCAGTGGATGACATTA-TCCTT
66 TGTCTGAGGATGAAACTGCTCCTTCGCGTTGA-GTAGATCTGGTC-GTGGATAACATTATTCCTT
** *
12807926 TATGATAAGG
129 CGTGATGAGG
*
12807936 ACGTCTAG-CAGTATTTAGGGATAATTTGGAGACAA
1 ACGTCTAGCCA-TCTTTAGGGATAATTTGGAGACAA
12807971 ATCTCAAGTG
Statistics
Matches: 268, Mismatches: 40, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
137 1 0.00
138 41 0.15
139 223 0.83
140 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (138 bp):
ACGTCTAGCCATCTTTAGGGATAATTTGGAGACAACACGGTTCATTCGTGATGAGGAAGTCTGAT
TGTCTGAGGATGAAACTGCTCCTTCGCGTTGAGTAGATCTGGTCGTGGATAACATTATTCCTTCG
TGATGAGG
Found at i:12808165 original size:35 final size:35
Alignment explanation
Indices: 12808125--12808379 Score: 108
Period size: 35 Copynumber: 7.4 Consensus size: 35
12808115 CAAATGTTTA
12808125 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT
** * * **
12808160 TGTTTCAAGAGAAACAATATTAA---AG---GTTT
1 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT
12808189 ATGTTTCAAGAGAAACTGT-TCAAGCT-AGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAG-TGAGAC-AAATT
** **
12808225 TGTTTCAAGAGAAACAATCTCAA---AG---GTTT
1 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT
* * *
12808254 ATGTTTCAAGGGAATCTGTCTCAAGCGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGTGAGAC-AAATT
** ** *
12808291 TGTTTTTAGAGAAAACAATCTCAAGTGAGATCAATTT
1 TGTTTCAAGAG-AAACTGTCTCAAGTGAGA-CAAATT
* **
12808328 TGTTTCAAGA-AAAATGATCTCAAACGAGACAAAACTT
1 TGTTTCAAGAGAAACTG-TCTCAAGTGAGAC-AAA-TT
* *
12808365 TATTTCGAGAGAAAC
1 TGTTTCAAGAGAAAC
12808380 AATCTCTAAG
Statistics
Matches: 157, Mismatches: 40, Indels: 43
0.65 0.17 0.18
Matches are distributed among these distances:
29 7 0.04
30 35 0.22
32 4 0.03
33 4 0.03
35 39 0.25
36 26 0.17
37 38 0.24
38 4 0.03
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT
Found at i:12808193 original size:65 final size:66
Alignment explanation
Indices: 12807993--12808391 Score: 444
Period size: 65 Copynumber: 5.9 Consensus size: 66
12807983 ATTAATTTTA
* * * * **
12807993 TTTCACGAGAAATTGTCTCAAGCAAGACAAAACTTTATTTTGAGAGAAACAATCTCAAAGGTTTA
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTTTA
*
12808058 CG
65 TG
* * * *
12808060 TTTCAAGAGAAAATGTCTCAAACGAGACAAAACTTTGTTTCAAGAGAAACAATCCCAAATGTTTA
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTTTA
12808125 TG
65 TG
* * *
12808127 TTTCAAGAGAAACTGTCTCAAGTGAGAC-AAATTTGTTTCAAGAGAAACAATATTAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
12808191 G
66 G
*
12808192 TTTCAAGAGAAACTGT-TCAAGCTAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
12808256 G
66 G
* * ** *
12808257 TTTCAAGGGAATCTGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACAATCTCAAGTGAGAT
1 TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAG-AAACAATCTCAA---AGGT
*
12808322 CAATTTTG
62 ---TTATG
* * * * *
12808330 TTTCAAGA-AAAATGATCTCAAACGAGACAAAACTTTATTTCGAGAGAAACAATCTCTAAGGT
1 TTTCAAGAGAAACTG-TCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGT
12808392 GACAAACAAT
Statistics
Matches: 284, Mismatches: 37, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
64 9 0.03
65 95 0.33
66 28 0.10
67 94 0.33
70 6 0.02
72 4 0.01
73 38 0.13
74 10 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (66 bp):
TTTCAAGAGAAACTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTAT
G
Found at i:12808259 original size:30 final size:30
Alignment explanation
Indices: 12808095--12808263 Score: 94
Period size: 30 Copynumber: 5.3 Consensus size: 30
12808085 GACAAAACTT
* *
12808095 TGTTTCAAGAGAAACAATCCCAAATGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
** **
12808125 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG---GTTTA
* *
12808160 TGTTTCAAGAGAAACAATATTAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* *
12808190 TGTTTCAAGAGAAACTGTTCAAGCTAGACAAA--ATT-
1 TGTTTCAAGAGAAA-----CAATCT---CAAAGGTTTA
12808225 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
12808255 TGTTTCAAG
1 TGTTTCAAG
12808264 GGAATCTGTC
Statistics
Matches: 103, Mismatches: 18, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
27 4 0.04
29 4 0.04
30 48 0.47
32 2 0.02
33 1 0.01
35 37 0.36
36 4 0.04
38 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:12808313 original size:37 final size:37
Alignment explanation
Indices: 12808272--12808385 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
12808262 AGGGAATCTG
12808272 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACAA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACAA
* * ** **
12808309 TCTCAAGTGAGATC-AATTTTGTTTCAAGA-AAAATGA
1 TCTCAAGCGAGA-CAAAATTTGTTTTTAGAGAAAACAA
* * * *
12808345 TCTCAAACGAGACAAAACTT-TATTTCGAGAGAAACAA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGA-AAACAA
12808382 TCTC
1 TCTC
12808386 TAAGGTGACA
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
35 5 0.09
36 20 0.35
37 31 0.54
38 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (37 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAACAA
Found at i:12811468 original size:17 final size:16
Alignment explanation
Indices: 12811416--12811469 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
12811406 TCTCTTTATT
12811416 TTTTTC-TT-CTCTTC
1 TTTTTCTTTGCTCTTC
*
12811430 TTTTCTCTTTGCTCATTG
1 TTTT-TCTTTGCTC-TTC
12811448 TTTTTCTTTGCTCTCTC
1 TTTTTCTTTGCTCT-TC
12811465 TTTTT
1 TTTTT
12811470 TTTCTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 3 0.09
17 18 0.55
18 6 0.18
ACGTcount: A:0.02, C:0.24, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTTCTTTGCTCTTC
Found at i:12811470 original size:19 final size:19
Alignment explanation
Indices: 12811406--12811471 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 19
12811396 TCTTCTTTTT
12811406 TCTCTTTATTTT-TTT-CT-
1 TCTCTTT-TTTTCTTTGCTC
12811423 TCTCTTCTTTTCTCTTTGCTC
1 TCTCTT-TTTT-TCTTTGCTC
* *
12811444 -AT-TGTTTTTCTTTGCTC
1 TCTCTTTTTTTCTTTGCTC
12811461 TCTCTTTTTTT
1 TCTCTTTTTTT
12811472 TCTATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
17 18 0.47
18 7 0.18
19 10 0.26
20 3 0.08
ACGTcount: A:0.03, C:0.23, G:0.05, T:0.70
Consensus pattern (19 bp):
TCTCTTTTTTTCTTTGCTC
Found at i:12811489 original size:20 final size:19
Alignment explanation
Indices: 12811466--12811504 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12811456 TGCTCTCTCT
*
12811466 TTTTTTTCTATTTTTCTTTG
1 TTTTTTTCT-CTTTTCTTTG
12811486 TTTTTTTCTCTTTTCTTTG
1 TTTTTTTCTCTTTTCTTTG
12811505 ATTTAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTTTTCTCTTTTCTTTG
Found at i:12816349 original size:22 final size:20
Alignment explanation
Indices: 12816297--12816369 Score: 94
