Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 149 of 199
Found at i:44001300 original size:197 final size:197
Alignment explanation
Indices: 44001064--44001424 Score: 508
Period size: 197 Copynumber: 1.8 Consensus size: 197
44001054 CATGTCTGGG
* * * *
44001064 ACATGGCGTTGGCACCAAGATGAGAGGTCCCACGTAAGACCATGTCTTGAACATGGCGTTGGCAC
1 ACATGGCGTTGACACCAAGATGAAAGGACCCACGTAAGACCATGTCTGGAACATGGCGTTGGCAC
* * * **
44001129 CGAGATAAGAGGTCCCATATAAGACCATGTCTGGGACATGGTC-TTGGCACCAAGATGAGAGGTC
66 CGAGATAAGAGGTCCCACATAAGACCATGTCTGGGACAT-GACATGGGCACCAAGATGAGAACTC
** *
44001193 CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCTATGGACCATGTTT
130 CCATGTAAGACCATACCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTATGGACCATGTTT
44001258 GAT
195 GAT
* * *
44001261 ACATGGCGTTGACACCGAGATGAAAGGACCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 ACATGGCGTTGACACCAAGATGAAAGGACCCACGTAAGACCATGTCTGGAACATGGCGTTGGCAC
* * * * * *
44001326 CGAGATTAGAGGTCCCCCGTAAGACCATGTTTGGGACATGACATGGGCACCGATATGAGAACTCC
66 CGAGATAAGAGGTCCCACATAAGACCATGTCTGGGACATGACATGGGCACCAAGATGAGAACTCC
*
44001391 CATGTAAGACCATACCTGGGATATGGCATTGGCA
131 CATGTAAGACCATACCTGGGACATGGCATTGGCA
44001425 GTACAGGACA
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
196 2 0.01
197 139 0.99
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (197 bp):
ACATGGCGTTGACACCAAGATGAAAGGACCCACGTAAGACCATGTCTGGAACATGGCGTTGGCAC
CGAGATAAGAGGTCCCACATAAGACCATGTCTGGGACATGACATGGGCACCAAGATGAGAACTCC
CATGTAAGACCATACCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTATGGACCATGTTTG
AT
Found at i:44007283 original size:20 final size:20
Alignment explanation
Indices: 44007258--44007316 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
44007248 TTGTACAAGA
44007258 TTTGCACTTTGGTGCCCCTG
1 TTTGCACTTTGGTGCCCCTG
**
44007278 TTTGCACATTT-GTGAACCTG
1 TTTGCAC-TTTGGTGCCCCTG
*
44007298 TCTGCACTTTGGTGCCCCT
1 TTTGCACTTTGGTGCCCCT
44007317 ATTATTCATC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.10, C:0.29, G:0.22, T:0.39
Consensus pattern (20 bp):
TTTGCACTTTGGTGCCCCTG
Found at i:44029567 original size:56 final size:50
Alignment explanation
Indices: 44029501--44029742 Score: 184
Period size: 50 Copynumber: 4.7 Consensus size: 50
44029491 AGGAATGAGA
* **
44029501 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGA-G--ATGAGAGG
* *
44029557 TCCCACGTAAGACCATTTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * **
44029607 TCCCCCGTAAGACCATGTCTGGGACATGCCA-TGGACACCGATATTAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATGAGAGG
** * * * * * **
44029657 TCCCATATAAGACCATATCTGGGAAATGGCATTGGCA--GTACAGGAAACA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* * *
44029706 TTCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
44029743 TGTTATTATC
Statistics
Matches: 153, Mismatches: 30, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 39 0.25
50 73 0.48
51 3 0.02
52 1 0.01
53 3 0.02
56 33 0.22
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:44029970 original size:20 final size:20
Alignment explanation
Indices: 44029945--44029993 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44029935 TGAGTTATTA
44029945 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
44029965 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
44029985 AAG-AAGCAA
1 AAGTAAGCAA
44029994 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:44030121 original size:14 final size:14
Alignment explanation
Indices: 44030102--44030129 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44030092 CTTTATTTTC
44030102 CTTCTTTTCTTATA
1 CTTCTTTTCTTATA
44030116 CTTCTTTTCTTATA
1 CTTCTTTTCTTATA
44030130 GTATGGCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
CTTCTTTTCTTATA
Found at i:44034721 original size:47 final size:47
Alignment explanation
Indices: 44034658--44035154 Score: 718
Period size: 47 Copynumber: 10.6 Consensus size: 47
44034648 CCCTTCGGGA
* * *
44034658 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
44034705 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
44034752 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
44034799 CTTCTCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
44034846 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* * *
44034893 CTTATCTCACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
44034940 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
44034989 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
44035036 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * *
44035083 C-CA-CATATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
44035128 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
44035155 TATTCAAATA
Statistics
Matches: 422, Mismatches: 22, Indels: 12
0.93 0.05 0.03
Matches are distributed among these distances:
45 41 0.10
46 3 0.01
47 334 0.79
49 43 0.10
50 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:44036676 original size:56 final size:56
Alignment explanation
Indices: 44036609--44036728 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
44036599 TATTAGTTTA
44036609 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
44036665 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
44036721 TTGCCCAT
1 TTGCCCAT
44036729 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:44041524 original size:20 final size:21
Alignment explanation
Indices: 44041501--44041541 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44041491 ATCACTTTAA
*
44041501 TATCAA-ATTAATATAATATT
1 TATCAAGATAAATATAATATT
*
44041521 TATCAAGATAAATATTATATT
1 TATCAAGATAAATATAATATT
44041542 GAATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
TATCAAGATAAATATAATATT
Found at i:44051580 original size:36 final size:36
Alignment explanation
Indices: 44051524--44051644 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
44051514 TACTCTCTAT
*
44051524 TTTAGTGTG-TTTCGATTGGATTAGCTCTTCCGAGCCA
1 TTTAGTGTGTTTTCGA-TGGATTAGCTCTTACGAG-CA
* * *
44051561 -TTAGTGTGTTTTTGATGGATTAGCTCGTATGAGCA
1 TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
* * * *
44051596 TTTGGTGTGTTTTGGATGGACTAGCTCTTATGAGCA
1 TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
* *
44051632 TCTGGTGTGTTTT
1 TTTAGTGTGTTTT
44051645 GGTGGGATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 2 0.03
36 66 0.90
37 5 0.07
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (36 bp):
TTTAGTGTGTTTTCGATGGATTAGCTCTTACGAGCA
Found at i:44051645 original size:36 final size:36
Alignment explanation
Indices: 44051564--44051646 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
44051554 CGAGCCATTA
* * *
44051564 GTGTGTTTTTGATGGATTAGCTCGTATGAGCATTTG
1 GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
*
44051600 GTGTGTTTTGGATGGACTAGCTCTTATGAGCATCTG
1 GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
44051636 GTGTGTTTTGG
1 GTGTGTTTTGG
44051647 TGGGATTACC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.14, C:0.10, G:0.33, T:0.43
Consensus pattern (36 bp):
GTGTGTTTTGGATGGACTAGCTCGTATGAGCATCTG
Found at i:44056805 original size:22 final size:21
Alignment explanation
Indices: 44056780--44056837 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
44056770 TTAATCCAGC
*
44056780 CCAATACATAATTTTATATTTT
1 CCAATAAATAATTTTA-ATTTT
*
44056802 CCAA-AAATAATATTAATTTT
1 CCAATAAATAATTTTAATTTT
*
44056822 CTAATTAAATAATTTT
1 CCAA-TAAATAATTTT
44056838 CTCATCTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.27
21 9 0.30
22 13 0.43
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (21 bp):
CCAATAAATAATTTTAATTTT
Found at i:44057058 original size:6 final size:6
Alignment explanation
Indices: 44057043--44057097 Score: 83
Period size: 6 Copynumber: 9.0 Consensus size: 6
44057033 CAAAAATGAA
* *
44057043 TCATTT CTCATTC TCATTT TCATTT TCATTT TCATTT TCAATT TCATTT
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT
44057092 TCATTT
1 TCATTT
44057098 CAAGAAAACC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
6 39 0.89
7 5 0.11
ACGTcount: A:0.18, C:0.20, G:0.00, T:0.62
Consensus pattern (6 bp):
TCATTT
Found at i:44057725 original size:6 final size:6
Alignment explanation
Indices: 44057708--44057746 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
44057698 ACACACCATC
44057708 TTTCAGT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TT
1 TTTCA-T TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TT
44057747 CAAGAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (6 bp):
TTTCAT
Found at i:44066703 original size:56 final size:56
Alignment explanation
Indices: 44066643--44066754 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
44066633 ACACATACTG
*
44066643 TCACCACCATATAGTCCTAATTATTATGTTCCTCACTAAGTAACTAATCAGTCCTA
1 TCACCACCATACAGTCCTAATTATTATGTTCCTCACTAAGTAACTAATCAGTCCTA
* * *
44066699 TCACCACCATACAGTCCTAATTATTCTGTTCCTCACTATGTAACTAATCGGTCCTA
1 TCACCACCATACAGTCCTAATTATTATGTTCCTCACTAAGTAACTAATCAGTCCTA
44066755 ATCTAACCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (56 bp):
TCACCACCATACAGTCCTAATTATTATGTTCCTCACTAAGTAACTAATCAGTCCTA
Found at i:44069714 original size:20 final size:20
Alignment explanation
Indices: 44069677--44069725 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
44069667 CATATCATGC
*
44069677 ATTCATTTGTGATCTCATAT
1 ATTCATTTTTGATCTCATAT
* *
44069697 ATTCATTTTTTATTTCATAT
1 ATTCATTTTTGATCTCATAT
44069717 ATTCATTTT
1 ATTCATTTT
44069726 CAACCAGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTCATTTTTGATCTCATAT
Found at i:44069799 original size:24 final size:24
Alignment explanation
Indices: 44069771--44069817 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
44069761 ATGCAGGATA
* *
44069771 ATAATGCTCATATGAGCTATGAAT
1 ATAATGCTCACACGAGCTATGAAT
44069795 ATAATGCTCACACGAGCTATGAA
1 ATAATGCTCACACGAGCTATGAA
44069818 ATGGGCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (24 bp):
ATAATGCTCACACGAGCTATGAAT
Found at i:44071475 original size:14 final size:13
Alignment explanation
Indices: 44071451--44071484 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
44071441 AATCACTATT
*
44071451 CATATATAGCTCA
1 CATATAGAGCTCA
44071464 CAATATAGAGCTCA
1 C-ATATAGAGCTCA
44071478 CATATAG
1 CATATAG
44071485 TTTAACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (13 bp):
CATATAGAGCTCA
Found at i:44073016 original size:27 final size:27
Alignment explanation
Indices: 44072986--44073163 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
44072976 ATATTGAGCC
* *
44072986 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
44073013 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
44073040 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
44073068 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
44073095 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
44073122 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
44073149 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44073164 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:44073098 original size:55 final size:54
Alignment explanation
Indices: 44072986--44073163 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
44072976 ATATTGAGCC
* * * * *
44072986 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
44073040 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
44073095 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
44073149 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44073164 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:44081022 original size:27 final size:27
Alignment explanation
Indices: 44080992--44081169 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
44080982 ATATTGAGCC
* *
44080992 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
44081019 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
44081046 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
44081074 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
44081101 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
44081128 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
44081155 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44081170 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:44081104 original size:55 final size:54
Alignment explanation
Indices: 44080992--44081169 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
44080982 ATATTGAGCC
* * * * *
44080992 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
44081046 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
44081101 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
44081155 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44081170 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:44083108 original size:18 final size:18
Alignment explanation
Indices: 44083087--44083124 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
44083077 CATTCAAAAG
44083087 AATATGAAATTTCAATAA
1 AATATGAAATTTCAATAA
*
44083105 AATATGAAATTTTAATAA
1 AATATGAAATTTCAATAA
44083123 AA
1 AA
44083125 AATAGTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (18 bp):
AATATGAAATTTCAATAA
Found at i:44083128 original size:20 final size:20