Period size: 22 Copynumber: 3.6 Consensus size: 20
12816287 ATGCAAAAAC
*
12816297 GGTATCGATACCATAG-GAG
1 GGTATCGATACCATAGTAAG
*
12816316 GGTATCGGTACCATAGTAAG
1 GGTATCGATACCATAGTAAG
*
12816336 GTAGTATCGATACCATTGTAAG
1 G--GTATCGATACCATAGTAAG
12816358 GGTATCGATACC
1 GGTATCGATACC
12816370 CGGTAACATC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 15 0.32
20 14 0.30
22 18 0.38
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:12816869 original size:59 final size:59
Alignment explanation
Indices: 12816795--12817079 Score: 437
Period size: 59 Copynumber: 4.8 Consensus size: 59
12816785 ATGGAACTAA
* *
12816795 GTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
12816854 GTGTGCTAAAGTGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTTTTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
12816913 GTGTGCTGAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTAT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
12816972 GTGTGCTAAAATGTTAAGAAATTCATATTAAGTATATGAATTTCTGTATTGGGCACCTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
12817031 GTGTGC-AAACATGTTAAGAAATTTATACTAGGTGTATGAATTTCTGTAT
1 GTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
12817080 GGGAAATATA
Statistics
Matches: 207, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 3 0.01
59 204 0.99
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:12816976 original size:118 final size:118
Alignment explanation
Indices: 12816795--12817130 Score: 437
Period size: 118 Copynumber: 2.9 Consensus size: 118
12816785 ATGGAACTAA
* * *
12816795 GTGTGCTAAAATGTTAAGAAATTCATAATAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGC
* * * *
12816860 TAAAGTGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTTTTGGGCACTTT
66 TAAAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTT
*
12816913 GTGTGCTGAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGC
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGC
* *
12816978 TAAAATGTTAAGAAATTCATATTAAGTATATGAATTTCTGTATTGGGCACCTT
66 TAAAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTT
* * * * * *
12817031 GTGTGC-AAACATGTTAAGAAATTTATACTAGGTGTATGAATTTCTGTA-TGGGAAATATATGTG
1 GTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTG
** * * *
12817094 -TATAAA-CATAAGAAATTCATAATAAGGAAATGAATTT
65 CTA-AAATGTTAAGAAATTCATACTAAGTATATGAATTT
12817131 TTATATTGTT
Statistics
Matches: 194, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
116 28 0.14
117 17 0.09
118 149 0.77
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (118 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGC
TAAAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTT
Found at i:12823325 original size:20 final size:20
Alignment explanation
Indices: 12823283--12823329 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12823273 ATTCAATCAT
*
12823283 TATCGATACCAAAAGGGGAG
1 TATCGATACCAAAAGGGAAG
*
12823303 TATCGATACC-GAAGGGAAGG
1 TATCGATACCAAAAGGGAA-G
12823323 TATCGAT
1 TATCGAT
12823330 TCCATTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (20 bp):
TATCGATACCAAAAGGGAAG
Found at i:12823918 original size:59 final size:59
Alignment explanation
Indices: 12823853--12824137 Score: 455
Period size: 59 Copynumber: 4.8 Consensus size: 59
12823843 ATGGCACTAA
*
12823853 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
12823912 GTGTGCTAAAGTGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
12823971 GCGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTAT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
12824030 GTGTGCTAAAATGTTAAGAAATTCATATTAAGTATATGAATTTCTGTATTGGGCACCTT
1 GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
12824089 GTGTGC-AAACATGTTAAGAAATTTATACTAGGTGTATGAATTTCTGTAT
1 GTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
12824138 GGGAAATATA
Statistics
Matches: 210, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
58 3 0.01
59 207 0.99
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (59 bp):
GTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:12824034 original size:118 final size:118
Alignment explanation
Indices: 12823855--12824188 Score: 451
Period size: 118 Copynumber: 2.8 Consensus size: 118
12823845 GGCACTAAGT
* *
12823855 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCTA
1 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
* * *
12823920 AAGTGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGC
66 AAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTTGC
12823973 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
1 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
* * *
12824038 AAATGTTAAGAAATTCATATTAAGTATATGAATTTCTGTATTGGGCACCTTGT
66 AAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTTGC
* * * * * *
12824091 GTGC-AAACATGTTAAGAAATTTATACTAGGTGTATGAATTTCTGTA-TGGGAAATATATGTG-T
1 GTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCT
** * * *
12824153 ATAAA-CATAAGAAATTCATAATAAGGAAATGAATTT
65 A-AAATGTTAAGAAATTCATACTAAGTATATGAATTT
12824189 TTATATTGTT
Statistics
Matches: 195, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
116 28 0.14
117 18 0.09
118 149 0.76
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (118 bp):
GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
AAATGTTAAGAAATTCATACTAAGTATATGAATTTCCGTATTGGGCACCTTGC
Found at i:12824921 original size:16 final size:17
Alignment explanation
Indices: 12824884--12824926 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
12824874 CAGTTAGTAA
* *
12824884 TTAGTGGTTAGAATATG
1 TTAGTTGTTAGAATAAG
12824901 TTAGTTGTTAGAA-AAG
1 TTAGTTGTTAGAATAAG
12824917 TTAGTTGTTA
1 TTAGTTGTTA
12824927 ACAGTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (17 bp):
TTAGTTGTTAGAATAAG
Found at i:12824941 original size:16 final size:16
Alignment explanation
Indices: 12824922--12824962 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
12824912 AAAAGTTAGT
12824922 TGTTAACAGTTAGAAA
1 TGTTAACAGTTAGAAA
*
12824938 TGTTAGCAGTTAGAAA
1 TGTTAACAGTTAGAAA
*
12824954 AGTTAACAG
1 TGTTAACAG
12824963 AGTCTGGACC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (16 bp):
TGTTAACAGTTAGAAA
Found at i:12825334 original size:28 final size:29
Alignment explanation
Indices: 12825286--12825345 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
12825276 AGAGTGCAAA
*
12825286 AAAATAAAAATTAGTGGTTAA-TATGAAAT
1 AAAATAAAAATTAGTAGTTAACT-TGAAAT
*
12825315 AAAAT-AAATTTAGTAGTTAACTTGAAAT
1 AAAATAAAAATTAGTAGTTAACTTGAAAT
12825343 AAA
1 AAA
12825346 TAACATAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.32
Consensus pattern (29 bp):
AAAATAAAAATTAGTAGTTAACTTGAAAT
Found at i:12826765 original size:2 final size:2
Alignment explanation
Indices: 12826758--12826803 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
12826748 GATATAAAGA
12826758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12826800 AT AT
1 AT AT
12826804 GTTTATTATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12827741 original size:13 final size:14
Alignment explanation
Indices: 12827707--12827745 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
12827697 CCTCTCAAAT
12827707 CCAACCCTTACAAC
1 CCAACCCTTACAAC
* *
12827721 CGATCCCTTA-AAC
1 CCAACCCTTACAAC
12827734 CCAACCCTTACA
1 CCAACCCTTACA
12827746 TGTACATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.33, C:0.46, G:0.03, T:0.18
Consensus pattern (14 bp):
CCAACCCTTACAAC
Found at i:12827924 original size:13 final size:11
Alignment explanation
Indices: 12827897--12827930 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
12827887 TGGATTCGAA
12827897 TTGGTTTTTTC
1 TTGGTTTTTTC
12827908 TTGGTTTTCTCTC
1 TTGGTTTT-T-TC
12827921 TTGGTTTTTT
1 TTGGTTTTTT
12827931 TCGGTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.00, C:0.12, G:0.18, T:0.71
Consensus pattern (11 bp):
TTGGTTTTTTC
Found at i:12827936 original size:23 final size:24
Alignment explanation
Indices: 12827897--12827943 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
12827887 TGGATTCGAA
*
12827897 TTGGTTTTTTCTTGGTTTTCTCTC
1 TTGGTTTTTTCTCGGTTTTCTCTC
12827921 TTGGTTTTTT-TCGGTTTTCTCTC
1 TTGGTTTTTTCTCGGTTTTCTCTC
12827944 CCCGAATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.66
Consensus pattern (24 bp):
TTGGTTTTTTCTCGGTTTTCTCTC
Found at i:12828885 original size:137 final size:137
Alignment explanation
Indices: 12828639--12828967 Score: 480
Period size: 137 Copynumber: 2.4 Consensus size: 137
12828629 TAGGTAAATT
* * * * * * **
12828639 TGGAGATAACACAGTTCCTACGTGATGAGGAAATCTAGTTATCTAA-GAGTGATGCTTCTCCTAC
1 TGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGA-TGACGCAACTCCTAC
* * *
12828703 ACGATGAGGAGATCTGGTCAGTGGATGACATGGTTCCTACTTGATGAGGACATCTGACCATCTTT
65 ACGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACATGATGAGGACATCTGACCATATTT
12828768 AGGGATAA
130 AGGGATAA
*
12828776 TGGAGATAACACGGTTCCTACGCGATGAGGAAGTTTGGCTATCTAAGGATGACGCAACTCCTACA
1 TGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCAACTCCTACA
* * * *
12828841 TGATGAGGAGATCTGGTCGGTGGATGACACGGTTCCTACATGATGAGGACGTCTGGCCATATTTA
66 CGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACATGATGAGGACATCTGACCATATTTA
12828906 GGGATAA
131 GGGATAA
* *
12828913 TGGAGATAACACGGTTCCTACACGATGAGGAAGTCTGGCTATCTAAGGGTGACGC
1 TGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGC
12828968 GATGATGATA
Statistics
Matches: 172, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
137 170 0.99
138 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (137 bp):
TGGAGATAACACGGTTCCTACGCGATGAGGAAGTCTGGCTATCTAAGGATGACGCAACTCCTACA
CGATGAGGAGATCTGGTCAGTGGATGACACGGTTCCTACATGATGAGGACATCTGACCATATTTA
GGGATAA
Found at i:12829157 original size:68 final size:67
Alignment explanation
Indices: 12829043--12829303 Score: 332
Period size: 69 Copynumber: 3.8 Consensus size: 67
12829033 GGATAATTTA
* *
12829043 TTTCAAGAGAAACAGTCTCAAGCGAGACAAAACTT-TTTACATGGGAAACAATCTCTA-TCATTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTT-CA-GGGAAACAATCTCTAGT-ATTT
12829106 TTATG
63 TTATG
*
12829111 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TATGTTTCAAGGGAAACAATCTC-AGTGTTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT-TGTTTC-AGGGAAACAATCTCTAGTATTTT
12829174 TATG
64 TATG
* * * * *
12829178 TTTCAAGAGAAATTGTCTCAAGAGAGACAACACTTGTTTTCAGAGAAACAATCTCGAAGTTTTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTG-TTTCAGGGAAACAATCTC-TAGTATTTT
12829243 TATG
64 TATG
* *
12829247 TTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTGTTTCAGGAGAAACAATCTCTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAGG-GAAACAATCTCTA
12829304 AGGTTTATCA
Statistics
Matches: 173, Mismatches: 11, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
67 55 0.32
68 58 0.34
69 60 0.35
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (67 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAGGGAAACAATCTCTAGTATTTTTA
TG
Found at i:12829575 original size:36 final size:36
Alignment explanation
Indices: 12829528--12829673 Score: 136
Period size: 36 Copynumber: 4.1 Consensus size: 36
12829518 TTTCATGGGA
* * *
12829528 AAATTTTCTCAAACGAGACGAAATTTGTTTCGAGAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTCGAGAG
* * * *
12829564 AAATTGCCTCAAGCAAGACAAAATTTGTTTTGAAAG
1 AAATTGTCTCAAGCGAGACAAAATTTGTTTCGAGAG
* ** *
12829600 AAAACTGTCTCAAGCGAGAC--AATTT-TTTTAAGAA
1 -AAATTGTCTCAAGCGAGACAAAATTTGTTTCGAGAG
* *
12829634 AAATTATCTCAAGCGAGATAAAACTTTGTTTCGAGAG
1 AAATTGTCTCAAGCGAGACAAAA-TTTGTTTCGAGAG
12829671 AAA
1 AAA
12829674 CAATCTCAAA
Statistics
Matches: 86, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
33 16 0.19
34 6 0.07
35 7 0.08
36 32 0.37
37 25 0.29
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (36 bp):
AAATTGTCTCAAGCGAGACAAAATTTGTTTCGAGAG
Found at i:12832133 original size:17 final size:16
Alignment explanation
Indices: 12832111--12832171 Score: 79
Period size: 17 Copynumber: 3.7 Consensus size: 16
12832101 ACTTGATCCG
12832111 TTTTCTTT-CTTCTCGTT
1 TTTTCTTTGC-TCTC-TT
*
12832128 TTTTCTTTGCTCTTTGT
1 TTTTCTTTGCTCTCT-T
12832145 TTTTCTTTGCTCTCTT
1 TTTTCTTTGCTCTCTT
12832161 TTTTCTTTGCT
1 TTTTCTTTGCT
12832172 ATTTTCTTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 13 0.32
17 26 0.65
18 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.08, T:0.70
Consensus pattern (16 bp):
TTTTCTTTGCTCTCTT
Found at i:12832189 original size:13 final size:12
Alignment explanation
Indices: 12832158--12832198 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
12832148 TCTTTGCTCT
12832158 CTTTTTTCTTTG
1 CTTTTTTCTTTG
*
12832170 CTATTTTCTTTG
1 CTTTTTTCTTTG
*
12832182 TGTTTTTTCTTTG
1 -CTTTTTTCTTTG
12832195 CTTT
1 CTTT
12832199 GATTTGATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:12835107 original size:12 final size:13
Alignment explanation
Indices: 12835086--12835120 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
12835076 ATAACCATTT
12835086 TTTAAAAAAAAAA
1 TTTAAAAAAAAAA
12835099 TTTAAAAAAAAAA
1 TTTAAAAAAAAAA
12835112 TTTAAAAAA
1 TTTAAAAAA
12835121 TTTATGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TTTAAAAAAAAAA
Found at i:12835900 original size:2 final size:2
Alignment explanation