Alignment explanation
Indices: 44083082--44083128 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
44083072 TTTGTCATTC
44083082 AAAAGAATATGAAATTTCAAT
1 AAAA-AATATGAAATTTCAAT
*
44083103 --AAAATATGAAATTTTAAT
1 AAAAAATATGAAATTTCAAT
44083121 AAAAAATA
1 AAAAAATA
44083129 GTTTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 15 0.65
19 2 0.09
20 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAAAATATGAAATTTCAAT
Found at i:44083395 original size:26 final size:27
Alignment explanation
Indices: 44083366--44083435 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
44083356 ATGATTGCAA
*
44083366 CTCGCCAAGCCCACTGGC-GAC-CTCAG
1 CTCGCCAAGCCCACTAGCAGACACT-AG
* *
44083392 CTCG-CTAGACCCACTAGCATACACTAG
1 CTCGCCAAG-CCCACTAGCAGACACTAG
44083419 CTCGCCAAGCCC-CTAGC
1 CTCGCCAAGCCCACTAGC
44083436 TCCTAGGCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
25 3 0.08
26 17 0.47
27 11 0.31
28 5 0.14
ACGTcount: A:0.23, C:0.44, G:0.19, T:0.14
Consensus pattern (27 bp):
CTCGCCAAGCCCACTAGCAGACACTAG
Found at i:44097737 original size:25 final size:25
Alignment explanation
Indices: 44097705--44097759 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
44097695 TAATTTAATC
*
44097705 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
44097729 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
44097754 ATATAT
1 ATATAT
44097760 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:44102351 original size:19 final size:19
Alignment explanation
Indices: 44102309--44102368 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
44102299 CATGGGCTTA
*
44102309 GGCCGAAATGGGCCACGT-TG
1 GGCCGAAATGGG-C-TGTGTG
44102329 GGCCGAAATGGGCTGTGTG
1 GGCCGAAATGGGCTGTGTG
*
44102348 GGCC-TAATGGGCT-TGTG
1 GGCCGAAATGGGCTGTGTG
44102365 GGCC
1 GGCC
44102369 TACACGGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
17 8 0.22
18 10 0.27
19 7 0.19
20 12 0.32
ACGTcount: A:0.15, C:0.22, G:0.43, T:0.20
Consensus pattern (19 bp):
GGCCGAAATGGGCTGTGTG
Found at i:44102366 original size:17 final size:18
Alignment explanation
Indices: 44102335--44102370 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
44102325 GTTGGGCCGA
44102335 AATGGGCTGTGTGGGCCT
1 AATGGGCTGTGTGGGCCT
44102353 AATGGGCT-TGTGGGCCT
1 AATGGGCTGTGTGGGCCT
44102370 A
1 A
44102371 CACGGATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.14, C:0.17, G:0.42, T:0.28
Consensus pattern (18 bp):
AATGGGCTGTGTGGGCCT
Found at i:44102672 original size:28 final size:27
Alignment explanation
Indices: 44102601--44102701 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
44102591 CAAAATAGGT
* *
44102601 AAAATGACCAAAATACCCCTGAAGGAT-
1 AAAATGACTAAAATACCCCT-AAAGATG
* ***
44102628 AAAATAACTATTTTACCCCTAACAGATG
1 AAAATGACTAAAATACCCCTAA-AGATG
* *
44102656 AAAATGACTAAAATACCCCTATAG-GG
1 AAAATGACTAAAATACCCCTAAAGATG
*
44102682 TAAAATGACTGAAATACCCC
1 -AAAATGACTAAAATACCCC
44102702 CATAAGGTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
26 3 0.05
27 38 0.66
28 17 0.29
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.21
Consensus pattern (27 bp):
AAAATGACTAAAATACCCCTAAAGATG
Found at i:44102696 original size:27 final size:27
Alignment explanation
Indices: 44102656--44102880 Score: 276
Period size: 27 Copynumber: 8.3 Consensus size: 27
44102646 CTAACAGATG
* *
44102656 AAAATGACTAAAATACCCCTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
44102683 AAAATGACTGAAATACCCCCATAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
* * * *
44102710 AACATGACCGAAATACCCCCGTAAGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
44102737 AAAATGA-TCGAAATACCCCTATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
*
44102764 AAAATGACCGAAATACCCCCATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
*
44102791 AAAATGA-TCGAAATACCCCTATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
44102818 AAAATGA-TCGAAATACCCCCATAGGGT
1 AAAATGACT-GAAATACCCCCATAGGGT
* * **
44102845 AAAATGACCGAAATAACCTTATAGGGT
1 AAAATGACTGAAATACCCCCATAGGGT
44102872 AAAATGACT
1 AAAATGACT
44102881 TTTATACCCC
Statistics
Matches: 173, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
27 173 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
AAAATGACTGAAATACCCCCATAGGGT
Found at i:44102738 original size:54 final size:54
Alignment explanation
Indices: 44102656--44102879 Score: 324
Period size: 54 Copynumber: 4.1 Consensus size: 54
44102646 CTAACAGATG
** * * *
44102656 AAAATGACTAAAATACCCCTATAGGGTAAAATGA-CTGAAATACCCCCATAAGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCTATAGGGT
* * *
44102710 AACATGACCGAAATACCCCCGTAAGGTAAAATGATCGAAATACCCCTATAGGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGGT
44102764 AAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGGT
* * * *
44102818 AAAATGATCGAAATACCCCCATAGGGTAAAATGACCGAAATAACCTTATAGGGT
1 AAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGGT
44102872 AAAATGAC
1 AAAATGAC
44102880 TTTTATACCC
Statistics
Matches: 153, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
54 152 0.99
55 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.19
Consensus pattern (54 bp):
AAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTATAGGGT
Found at i:44102760 original size:81 final size:81
Alignment explanation
Indices: 44102666--44102879 Score: 320
Period size: 81 Copynumber: 2.6 Consensus size: 81
44102656 AAAATGACTA
* * *
44102666 AAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATAAGGTAACATGACCGAAATACCCCCG
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCCA
44102731 TAAGGTAAAATGATCG
66 TAAGGTAAAATGATCG
* * *
44102747 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCCA
*
44102812 TAGGGTAAAATGATCG
66 TAAGGTAAAATGATCG
* * ** *
44102828 AAATACCCCCATAGGGTAAAATGACCGAAATAACCTTATAGGGTAAAATGAC
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGAC
44102880 TTTTATACCC
Statistics
Matches: 121, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 121 1.00
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.19
Consensus pattern (81 bp):
AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGACCGAAATACCCCCA
TAAGGTAAAATGATCG
Found at i:44102902 original size:81 final size:83
Alignment explanation
Indices: 44102666--44102905 Score: 280
Period size: 81 Copynumber: 3.0 Consensus size: 83
44102656 AAAATGACTA
* * * *
44102666 AAATACCCCTATAGGGTAAAATGACTGAAATACCCCCATAAGGTAACATGAC-CGAAATACCCCC
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTAGAAATA-CCCC
* *
44102730 GTA--AGGTAAAATGATCG
65 ATAGGAGATAAAATGATCG
*