Indices: 12835893--12835926 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12835883 AAATTTAACG
12835893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12835927 CATGTATATC
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):
TA
Found at i:12837750 original size:3 final size:3
Alignment explanation
Indices: 12837744--12837801 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
12837734 AATAATAGTA
12837744 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12837792 ATT ATT ATT A
1 ATT ATT ATT A
12837802 CTATAATAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:12838059 original size:36 final size:36
Alignment explanation
Indices: 12838010--12838152 Score: 137
Period size: 37 Copynumber: 4.0 Consensus size: 36
12838000 AAGGGAAAAC
* *
12838010 TGTCTCAAACAAGACGAAATTTGTTTCGAGAGAAAT
1 TGTCTCAAGCAAGACGAAATTTGTTTTGAGAGAAAT
* * * *
12838046 TGTCTCAAGCAAGACAAAATTTGTTTTTAAAGAAAAC
1 TGTCTCAAGCAAGACGAAATTTGTTTTGAGAG-AAAT
* * * *
12838083 TATCTCAAGCAAGAC--AATTTTTTTTAAGAAAAAT
1 TGTCTCAAGCAAGACGAAATTTGTTTTGAGAGAAAT
* * *
12838117 TGTCTCTAGCGAGACGACACTTTGTTTTGAGAGAAA
1 TGTCTCAAGCAAGACGA-AATTTGTTTTGAGAGAAA
12838153 CAATCTCAAA
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
34 15 0.18
35 11 0.13
36 27 0.32
37 31 0.37
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCAAGACGAAATTTGTTTTGAGAGAAAT
Found at i:12838098 original size:37 final size:36
Alignment explanation
Indices: 12838004--12838114 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
12837994 CATTTCAAGG
* ** *
12838004 GAAAACTGTCTCAAACAAGACGAAATTTGTTTCGAGA
1 GAAAACTGTCTCAAGCAAGAC-AAATTTGTTTTTAAA
*
12838041 G-AAATTGTCTCAAGCAAGACAAAATTTGTTTTTAAA
1 GAAAACTGTCTCAAGCAAGAC-AAATTTGTTTTTAAA
*
12838077 GAAAACTATCTCAAGCAAGAC-AATTT-TTTTT-AA
1 GAAAACTGTCTCAAGCAAGACAAATTTGTTTTTAAA
12838110 GAAAA
1 GAAAA
12838115 ATTGTCTCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.11
34 5 0.08
35 5 0.08
36 30 0.46
37 18 0.28
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (36 bp):
GAAAACTGTCTCAAGCAAGACAAATTTGTTTTTAAA
Found at i:12840600 original size:9 final size:9
Alignment explanation
Indices: 12840588--12840628 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
12840578 ACTTGATTCG
12840588 TTTTCTTTC
1 TTTTCTTTC
*
12840597 TTTTCTTTT
1 TTTTCTTTC
*
12840606 TTTTCTTTG
1 TTTTCTTTC
12840615 TTTT-TTTC
1 TTTTCTTTC
12840623 TTTTCT
1 TTTTCT
12840629 CTTTGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:12840626 original size:19 final size:18
Alignment explanation
Indices: 12840588--12840638 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
12840578 ACTTGATTCG
* *
12840588 TTTTCTTTCTTTTCTTTT
1 TTTTCTTTGTTTTTTTTT
12840606 TTTTCTTTGTTTTTTTCTT
1 TTTTCTTTGTTTTTTT-TT
*
12840625 TTCTCTTTGTTTTT
1 TTTTCTTTGTTTTT
12840639 CTTCGCTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (18 bp):
TTTTCTTTGTTTTTTTTT
Found at i:12843568 original size:20 final size:20
Alignment explanation
Indices: 12843543--12843582 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12843533 GTCATAACCA
*
12843543 TTTTTTAAAAAATAATTATG
1 TTTTTTAAAAAACAATTATG
**
12843563 TTTTTTCTAAAACAATTATG
1 TTTTTTAAAAAACAATTATG
12843583 ACTTTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAAAACAATTATG
Found at i:12853937 original size:13 final size:13
Alignment explanation
Indices: 12853919--12853960 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
12853909 GTTTTTTTTC
12853919 GGTTTTCTCTCTT
1 GGTTTTCTCTCTT
*
12853932 GGTTTT-T-T-TC
1 GGTTTTCTCTCTT
12853942 GGTTTTCTCTCTT
1 GGTTTTCTCTCTT
12853955 GGTTTT
1 GGTTTT
12853961 TTTCGGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.00, C:0.17, G:0.19, T:0.64
Consensus pattern (13 bp):
GGTTTTCTCTCTT
Found at i:12853937 original size:23 final size:23
Alignment explanation
Indices: 12853911--12853975 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
12853901 TTCGAATGGT
12853911 TTTTTTTCGGTTTTCTCTCTTGG
1 TTTTTTTCGGTTTTCTCTCTTGG
12853934 TTTTTTTCGGTTTTCTCTCTTGG
1 TTTTTTTCGGTTTTCTCTCTTGG
*
12853957 TTTTTTTCGGTTCTCTCTC
1 TTTTTTTCGGTTTTCTCTC
12853976 CCCAAATGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.00, C:0.20, G:0.15, T:0.65
Consensus pattern (23 bp):
TTTTTTTCGGTTTTCTCTCTTGG
Found at i:12856025 original size:20 final size:20
Alignment explanation
Indices: 12856000--12856049 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12855990 CACTAGAGGA
12856000 TTATCTTCTT-TTTATT-TTAT
1 TTATCTT-TTATTTATTGTT-T
12856020 TTATCTTTTATTTATTGTTT
1 TTATCTTTTATTTATTGTTT
12856040 TTATCATTTT
1 TTATC-TTTT
12856050 TCATTGCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 2 0.07
20 19 0.70
21 6 0.22
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (20 bp):
TTATCTTTTATTTATTGTTT
Found at i:12858775 original size:15 final size:15
Alignment explanation
Indices: 12858751--12858793 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
12858741 TGAGTGTTTG
12858751 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
12858765 TTTGTTTTATTTTT-
1 TTTGTTTTATTTTTA
* *
12858779 TTAGTTTTAATTTTA
1 TTTGTTTTATTTTTA
12858794 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:12864810 original size:28 final size:29
Alignment explanation
Indices: 12864757--12864816 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
12864747 TGGTTATTAG
* **
12864757 ACTTTTCAATATTCTAATTAGTTCT-CAA
1 ACTTTTCAACATTCTAATTACATCTCCAA
*
12864785 ACTTTTCAACATTCTAATTTCATCTCCAA
1 ACTTTTCAACATTCTAATTACATCTCCAA
12864814 ACT
1 ACT
12864817 ATGTCCCTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (29 bp):
ACTTTTCAACATTCTAATTACATCTCCAA
Found at i:12865176 original size:12 final size:12
Alignment explanation
Indices: 12865158--12865192 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12865148 TCTTGAGGGA
12865158 CAAATTGCATCC
1 CAAATTGCATCC
*
12865170 TAAATTGCATCC
1 CAAATTGCATCC
12865182 CAAATTGCATC
1 CAAATTGCATC
12865193 ATTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.09, T:0.29
Consensus pattern (12 bp):
CAAATTGCATCC
Found at i:12869382 original size:21 final size:21
Alignment explanation
Indices: 12869358--12869397 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
12869348 GGTCAAGATC
*
12869358 TTTTGATAAAAGGACTTAATT
1 TTTTAATAAAAGGACTTAATT
* *
12869379 TTTTAATGAAATGACTTAA
1 TTTTAATAAAAGGACTTAA
12869398 CATTTTCATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTTAATAAAAGGACTTAATT
Found at i:12870084 original size:20 final size:19
Alignment explanation
Indices: 12870059--12870097 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
12870049 TTTTAGTTTA
12870059 TTAATTAAATTATTTTAAAT
1 TTAATTAAATTA-TTTAAAT
*
12870079 TTAATTATATTATTTAAAT
1 TTAATTAAATTATTTAAAT
12870098 ATTGAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAATTAAATTATTTAAAT
Found at i:12872051 original size:57 final size:57
Alignment explanation
Indices: 12871969--12872339 Score: 582
Period size: 57 Copynumber: 6.5 Consensus size: 57
12871959 AAATTCATAT
* * *
12871969 AATTTCTT-AGTTTTTGCATATAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
** *
12872025 AATTTCTTAACTTTTTGCACACAAAGTGCCCATAATGAAATTCATAAACTTATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* **
12872082 AATTTCTTAACTTTATGCACACAAAGTGCCCATACAAAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12872139 AATTTCTTAGCTTTTTGCACACAAATTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
*
12872196 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* * *
12872253 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATA
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12872310 AATTTCTTAACTTTTTGCAAACTAAGTGCC
1 AATTTCTTAACTTTTTGCACACAAAGTGCC
12872340 ATTTGGTAAT
Statistics
Matches: 292, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
56 8 0.03
57 284 0.97
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.35
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
Found at i:12872677 original size:20 final size:20
Alignment explanation
Indices: 12872648--12872704 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
12872638 TTTCAAAGTG
*
12872648 ATGCACCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
12872668 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
12872688 ATGCATCGATGCACCAA
1 ATGCATCGATGCACCAA
12872705 GGAAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:12872743 original size:65 final size:65
Alignment explanation
Indices: 12872667--12872822 Score: 187
Period size: 65 Copynumber: 2.4 Consensus size: 65
12872657 TGCACCAATC
*
12872667 CATGCATCGATGCACCAATCCATGCATCGATGCAC-CAAGGAAAATATTG-AACATCGAATGCAT
1 CATGCATCGATGCACCAATCCATGCATCGATGCACTCAAAG-AAATA-TGAAACATCGAATGCAT
12872730 TT
64 TT
* ***
12872732 CATGCATCGATGCA-C-ATACTATGCATCGATGCACTCAAAGTTTTATGAAAACATCGAATGCAT
1 CATGCATCGATGCACCAAT-CCATGCATCGATGCACTCAAAGAAATATG-AAACATCGAATGCAT
12872795 TT
64 TT
*
12872797 GATGCATCGATGCACCAA-CCATGCAT
1 CATGCATCGATGCACCAATCCATGCAT
12872823 TTGATGCAAC
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
63 4 0.05
64 18 0.23
65 54 0.69
66 1 0.01
67 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (65 bp):
CATGCATCGATGCACCAATCCATGCATCGATGCACTCAAAGAAATATGAAACATCGAATGCATTT
Found at i:12878725 original size:23 final size:23
Alignment explanation
Indices: 12878654--12878782 Score: 165
Period size: 23 Copynumber: 5.7 Consensus size: 23
12878644 ATCGATACAC
*
12878654 GTGCATGGATGCATC-CCTTTGAAT
1 GTGCATCGATGCA-CACC-TTGAAT
* * *
12878678 GTGCATCAAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
12878699 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
12878722 GTGCATCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
*
12878745 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
12878768 GTGCATCGATGCACA
1 GTGCATCGATGCACA
12878783 AGGCCATGCA
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
21 14 0.15
22 3 0.03
23 66 0.73
24 8 0.09
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:12878752 original size:46 final size:46
Alignment explanation
Indices: 12878654--12878782 Score: 183
Period size: 46 Copynumber: 2.8 Consensus size: 46
12878644 ATCGATACAC
* *
12878654 GTGCATGGATGCATC-CCTTTGAATGTGCATCAAT--ACACCATGAAG
1 GTGCATCGATGCA-CGCC-TTGAATGTGCATCGATGCACACCATGAAG
* *
12878699 GTGCATCGATGCACGCCTTGAATGTGCATCGATGCACACCTTGAAT
1 GTGCATCGATGCACGCCTTGAATGTGCATCGATGCACACCATGAAG
12878745 GTGCATCGATGCACGCCTTGAATGTGCATCGATGCACA
1 GTGCATCGATGCACGCCTTGAATGTGCATCGATGCACA
12878783 AGGCCATGCA
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
44 16 0.21
45 14 0.18
46 47 0.61
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (46 bp):
GTGCATCGATGCACGCCTTGAATGTGCATCGATGCACACCATGAAG
Found at i:12879218 original size:13 final size:13
Alignment explanation
Indices: 12879202--12879226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12879192 AAATCAAAAA
12879202 TCTAAATTTGATT
1 TCTAAATTTGATT
12879215 TCTAAATTTGAT
1 TCTAAATTTGAT
12879227 GTTTTTGATT
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
TCTAAATTTGATT
Found at i:12881562 original size:46 final size:45
Alignment explanation
Indices: 12881510--12881616 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
12881500 TGCATATACT
*
12881510 ATGCATCGATGCAGTCAGAG-T-TTTATGAAAACATCGAATGCATTTA
1 ATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTA
* *
12881556 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTA
12881601 ATGCATCGATGCACTC
1 ATGCATCGATGCACTC
12881617 TTAGTGCACC
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 34 0.61
46 19 0.34
47 3 0.05
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (45 bp):
ATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTA
Found at i:12881703 original size:21 final size:21
Alignment explanation
Indices: 12881673--12881728 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
12881663 TTTACACTTG
* **
12881673 ATGCACCGATGCACCTTGGGT
1 ATGCATCGATGCACCTTCAGT
**
12881694 ATGTGTCGATGCACCTTCAGT
1 ATGCATCGATGCACCTTCAGT
12881715 ATGCATCGATGCAC
1 ATGCATCGATGCAC
12881729 TGACGCTCCC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (21 bp):
ATGCATCGATGCACCTTCAGT
Found at i:12882776 original size:21 final size:21
Alignment explanation
Indices: 12882750--12882804 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
12882740 ACCCCCTTTT
12882750 GTATCGATACTGCTTGCATTA
1 GTATCGATACTGCTTGCATTA
12882771 GTATCGATACTGCTTGCATTA
1 GTATCGATACTGCTTGCATTA
12882792 GTATCGATACTGC
1 GTATCGATACTGC
12882805 CCAGCTGATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (21 bp):
GTATCGATACTGCTTGCATTA
Found at i:12889386 original size:57 final size:57
Alignment explanation
Indices: 12888845--12889378 Score: 899
Period size: 57 Copynumber: 9.4 Consensus size: 57
12888835 AAATTCATAT
* *
12888845 AATTTCTT-AGTTTTTGCACATAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12888901 GATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
*
12888958 AATTTCTTAACTTTATGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12889015 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12889072 AATTTCTTAACTTTTTGCACAAAAAGTGCCCATACGAAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12889129 AATTTCTTAGCTTTTTGCACACAAAGTGCTCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* **