44102747 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGA-TCGAAATACCCCT
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTAGAAATACCCC-
44102811 ATAGG-G-TAAAATGATCG
65 ATAGGAGATAAAATGATCG
* * ** ***
44102828 AAATACCCCCATAGGGTAAAATGACCGAAATAACCTTATAGGGTAAAATGACT-TTTATACCCC-
1 AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTAGAAATACCCCA
44102891 TAGGAGATAAAATGA
66 TAGGAGATAAAATGA
44102906 CTGTTATGAC
Statistics
Matches: 141, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
79 4 0.03
80 5 0.04
81 130 0.92
82 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (83 bp):
AAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGACTAGAAATACCCCA
TAGGAGATAAAATGATCG
Found at i:44103149 original size:26 final size:26
Alignment explanation
Indices: 44103113--44103167 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
44103103 TTTGCCACAT
*
44103113 ATACTGTTACTAGCAACTTTGCTACG
1 ATACTGATACTAGCAACTTTGCTACG
* * * *
44103139 ATACTGATACTGGTAGCTTTGCTGCG
1 ATACTGATACTAGCAACTTTGCTACG
44103165 ATA
1 ATA
44103168 TTAGTGTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (26 bp):
ATACTGATACTAGCAACTTTGCTACG
Found at i:44103327 original size:33 final size:33
Alignment explanation
Indices: 44103285--44103367 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
44103275 ACTGTATTGG
44103285 GCTAAGGCCCACACTGTACTATCACTTCATAGA
1 GCTAAGGCCCACACTGTACTATCACTTCATAGA
* *
44103318 GCTAAGGCCCACACTGTACTGTCACTTCATAGG
1 GCTAAGGCCCACACTGTACTATCACTTCATAGA
* *
44103351 GCTCAGGCCCAGACTGT
1 GCTAAGGCCCACACTGT
44103368 TACTGCATGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.23
Consensus pattern (33 bp):
GCTAAGGCCCACACTGTACTATCACTTCATAGA
Found at i:44104440 original size:29 final size:30
Alignment explanation
Indices: 44104382--44104440 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
44104372 TAAGTTAGAT
*
44104382 AAAGAAATTAGACACAAGCAGAATTAAAGA
1 AAAGAAATTAGACACAAGCAGAATAAAAGA
44104412 AAAGAAATT-GACAGCAAGCA-AATAAAAGA
1 AAAGAAATTAGACA-CAAGCAGAATAAAAGA
44104441 TAAGTCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.61, C:0.10, G:0.17, T:0.12
Consensus pattern (30 bp):
AAAGAAATTAGACACAAGCAGAATAAAAGA
Found at i:44108021 original size:20 final size:20
Alignment explanation
Indices: 44107996--44108036 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44107986 TAGTGAACGT
44107996 CCTCTCTGTACAACTTGTAA
1 CCTCTCTGTACAACTTGTAA
44108016 CCTCTCTGTACAACTTGTAA
1 CCTCTCTGTACAACTTGTAA
44108036 C
1 C
44108037 ATCTATGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (20 bp):
CCTCTCTGTACAACTTGTAA
Found at i:44109228 original size:16 final size:16
Alignment explanation
Indices: 44109207--44109240 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
44109197 CTACTGAAAC
44109207 AAAGTAAATGTTCCTA
1 AAAGTAAATGTTCCTA
*
44109223 AAAGTAAATGTTTCTA
1 AAAGTAAATGTTCCTA
44109239 AA
1 AA
44109241 TATTTTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (16 bp):
AAAGTAAATGTTCCTA
Found at i:44112591 original size:25 final size:25
Alignment explanation
Indices: 44112563--44112614 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
44112553 CGCTGAACAA
44112563 TCCTTGCATTTGAGATTGACAACTT
1 TCCTTGCATTTGAGATTGACAACTT
44112588 TCCTTGCATTTGAGATTGACAACTT
1 TCCTTGCATTTGAGATTGACAACTT
44112613 TC
1 TC
44112615 TCTAGAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.40
Consensus pattern (25 bp):
TCCTTGCATTTGAGATTGACAACTT
Found at i:44113777 original size:25 final size:25
Alignment explanation
Indices: 44113747--44113795 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
44113737 AGTGCTCTGA
44113747 CAGCAAAGTCACTTGCATAACACAG
1 CAGCAAAGTCACTTGCATAACACAG
44113772 CAGCAAAGTCACTTGCATAACACA
1 CAGCAAAGTCACTTGCATAACACA
44113796 ATAGTTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.16
Consensus pattern (25 bp):
CAGCAAAGTCACTTGCATAACACAG
Found at i:44120020 original size:41 final size:41
Alignment explanation
Indices: 44119953--44120085 Score: 203
Period size: 41 Copynumber: 3.2 Consensus size: 41
44119943 TTTATGGTTT
* * *
44119953 CCTTTTCATTTGTTGTCATTTTTGGATAACATCCTTTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
* *
44119994 CCTTTTCATTTGATATCCTTTCTGGATAACATCATTTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
*
44120035 CCTTTTTATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
1 CCTTTTCATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
*
44120076 TCTTTTCATT
1 CCTTTTCATT
44120086 GATTCAGAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.20, C:0.21, G:0.08, T:0.51
Consensus pattern (41 bp):
CCTTTTCATTTGTTATCCTTTCTGGATAACATCCTTTTCAA
Found at i:44124117 original size:25 final size:25
Alignment explanation
Indices: 44124089--44124146 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
44124079 ATATTACATT
44124089 ATTTAAATATAATATATATCAATAA
1 ATTTAAATATAATATATATCAATAA
* * *
44124114 ATTTATAA-ATAATTTATATTAATTA
1 ATTTA-AATATAATATATATCAATAA
*
44124139 ATTAAAAT
1 ATTTAAAT
44124147 TATTTGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
24 2 0.07
25 23 0.85
26 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTTAAATATAATATATATCAATAA
Found at i:44128819 original size:56 final size:56
Alignment explanation
Indices: 44128733--44128852 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
44128723 ACAAGGGATG
*
44128733 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATATTGTGTTAATGGAAAAATAAAATAAGAAGC
*
44128789 ATGGGCAAAACATGTCATGAAACATATTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATATTGTGTTAATGGAAAAATAAAATAAGAAGC
44128845 ATGGGCAA
1 ATGGGCAA
44128853 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATATTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:44130062 original size:40 final size:42
Alignment explanation
Indices: 44129979--44130124 Score: 164
Period size: 40 Copynumber: 3.6 Consensus size: 42
44129969 TCGAATGATG
* * *
44129979 TCCGGGCTAAG-TCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGATCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
44130019 TCCGGACTAAGAT-CCGAAGGCATTTGTTCGAGTTACTA-AA
1 TCCGGGCTAAGATCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44130059 TCCGGGTTAA-ATCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGATCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44130100 -CCGGGCTATG-TCCCGAAGGCATTTG
1 TCCGGGCTAAGATCCCGAAGGCATTTG
44130125 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
39 2 0.02
40 79 0.88
41 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.27
Consensus pattern (42 bp):
TCCGGGCTAAGATCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:44130116 original size:80 final size:80
Alignment explanation
Indices: 44129979--44130157 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
44129969 TCGAATGATG
* * *
44129979 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAATCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
44130044 GTTCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
44130059 TCCGGGTTAAATCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAATCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
44130122 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
*
44130139 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAATCCCGAAGG
44130158 TACGTGATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 18 0.21
80 59 0.70
81 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAATCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:44130131 original size:40 final size:40
Alignment explanation
Indices: 44129979--44130157 Score: 143
Period size: 40 Copynumber: 4.5 Consensus size: 40
44129969 TCGAATGATG
* * * * * *
44129979 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAATCCCGAAGGCATTTGTAC-GAGTTACTAAA
* *
44130019 TCCGGACTAAGAT-CCGAAGGCATTTGTTCGAGTTACTAAA
1 TCCGGGCTAA-ATCCCGAAGGCATTTGTACGAGTTACTAAA
* *
44130059 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAATCCCGAAGGCATTTGTACGAGTTACTA-AA
** * *
44130100 -CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAATCCCGAAGGCATTTGTACGAGTTA-CTAAA
* *
44130139 TCC-GGTTAAATTCCGAAGG
1 TCCGGGCTAAATCCCGAAGG
44130158 TACGTGATTT
Statistics
Matches: 113, Mismatches: 20, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
39 17 0.15
40 87 0.77
41 9 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAATCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:44136683 original size:56 final size:56
Alignment explanation
Indices: 44136597--44136716 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
44136587 ACAAGGGATG
44136597 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
44136653 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
44136709 ATGGGCAA
1 ATGGGCAA
44136717 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:44137995 original size:80 final size:80
Alignment explanation
Indices: 44137843--44138021 Score: 188
Period size: 80 Copynumber: 2.2 Consensus size: 80
44137833 TCGAATGATG
*
44137843 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
**
44137908 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
44137923 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAAT-CGGGCTATG-TCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-ATCCGGACTAAGAT-CCGAAGGCA
*
44137985 TTTGAACGAGTAGCTATA
63 TTTGAACGAGTAGCTAAA
* *
44138003 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
44138022 TACGTGATTT
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
79 17 0.20
80 58 0.69
81 9 0.11
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:44138002 original size:40 final size:41
Alignment explanation
Indices: 44137843--44137988 Score: 185
Period size: 40 Copynumber: 3.6 Consensus size: 41
44137833 TCGAATGATG
* * *
44137843 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
*
44137883 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44137923 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
44137964 T-CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
44137989 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.01
40 81 0.87
41 11 0.12
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:44141911 original size:16 final size:16
Alignment explanation
Indices: 44141887--44141924 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
44141877 TTTGGTTCAC
* *
44141887 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
44141903 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
44141919 TGTAAT
1 TGTAAT
44141925 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:44142009 original size:39 final size:43
Alignment explanation
Indices: 44141903--44142012 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
44141893 GGATTAGAGG
44141903 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
** * ***
44141948 TGTAATGGAATAGAGGCATAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
44141988 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
44142013 TAATGGAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
39 19 0.35
40 2 0.04
43 1 0.02
44 11 0.20
45 22 0.40
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:44142166 original size:25 final size:25
Alignment explanation
Indices: 44142134--44142188 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
44142124 TAATTTAATC
*
44142134 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
44142158 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
44142183 ATATAT
1 ATATAT
44142189 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:44146561 original size:50 final size:50
Alignment explanation
Indices: 44146515--44147200 Score: 841
Period size: 50 Copynumber: 13.5 Consensus size: 50
44146505 TATCCCAAGT
* ** * * *
44146515 ATGGTCTTACATGAGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*** *
44146565 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
44146615 ATGGTCTTACATGAGACCTCTCATCTCGGTGTCAACACCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
44146665 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* ** * * * *
44146715 ATGGTCTTACATGGTAGTTCTCATATCAGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
***
44146765 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* *
44146815 ATGGTCTTACATGGGACCTCTCATCTCGGTGTCAACGTCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* * *
44146865 ATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGTCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* ** * * *
44146915 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
***
44146965 ATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
** *
44147015 ATGGTCTTACATGGGACCTCTCATCTTAGTGCCAACGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
44147065 ATGGTCTTACATGGGACCTCTCATCGGACCTCTCATCTTGGTGCCAACGCCATGTTCCAGAC
1 ATGGTCTTACATGGGA-C-CTC-TC--A----TC-TC--GGTGCCAACGCCATGTCCCAGAC
* *
44147127 ATGGTCTTACATGAGACCTCTCATCTTGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
44147177 ATGGTCTTACATGAGACCTCTCAT
1 ATGGTCTTACATGGGACCTCTCAT
44147201 AATTTCAATA
Statistics
Matches: 544, Mismatches: 80, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
50 489 0.90
51 1 0.00
52 4 0.01
53 4 0.01
55 1 0.00