12889186 AATTTCTTAACTTTTTGCACACAAAGTGCTCATACATAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
**
12889243 AATTTCTTAGTTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
* *
12889300 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATATGGAAATTCATAAACTAATTATG
1 AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
12889357 AATTTCTTAACTTTTTGCACAC
1 AATTTCTTAACTTTTTGCACAC
12889379 TCAGTGCCAT
Statistics
Matches: 450, Mismatches: 27, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
56 7 0.02
57 443 0.98
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (57 bp):
AATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTAATTATG
Found at i:12889754 original size:22 final size:19
Alignment explanation
Indices: 12889726--12889779 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 19
12889716 TACCCCTACC
12889726 ATGGTATCGATACTACTATACT
1 ATGGTATCGATACT-CTAT--T
*
12889748 ATGGTATTGATACTCTATT
1 ATGGTATCGATACTCTATT
*
12889767 ACGGTATCGATAC
1 ATGGTATCGATAC
12889780 CATTTTTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 12 0.41
21 4 0.14
22 13 0.45
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (19 bp):
ATGGTATCGATACTCTATT
Found at i:12901018 original size:42 final size:42
Alignment explanation
Indices: 12900940--12901019 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
12900930 TTGACATTTA
* **
12900940 GTGATACCAAATATAGATGTTATTTATAATAATTGATGATGT
1 GTGATACCAAATATAGATATTAAATATAATAATTGATGATGT
* * *
12900982 GTGATACCAAGTATAGATATTAAATATGATACTTGATG
1 GTGATACCAAATATAGATATTAAATATAATAATTGATG
12901020 TTATATGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (42 bp):
GTGATACCAAATATAGATATTAAATATAATAATTGATGATGT
Found at i:12901029 original size:42 final size:42
Alignment explanation
Indices: 12900941--12901030 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
12900931 TGACATTTAG
* ** * *
12900941 TGATACCAAATATAGATGTTATTTATAATAATTGATGATGTG
1 TGATACCAAATATAGATATTAAATATAATAATTGATGATATA
* * * *
12900983 TGATACCAAGTATAGATATTAAATATGATACTTGATGTTATA
1 TGATACCAAATATAGATATTAAATATAATAATTGATGATATA
12901025 TGATAC
1 TGATAC
12901031 AATATATCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (42 bp):
TGATACCAAATATAGATATTAAATATAATAATTGATGATATA
Found at i:12902799 original size:15 final size:15
Alignment explanation
Indices: 12902779--12902820 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12902769 TTAGTTGGGC
*
12902779 GGGCGGATGTGGGGA
1 GGGCGGATGCGGGGA
*
12902794 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGA
*
12902809 GGGTGGATGCGG
1 GGGCGGATGCGG
12902821 TGCGGATGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.67, T:0.12
Consensus pattern (15 bp):
GGGCGGATGCGGGGA
Found at i:12906130 original size:20 final size:20
Alignment explanation
Indices: 12906107--12906172 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
12906097 AATTTGTAAA
*
12906107 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
12906127 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
12906147 TCGCAATATAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
12906167 TCGCAA
1 TCGCAA
12906173 AGCGCGTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.45, C:0.23, G:0.12, T:0.20
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:12906732 original size:20 final size:20
Alignment explanation
Indices: 12906706--12906873 Score: 179
Period size: 20 Copynumber: 8.7 Consensus size: 20
12906696 CGCAACGCGA
12906706 TTTCGCGTTGCGATTTTC-T
1 TTTCGCGTTGCGATTTTCAT
*
12906725 AGTTCGCGTTGCGA---T-A-
1 -TTTCGCGTTGCGATTTTCAT
* *
12906741 TTT-GCGTTGCGGTTTTCTAG
1 TTTCGCGTTGCGATTTTC-AT
*
12906761 TTTCGCGTTGCGATTTTAAT
1 TTTCGCGTTGCGATTTTCAT
* *
12906781 TTTCACGTTGCGATTTTAAT
1 TTTCGCGTTGCGATTTTCAT
* *
12906801 TTTTGCATTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
12906821 GTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
12906841 TTTCGCGTTGTGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
12906861 TTTCGCGTTGCGA
1 TTTCGCGTTGCGA
12906874 ATTTAAGTTT
Statistics
Matches: 123, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
14 8 0.07
15 2 0.02
17 2 0.02
19 1 0.01
20 98 0.80
21 12 0.10
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:12906773 original size:35 final size:35
Alignment explanation
Indices: 12906705--12906774 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
12906695 TCGCAACGCG
12906705 ATTTCGCGTTGCGATTTTCTAGTTCGCGTTGCGAT
1 ATTTCGCGTTGCGATTTTCTAGTTCGCGTTGCGAT
*
12906740 ATTT-GCGTTGCGGTTTTCTAGTTTCGCGTTGCGAT
1 ATTTCGCGTTGCGATTTTCTAG-TTCGCGTTGCGAT
12906775 TTTAATTTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 16 0.48
35 17 0.52
ACGTcount: A:0.10, C:0.19, G:0.27, T:0.44
Consensus pattern (35 bp):
ATTTCGCGTTGCGATTTTCTAGTTCGCGTTGCGAT
Found at i:12909028 original size:21 final size:21
Alignment explanation
Indices: 12909002--12909052 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
12908992 TGCACCTATC
*
12909002 ATCGTTCAAAAGGTGCCTCCT
1 ATCGTTCAAAAGGCGCCTCCT
12909023 ATCGTTCAAAAGGCGCCTCCT
1 ATCGTTCAAAAGGCGCCTCCT
12909044 ATCGTTCAA
1 ATCGTTCAA
12909053 GAGACCCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (21 bp):
ATCGTTCAAAAGGCGCCTCCT
Found at i:12909062 original size:21 final size:21
Alignment explanation
Indices: 12909002--12909062 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
12908992 TGCACCTATC
***
12909002 ATCGTTCAAAAGGTGCCTCCT
1 ATCGTTCAAAAGACCCCTCCT
* *
12909023 ATCGTTCAAAAGGCGCCTCCT
1 ATCGTTCAAAAGACCCCTCCT
*
12909044 ATCGTTCAAGAGACCCCTC
1 ATCGTTCAAAAGACCCCTC
12909063 TCATCATTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAAAGACCCCTCCT
Found at i:12909136 original size:42 final size:42
Alignment explanation
Indices: 12909048--12909139 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
12909038 CCTCCTATCG
* *
12909048 TTCAAGAGACCCCTCTCATCATTGAAGGGGCTCCACCCACCG
1 TTCAAGAGACCCCTCTCATCATTCAAGGGGCTCCACCCACCA
* * * **
12909090 TTCAAGAGGCCCCTGTCATCATTCAAGAGG-TCTCGTCCACCA
1 TTCAAGAGACCCCTCTCATCATTCAAGGGGCTC-CACCCACCA
12909132 TTCAAGAG
1 TTCAAGAG
12909140 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (42 bp):
TTCAAGAGACCCCTCTCATCATTCAAGGGGCTCCACCCACCA
Found at i:12910729 original size:20 final size:21
Alignment explanation
Indices: 12910704--12910750 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
12910694 TCGCGTTGCA
*
12910704 ATTTTCGGT-TTGCGATTTTG
1 ATTTTCGGTATTGCGAATTTG
12910724 ATTTTC-GTATTGCGAATTTG
1 ATTTTCGGTATTGCGAATTTG
*
12910744 ACTTTCG
1 ATTTTCG
12910751 TGTTGTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (21 bp):