57 1 0.00
59 4 0.01
60 4 0.01
61 1 0.00
62 35 0.06
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:44146798 original size:200 final size:200
Alignment explanation
Indices: 44146515--44147089 Score: 1044
Period size: 200 Copynumber: 2.9 Consensus size: 200
44146505 TATCCCAAGT
44146515 ATGGTCTTACATGAG-AGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGG
1 ATGGTCTTACATG-GTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGG
* *
44146579 GACCTCTCATCTCGGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATCTCGG
65 GACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
44146644 TGTCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTC
130 TGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTC
44146709 CCAAAC
195 CCAAAC
*
44146715 ATGGTCTTACATGGTAGTTCTCATATCAGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
1 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
44146780 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
66 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* *
44146845 GTCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGTCATGTCC
131 GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCC
44146910 CAAAC
196 CAAAC
44146915 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
1 ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
**
44146980 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTAGT
66 ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
* *
44147045 GCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATC
131 GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
44147090 GGACCTCTCA
Statistics
Matches: 362, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
199 1 0.00
200 361 1.00
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.27
Consensus pattern (200 bp):
ATGGTCTTACATGGTAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTCTTATGGGGG
ACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGT
GTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGACATGTCC
CAAAC
Found at i:44147118 original size:112 final size:112
Alignment explanation
Indices: 44146978--44147200 Score: 392
Period size: 112 Copynumber: 2.0 Consensus size: 112
44146968 GTCTTATGGG
*
44146978 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTA
1 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTTA
*
44147043 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATC
66 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATC
* * *
44147090 GGACCTCTCATCTTGGTGCCAACGCCATGTTCCAGACATGGTCTTACATGAGACCTCTCATCTTG
1 GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTTA
*
44147155 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT
66 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCAT
44147201 AATTTCAATA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 105 1.00
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.26
Consensus pattern (112 bp):
GGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTTA
GTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATC
Found at i:44151962 original size:39 final size:40
Alignment explanation
Indices: 44151895--44152005 Score: 111
Period size: 39 Copynumber: 2.8 Consensus size: 40
44151885 TTTAAGTATA
* * * * **
44151895 TAATTATGTCATAATCTGAACATATTTAATA-AGATTTTT
1 TAATTATGTCATAGTTTGGACATATTTAATATACATAATT
44151934 TAATTATGTCATAGTTTAGGACAT-TTTAA-ATACATAATT
1 TAATTATGTCATAGTTT-GGACATATTTAATATACATAATT
* * *
44151973 TAATTATGTCCTAGTTTGGAAATCTTTAATATA
1 TAATTATGTCATAGTTTGGACATATTTAATATA
44152006 TGTGTTTAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
38 6 0.10
39 46 0.77
40 8 0.13
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (40 bp):
TAATTATGTCATAGTTTGGACATATTTAATATACATAATT
Found at i:44158143 original size:28 final size:28
Alignment explanation
Indices: 44158091--44158185 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 28
44158081 AGAAGAAAAT
44158091 CCTTTGTGGCAAAACTTTGGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
* *
44158120 CCTTTGTGGCAAACCTATT-AAAGG-ATAA
1 CCTTTGTGGCAAAACT-TTGAAAGGCA-AG
*
44158148 CCTTTGTTGCAAAACTTTAGAAAGGCAAG
1 CCTTTGTGGCAAAACTTT-GAAAGGCAAG
44158177 CCTTTGTGG
1 CCTTTGTGG
44158186 TGAACCTATT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
27 3 0.05
28 20 0.36
29 29 0.53
30 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (28 bp):
CCTTTGTGGCAAAACTTTGAAAGGCAAG
Found at i:44158179 original size:57 final size:57
Alignment explanation
Indices: 44158091--44158211 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 57
44158081 AGAAGAAAAT
* *
44158091 CCTTTGTGGCAAAACTTTGGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGATAA
1 CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
* **
44158148 CCTTTGTTGCAAAACTTTAGAAAGGCAAGCCTTTGTGGTGAACCTATTAAAGGACAA
1 CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
*
44158205 CTTTTGT
1 CCTTTGT
44158212 AGCAGTGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (57 bp):
CCTTTGTGGCAAAACTTTAGAAAGGCAAGCCTTTGTGGCAAACCTATTAAAGGACAA
Found at i:44167085 original size:48 final size:48
Alignment explanation
Indices: 44166995--44167191 Score: 223
Period size: 48 Copynumber: 4.1 Consensus size: 48
44166985 AATAGATTTC
* * * * *
44166995 TCGGTGGCCTGCACACAGTCTGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * * *
44167043 TCAGTGGCCTGCACATAGTCCGTGTCACCCTTGTATCTTAACAAATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * * * *
44167091 TTGGTGGCCTACACATACTCTGTGCCACCCTTGTGTCACAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
*
44167139 TCGGTGGCTTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
44167187 TCGGT
1 TCGGT
44167192 ACGGATAGTA
Statistics
Matches: 119, Mismatches: 30, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Found at i:44178575 original size:12 final size:12
Alignment explanation
Indices: 44178558--44178582 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44178548 TCTATATCGA
44178558 GCCTAGCACACG
1 GCCTAGCACACG
44178570 GCCTAGCACACG
1 GCCTAGCACACG
44178582 G
1 G
44178583 ACGTGTGAGG
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:0.24, C:0.40, G:0.28, T:0.08
Consensus pattern (12 bp):
GCCTAGCACACG
Found at i:44179109 original size:29 final size:25
Alignment explanation
Indices: 44179077--44179134 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 25
44179067 TTGTACTCGT
44179077 TTTTTCTCTTCTTTATTATCATTATTTTC
1 TTTTTCTCTTCTTT-TT-TC-TT-TTTTC
*
44179106 TTTTTCTTTTCTTTTTTCTTTTTTC
1 TTTTTCTCTTCTTTTTTCTTTTTTC
44179131 TTTT
1 TTTT