ATTTTCGGTATTGCGAATTTG
Found at i:12910751 original size:20 final size:20
Alignment explanation
Indices: 12910713--12910770 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
12910703 AATTTTCGGT
* *
12910713 TTGCGATTTTGATTTTCGTA
1 TTGCGAATTTGACTTTCGTA
*
12910733 TTGCGAATTTGACTTTCGTG
1 TTGCGAATTTGACTTTCGTA
* *
12910753 TTGTGAATTTAACTTTCG
1 TTGCGAATTTGACTTTCG
12910771 CAACAATCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.12, G:0.21, T:0.50
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGTA
Found at i:12911035 original size:18 final size:18
Alignment explanation
Indices: 12911012--12911047 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12911002 AAACCGGTTG
*
12911012 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
12911030 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
12911048 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:12913347 original size:24 final size:24
Alignment explanation
Indices: 12913320--12913365 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12913310 AAAATCCGAT
12913320 TATTGACCAAGATCAAAGTTCGGG
1 TATTGACCAAGATCAAAGTTCGGG
*
12913344 TATTGACCAAGATCAAATTTCG
1 TATTGACCAAGATCAAAGTTCG
12913366 AATACTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTTCGGG
Found at i:12914308 original size:19 final size:20
Alignment explanation
Indices: 12914284--12914371 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
12914274 AACTAAAACC
12914284 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTAAAATTCG
*
12914303 TGTTGCG-AATTCAAAAATCG
1 TGTTGCGAAATT-AAAATTCG
* *
12914323 AGTTGCG-AATTCGAAATTC-
1 TGTTGCGAAATT-AAAATTCG
* *
12914342 AGTTGCGAATTTAAAATTCAG
1 TGTTGCGAAATTAAAATTC-G
12914363 TGTTGCGAA
1 TGTTGCGAA
12914372 TTTGACTTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
18 4 0.07
19 20 0.35
20 25 0.44
21 8 0.14
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:12914329 original size:20 final size:20
Alignment explanation
Indices: 12914296--12914373 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
12914286 TTGCGAAATT
*
12914296 AAATTCGTGTTGCGAATTCA
1 AAATTCGAGTTGCGAATTCA
* *
12914316 AAAATCGAGTTGCGAATTCG
1 AAATTCGAGTTGCGAATTCA
*
12914336 AAATTC-AGTTGCGAATTTA
1 AAATTCGAGTTGCGAATTCA
*
12914355 AAATTCAGTGTTGCGAATT
1 AAATTC-GAGTTGCGAATT
12914374 TGACTTCTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
19 17 0.35
20 22 0.45
21 10 0.20
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
AAATTCGAGTTGCGAATTCA
Found at i:12914330 original size:39 final size:40
Alignment explanation
Indices: 12914285--12914393 Score: 107
Period size: 39 Copynumber: 2.7 Consensus size: 40
12914275 ACTAAAACCT
12914285 GTTGCGAAATTAAATTCGTGTTGCGAATTCAAAAATC-GA
1 GTTGCGAAATTAAATTCGTGTTGCGAATTCAAAAATCAGA
* * * *
12914324 GTTGCG-AATTCGAAATTC-AGTTGCGAATTTAAAATTCAGT
1 GTTGCGAAATT--AAATTCGTGTTGCGAATTCAAAAATCAGA
* * *
12914364 GTTGCGAATTTGACTTCTGTGTTGCGAATT
1 GTTGCGAAATTAAATTC-GTGTTGCGAATT
12914394 TGACTTTTGT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
38 4 0.07
39 26 0.46
40 13 0.23
41 13 0.23
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (40 bp):
GTTGCGAAATTAAATTCGTGTTGCGAATTCAAAAATCAGA
Found at i:12914387 original size:20 final size:20
Alignment explanation
Indices: 12914343--12914410 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
12914333 TCGAAATTCA
* * *
12914343 GTTGCGAATTTAAAATTCAGT
1 GTTGCGAATTT-GACTTCTGT
12914364 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTCTGT
*
12914384 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTCTGT
12914404 GTTGCGA
1 GTTGCGA
12914411 TTTACATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 32 0.74
21 11 0.26
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTCTGT
Found at i:12914850 original size:80 final size:75
Alignment explanation
Indices: 12914766--12914919 Score: 191
Period size: 76 Copynumber: 2.0 Consensus size: 75
12914756 GTTACCGACC
* * * * *
12914766 GCCAGTATTCTTTTTTTTCTTTTTTTTTTTTTTCTATATCATATTTTTAATTTCTTTTGTTTTTT
1 GCCAGTATTCTTTATTTTC----TTTTTCTTTTCTATATCATATCTTTAATTTATTTTATTTTTT
*
12914831 GATTTTTAATAAGTT
62 -ATTTTCAATAAGTT
* *
12914846 GCCAGTATTCTTTATTTTCTTTTTCTTTTCTATATCGTATCTTTATTTTATTTTATTTTTTATTT
1 GCCAGTATTCTTTATTTTCTTTTTCTTTTCTATATCATATCTTTAATTTATTTTATTTTTTATTT
12914911 TCAATAAGT
66 TCAATAAGT
12914920 CTGTCTGTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
75 12 0.18
76 36 0.55
80 18 0.27
ACGTcount: A:0.18, C:0.10, G:0.06, T:0.66
Consensus pattern (75 bp):
GCCAGTATTCTTTATTTTCTTTTTCTTTTCTATATCATATCTTTAATTTATTTTATTTTTTATTT
TCAATAAGTT
Found at i:12915576 original size:17 final size:18
Alignment explanation
Indices: 12915542--12915587 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12915532 AATTTTATTT
*
12915542 AAATAATTCAAAGCCATA
1 AAATAATTTAAAGCCATA
*
12915560 AAATAATTTAAA-TCATA
1 AAATAATTTAAAGCCATA
12915577 AAATAAATTTA
1 AAAT-AATTTA
12915588 TAATTCCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (18 bp):
AAATAATTTAAAGCCATA
Found at i:12920561 original size:29 final size:29
Alignment explanation
Indices: 12920523--12920581 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
12920513 CCTAAATTAA
*
12920523 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGAAGTCATTGCTTACATCAATTTAGT
12920552 TTTGAAGTCATTGCTTACATCAATTTAGT
1 TTTGAAGTCATTGCTTACATCAATTTAGT
12920581 T
1 T
12920582 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (29 bp):
TTTGAAGTCATTGCTTACATCAATTTAGT
Found at i:12925239 original size:29 final size:29
Alignment explanation
Indices: 12925205--12925263 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12925195 CCTAAATTAA
12925205 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12925234 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
12925263 T
1 T
12925264 AGGTGAAAAT
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:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:12926324 original size:187 final size:186
Alignment explanation
Indices: 12925996--12926371 Score: 671
Period size: 187 Copynumber: 2.0 Consensus size: 186
12925986 TTCCAACAAG
* *
12925996 TTAATTAATCTATAGAGCGAAATTCTAGATCTGACGGTCATATCAATTTAGTTTGTTAACTTACG
1 TTAATTAATCTATAGAGCGAAATTCTAGATCTAACGATCATATCAATTTAGTTTGTTAACTTACG
*
12926061 AATAATTATAATGACATATGTCTAACACCTTCATATAAAGCCATTATAAATTTTTCGCAACCATG
66 AATAACTATAATGACATATGTCTAACACCTTCATATAAAGCCATTATAAATTTTTCGCAACCATG
12926126 ATTAAGGAGAGAATCCATTTTTCCTCATCATTGTCTCCTATATCCCCATTACATCT
131 ATTAAGGAGAGAATCCATTTTTCCTCATCATTGTCTCCTATATCCCCATTACATCT
12926182 TTAATTAATCTATCAGAGCGAAATTCTAGATCTAACGATCATATCAATTTAGTTTGTTAACTTAC