44179135 AGCATGTCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.32
26 2 0.07
27 2 0.07
28 2 0.07
29 13 0.46
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCTCTTCTTTTTTCTTTTTTC
Found at i:44185246 original size:51 final size:50
Alignment explanation
Indices: 44185125--44185247 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 50
44185115 CTGCTTTTTC
* * * *
44185125 AATATCTTGTTTATATAATTATTTTTTAGATTTGATGTTTTAAATAAATATT
1 AATAT-TTGTTTATATTATT-TTGTTTAGATCTGATGTTTTAAACAAATATT
* *
44185177 AATATTTATTTA-ATTTATTTTGTTTAGATCTGATGTTTTTACACAAATA-T
1 AATATTTGTTTATA-TTATTTTGTTTAGATCTGATG-TTTTAAACAAATATT
*
44185227 AGATATTTGGTTATATTATTT
1 A-ATATTTGTTTATATTATTT
44185248 GTTCAAGATA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
50 17 0.29
51 36 0.61
52 6 0.10
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (50 bp):
AATATTTGTTTATATTATTTTGTTTAGATCTGATGTTTTAAACAAATATT
Found at i:44185559 original size:82 final size:82
Alignment explanation
Indices: 44185449--44185685 Score: 302
Period size: 82 Copynumber: 2.9 Consensus size: 82
44185439 ATGATTGTCG
* * *
44185449 TTCAATAGATTTTATTCCT-TTTTTATTTTGTTTCCAAACAAGAATTAATTGAATAATTCTATTT
1 TTCAACAGATTTTATT-CTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
*
44185513 C-AGAATTTATTCTCG-CA
65 CGAG-ATTTATTCCCGCCA
* *
44185530 TCTCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAATAATTAAATAAATAATTCTATTT
1 T-TCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
44185595 CGAGATTTATTCCCGCCA
65 CGAGATTTATTCCCGCCA
* * * * *
44185613 TTTAACAGATTTTATT-TGATTGTGATTTTGTTTCCAAACAAGATTTAATTAAATAATTTTGTTT
1 TTCAACAGATTTTATTCT-ATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTT
*
44185677 CAAGATTTA
65 CGAGATTTA
44185686 ATCCTGTCGG
Statistics
Matches: 137, Mismatches: 14, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
81 4 0.03
82 128 0.93
83 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (82 bp):
TTCAACAGATTTTATTCTATTTTGATTTTGTTTCCAAACAAGAATTAATTAAATAATTCTATTTC
GAGATTTATTCCCGCCA
Found at i:44185808 original size:12 final size:13
Alignment explanation
Indices: 44185791--44185821 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
44185781 TTTTTTATTT
44185791 ATTGTGGCTTT-A
1 ATTGTGGCTTTAA
44185803 ATTGTGGCTTTAA
1 ATTGTGGCTTTAA
44185816 ATTGTG
1 ATTGTG
44185822 AAAGCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (13 bp):
ATTGTGGCTTTAA
Found at i:44185828 original size:28 final size:29
Alignment explanation
Indices: 44185797--44185851 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
44185787 ATTTATTGTG
* * *
44185797 GCTTTAATTGTGGCTTTAAA-TTGTGAAA
1 GCTTAAATTGTAGCTTCAAACTTGTGAAA
44185825 GCTTAAATTGTAGCTTCAAACTTGTGA
1 GCTTAAATTGTAGCTTCAAACTTGTGA
44185852 CATCAAAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (29 bp):
GCTTAAATTGTAGCTTCAAACTTGTGAAA
Found at i:44190785 original size:50 final size:48
Alignment explanation
Indices: 44190670--44190786 Score: 146
Period size: 51 Copynumber: 2.4 Consensus size: 48
44190660 CAAGATCTTG
*
44190670 TTTATTTAATTATTT-TTTAGATATGATGTTTTAAATAAATATAAATA
1 TTTATTTAATTATTTGTTTAGATACGATGTTTTAAATAAATATAAATA
* * *
44190717 TTTATTTAATTGATTTTGTTTAGATCCGGTGTTTTTACATAAATATAAATA
1 TTTATTTAATT-A-TTTGTTTAGATACGATG-TTTTAAATAAATATAAATA
*
44190768 TTTGTTTATATTATTTGTT
1 TTTATTTA-ATTATTTGTT
44190787 CAAGATCTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
47 11 0.18
48 1 0.02
49 3 0.05
50 16 0.27
51 26 0.43
52 3 0.05
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (48 bp):
TTTATTTAATTATTTGTTTAGATACGATGTTTTAAATAAATATAAATA
Found at i:44195355 original size:19 final size:19
Alignment explanation
Indices: 44195331--44195374 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
44195321 CTTCTTAGAA
44195331 GTATTTTTTAAGATAAAAT
1 GTATTTTTTAAGATAAAAT
*
44195350 GTA-TTTTTGAGATAAAAT
1 GTATTTTTTAAGATAAAAT
*
44195368 ATATTTT
1 GTATTTT
44195375 AAAAAAGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
GTATTTTTTAAGATAAAAT
Found at i:44198269 original size:22 final size:23
Alignment explanation
Indices: 44198234--44198277 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
44198224 AAATAATGGT
44198234 TTAAAACATGTAAAACATTTTTC
1 TTAAAACATGTAAAACATTTTTC
* *
44198257 TTAAAAC-TTTAAAATATTTTT
1 TTAAAACATGTAAAACATTTTT
44198278 AAATTACATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (23 bp):
TTAAAACATGTAAAACATTTTTC
Found at i:44198767 original size:26 final size:24
Alignment explanation
Indices: 44198736--44198786 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
44198726 GCCCATTTTT
* *
44198736 AATAAACATTAAAAAATTATTTTAAA
1 AATAAAAAATAAAAAA--ATTTTAAA
44198762 AATAAAAAATAAAAAAATTTTAAA
1 AATAAAAAATAAAAAAATTTTAAA
44198786 A
1 A
44198787 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
26 14 0.61
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (24 bp):
AATAAAAAATAAAAAAATTTTAAA
Found at i:44199585 original size:17 final size:18
Alignment explanation
Indices: 44199556--44199590 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
44199546 TTATATTTAT
44199556 TTTAAAAATAATAAAAAA
1 TTTAAAAATAATAAAAAA
44199574 TTTAAAAA-AATAAAAAA
1 TTTAAAAATAATAAAAAA
44199591 GGCATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TTTAAAAATAATAAAAAA
Found at i:44199739 original size:10 final size:10
Alignment explanation
Indices: 44199726--44199784 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
44199716 TAGAATTTAG
44199726 AAAAATTATAA
1 AAAAATTAT-A
*
44199737 AAAAATCATA
1 AAAAATTATA
*
44199747 AAAAATTGTA
1 AAAAATTATA
* *
44199757 AATATAATTTTT
1 AA-A-AATTATA
44199769 AAAAATTATA
1 AAAAATTATA
44199779 AAAAAT
1 AAAAAT
44199785 GGAAATATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 22 0.56
11 10 0.26
12 7 0.18
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAAATTATA
Found at i:44199815 original size:26 final size:25
Alignment explanation
Indices: 44199767--44199859 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 25
44199757 AATATAATTT
*
44199767 TTAAAAATTATAAAAAATGGAAATA
1 TTAAAAATTATAAAAAATAGAAATA
44199792 TTAAAATATTA-AAAATAATAGAAATCA
1 TTAAAA-ATTATAAAA-AATAGAAAT-A
* ** * *
44199819 TTTAGAAA--ATAAAATTTAAAAATT
1 -TTAAAAATTATAAAAAATAGAAATA
*
44199843 TTAAAAATTTTAAAAAA
1 TTAAAAATTATAAAAAA
44199860 ATTTAAAAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
23 6 0.12
25 22 0.43
26 16 0.31
27 2 0.04
28 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (25 bp):
TTAAAAATTATAAAAAATAGAAATA
Found at i:44199858 original size:10 final size:10
Alignment explanation