1 TTAATTAATCTAT-AGAGCGAAATTCTAGATCTAACGATCATATCAATTTAGTTTGTTAACTTAC
* * * *
12926247 GAGTAACTATAATGACATATGTCTGATACCTTCATATAAAGCCATTATAAATTTTTCTCAACCAT
65 GAATAACTATAATGACATATGTCTAACACCTTCATATAAAGCCATTATAAATTTTTCGCAACCAT
*
12926312 GATTAAGGAGAGAATCCATTTTTCCTCATCATTGTCTCCTATATCCCCATTATATCT
130 GATTAAGGAGAGAATCCATTTTTCCTCATCATTGTCTCCTATATCCCCATTACATCT
12926369 TTA
1 TTA
12926372 TCCCTATTGC
Statistics
Matches: 181, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
186 13 0.07
187 168 0.93
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (186 bp):
TTAATTAATCTATAGAGCGAAATTCTAGATCTAACGATCATATCAATTTAGTTTGTTAACTTACG
AATAACTATAATGACATATGTCTAACACCTTCATATAAAGCCATTATAAATTTTTCGCAACCATG
ATTAAGGAGAGAATCCATTTTTCCTCATCATTGTCTCCTATATCCCCATTACATCT
Found at i:12932105 original size:30 final size:30
Alignment explanation
Indices: 12932049--12932117 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
12932039 GATTTATTTA
**
12932049 GTGACCAAATTATAAATTTGGTAAAGTTTG
1 GTGACCAAATTATAAATTTGAAAAAGTTTG
*
12932079 GTGATCAAATTATAAACTTT-AAAAAGTTTAG
1 GTGACCAAATTATAAA-TTTGAAAAAGTTT-G
12932110 G-GACCAAA
1 GTGACCAAA
12932118 ATGTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (30 bp):
GTGACCAAATTATAAATTTGAAAAAGTTTG
Found at i:12933321 original size:24 final size:24
Alignment explanation
Indices: 12933294--12933339 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12933284 GCATGACATG
**
12933294 GTACATAGATGTTTTATACATCGT
1 GTACATAGAAATTTTATACATCGT
12933318 GTACATAGAAATTTTATACATC
1 GTACATAGAAATTTTATACATC
12933340 ATCTGAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (24 bp):
GTACATAGAAATTTTATACATCGT
Found at i:12934190 original size:22 final size:22
Alignment explanation
Indices: 12934137--12934190 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
12934127 GGCACAATGT
12934137 TCACTGTTCACAGTACAGTTCA
1 TCACTGTTCACAGTACAGTTCA
* * *
12934159 TCAATGTTCACGGTACTGTTCA
1 TCACTGTTCACAGTACAGTTCA
*
12934181 TCACTATTCA
1 TCACTGTTCA
12934191 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (22 bp):
TCACTGTTCACAGTACAGTTCA
Found at i:12940283 original size:24 final size:24
Alignment explanation
Indices: 12940256--12940301 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
12940246 GCATGACATG
12940256 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
12940280 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
12940302 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:12941573 original size:2 final size:2
Alignment explanation
Indices: 12941566--12941607 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
12941556 GGTGGGGACA
* *
12941566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12941608 TAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12944397 original size:36 final size:35
Alignment explanation
Indices: 12944310--12944414 Score: 167
Period size: 35 Copynumber: 3.0 Consensus size: 35
12944300 TGGCAACCAA
* *
12944310 CTTTGAAAATGGTTTCCAAAGTTTAGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
12944345 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
12944380 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAA-GTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
12944415 GATAGATGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 42 0.64
36 24 0.36
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:12945648 original size:15 final size:15
Alignment explanation
Indices: 12945624--12945655 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12945614 AGGCAGATCG
*
12945624 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
12945639 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
12945654 AA
1 AA
12945656 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:12948965 original size:35 final size:35
Alignment explanation
Indices: 12948926--12949004 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
12948916 TGGCAACCAA
12948926 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
12948961 CTTTGAAAATGGTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
12948996 -GTTGAAAAT
1 CTTTGAAAAT
12949005 AGGAATTGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
34 8 0.19
35 34 0.81
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.44
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:12954444 original size:13 final size:12
Alignment explanation
Indices: 12954415--12954448 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12954405 AATGAGATTT
12954415 TAATT-TTTTAA
1 TAATTATTTTAA
12954426 TAATTATTTTAA
1 TAATTATTTTAA
12954438 TATATTATTTT
1 TA-ATTATTTT
12954449 GAGTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.24
12 8 0.38
13 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TAATTATTTTAA
Found at i:12955540 original size:13 final size:14
Alignment explanation
Indices: 12955517--12955546 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
12955507 TTATTCTTAA
12955517 TATTTATATATTTT
1 TATTTATATATTTT
12955531 TATTTA-ATATTTT
1 TATTTATATATTTT
12955544 TAT
1 TAT
12955547 CCAATAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:12959783 original size:22 final size:22
Alignment explanation
Indices: 12959739--12959784 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12959729 TTTTAACATG
* * *
12959739 TTGAAAGTAAGTCTTCATTTTT
1 TTGAAAGTAAGTATGCATATTT
12959761 TTGAAAGTAAGTATGCATATTT
1 TTGAAAGTAAGTATGCATATTT
12959783 TT
1 TT
12959785 AAACGTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (22 bp):
TTGAAAGTAAGTATGCATATTT
Found at i:12961682 original size:23 final size:24
Alignment explanation
Indices: 12961645--12961704 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
12961635 CAGCTCGTAT
12961645 AAATGCACC-TAAGTGCCACATAG
1 AAATGCACCGTAAGTGCCACATAG
* * *
12961668 AATTGCACCGT-AGTGCCGCGTAG
1 AAATGCACCGTAAGTGCCACATAG
12961691 AAATGCACCG-AAGT
1 AAATGCACCGTAAGT
12961705 ACCATATAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.18
Consensus pattern (24 bp):
AAATGCACCGTAAGTGCCACATAG
Found at i:12962322 original size:22 final size:22
Alignment explanation
Indices: 12962286--12962356 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 22
12962276 TTTTATTTCA
*
12962286 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-ATATTATTATTAT
12962309 TTTGTTTTAATATTATTATTAT
1 TTTGTTTTAATATTATTATTAT
* *
12962331 TATTATTATATTATATTATTATTAT
1 T-TTGTT-T-TAATATTATTATTAT
12962356 T
1 T
12962357 AAATAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.31
23 13 0.31
24 1 0.02
25 15 0.36
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (22 bp):
TTTGTTTTAATATTATTATTAT
Done.