Indices: 44199836--44199871 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
44199826 AATAAAATTT
44199836 AAAAATTTT-
1 AAAAATTTTA
44199845 AAAAATTTTA
1 AAAAATTTTA
*
44199855 AAAAAATTTA
1 AAAAATTTTA
44199865 AAAAATT
1 AAAAATT
44199872 AGATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:44204762 original size:66 final size:66
Alignment explanation
Indices: 44204648--44204784 Score: 202
Period size: 66 Copynumber: 2.1 Consensus size: 66
44204638 TTGCAGGGAA
* * * *
44204648 ACTTGGAAGCGTTTTCAACATGTTGCATTGAAAACGCTTCCAGCTAGAATCGCTTTCTACTAAGT
1 ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
44204713 C
66 C
* * * *
44204714 ACTTGGAAGCATTTTTAACATATTGCATGGAAAACGCTTTCAGTTAGAATCACTTTCTGCTAAGT
1 ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
44204779 C
66 C
44204780 ACTTG
1 ACTTG
44204785 AAAATGCTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (66 bp):
ACTTGGAAGCATTTTCAACATATTGCATGGAAAACGCTTCCAGCTAGAATCACTTTCTACTAAGT
C
Found at i:44207711 original size:20 final size:18
Alignment explanation
Indices: 44207661--44207712 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
44207651 CTACAAGATA
44207661 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
44207678 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
*
44207698 GATATTAAATTAATA
1 AATATTAAATTAATA
44207713 AAATATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 11 0.38
18 1 0.03
19 3 0.10
20 14 0.48
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:44211359 original size:89 final size:89
Alignment explanation
Indices: 44211203--44211380 Score: 311
Period size: 89 Copynumber: 2.0 Consensus size: 89
44211193 GCTGAAGCTT
*
44211203 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGTAGAGCCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
44211268 TTCGTTCCACTACGACTATTACCC
66 TTCGTTCCACTACGACTATTACCC
* * * *
44211292 CCTCTCGAGCACGGATCGCATGAGCTTTAGTCGACACTGGTGCCTCAGATCTCACAGCAGAGTCT
1 CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
44211357 TTCGTTCCACTACGACTATTACCC
66 TTCGTTCCACTACGACTATTACCC
44211381 GCATTACCAG
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.26
Consensus pattern (89 bp):
CCTCTCGAGCACAGATCGCATAAGCTTTAGTCGACACTGGTGCCTCAAATCTCACAGCAGAGCCT
TTCGTTCCACTACGACTATTACCC
Found at i:44225012 original size:5 final size:5
Alignment explanation
Indices: 44225004--44225053 Score: 75
Period size: 5 Copynumber: 10.0 Consensus size: 5
44224994 TTTAAAAACA
*
44225004 CATAT CATAT TATAT CATAT CATAT CA-AT ACATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT -CATAT CATAT CATAT CATAT
44225054 AATAAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 2 0.05
5 37 0.90
6 2 0.05
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (5 bp):
CATAT
Found at i:44230915 original size:20 final size:18
Alignment explanation
Indices: 44230868--44230916 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
44230858 CAATATAAAC
44230868 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
44230885 ATTAAGA-TAATAGCTTTAAT
1 ATTAA-ATTAATA--TTTAAT
44230905 ATTAAATTAATA
1 ATTAAATTAATA
44230917 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 8 0.30
18 2 0.07
19 1 0.04
20 16 0.59
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:44238484 original size:39 final size:39
Alignment explanation
Indices: 44238403--44238506 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 39
44238393 AAATCATTGT
* * * *
44238403 TATAATTGTTGTAATTATAA-TTTACGATCGAATATTAT
1 TATAATTATTGTAATTATAATTTTACGATCAAACATTAC
*
44238441 TATAATTATTGTAATTATAATTTTTCGATCAAACATTAC
1 TATAATTATTGTAATTATAATTTTACGATCAAACATTAC
* *
44238480 TATAACTATGGTAATTATAATTATTAC
1 TATAATTATTGTAATTATAATT-TTAC
44238507 ATTCGGTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 19 0.34
39 34 0.61
40 3 0.05
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (39 bp):
TATAATTATTGTAATTATAATTTTACGATCAAACATTAC
Found at i:44239529 original size:29 final size:29
Alignment explanation
Indices: 44239497--44239558 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
44239487 ACTGGAAGTG
* *
44239497 TTTTCCAAAAAAT-GGTCTATTCCCGTAAT
1 TTTTCC-AAAAATCGGCCTATTCACGTAAT
*
44239526 TTTTCCTAAAATCGGCCTATTCACGTAAT
1 TTTTCCAAAAATCGGCCTATTCACGTAAT
44239555 TTTT
1 TTTT
44239559 TTGACATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (29 bp):
TTTTCCAAAAATCGGCCTATTCACGTAAT
Found at i:44245379 original size:26 final size:26
Alignment explanation
Indices: 44245319--44245379 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
44245309 TATCCGGAGC
* *
44245319 TCCTGATTAAAAGCTCTTCGTGAGCT
1 TCCTGATTAAAAGCTCTTCATGAACT
* * * *
44245345 TCTTAATTAAAAGTTCTTTATGAACT
1 TCCTGATTAAAAGCTCTTCATGAACT
44245371 TCCTGATTA
1 TCCTGATTA
44245380 TTACTCTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (26 bp):
TCCTGATTAAAAGCTCTTCATGAACT
Found at i:44255130 original size:24 final size:24
Alignment explanation
Indices: 44255098--44255145 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
44255088 CAGAGATAGA
44255098 CCCATCAGAAAACATGTAGTGCCT
1 CCCATCAGAAAACATGTAGTGCCT
44255122 CCCATCAGAAAACATGTAGTGCCT
1 CCCATCAGAAAACATGTAGTGCCT
44255146 AATTTGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (24 bp):
CCCATCAGAAAACATGTAGTGCCT
Found at i:44259361 original size:41 final size:43
Alignment explanation
Indices: 44259247--44259380 Score: 166
Period size: 45 Copynumber: 3.1 Consensus size: 43
44259237 TAGGATTTTT
* *
44259247 TATATGTGTTCTCGTGTAAGACCACGTCTGGGACGATGGCATCGA
1 TATATGTGAT-TCGTGTAAGACCATGTCTGGGAC-ATGGCATCGA
*
44259292 TATATGTGATTACGTGTAAGACCATGTCTAGGACATTGGCATCG-
1 TATATGTGATT-CGTGTAAGACCATGTCTGGGACA-TGGCATCGA
*
44259336 TAT-T-TGATTCGTGTAAGACCTTGTCTGGGACAGTGGCATCGA
1 TATATGTGATTCGTGTAAGACCATGTCTGGGACA-TGGCATCGA
44259378 TAT
1 TAT
44259381 GAGATAGCAT
Statistics
Matches: 80, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
41 29 0.36
42 8 0.10
43 1 0.01
44 5 0.06
45 37 0.46
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TATATGTGATTCGTGTAAGACCATGTCTGGGACATGGCATCGA
Found at i:44268728 original size:46 final size:46
Alignment explanation
Indices: 44268667--44268755 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 46
44268657 CACGAATAAT
* *
44268667 GAATCATAGTGTCTGGTCA-CC-TGTAAGGGTTGAACCTATACAAATC
1 GAATAATAGTGTCTGGTCACCCAT-TAA-GGTTGAACCTACACAAATC
44268713 GAATAATAGTGTCTGGTCACCCATTAAGGTTGAACCTACACAA
1 GAATAATAGTGTCTGGTCACCCATTAAGGTTGAACCTACACAA
44268756 CAAATTGTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 33 0.85
47 5 0.13
48 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (46 bp):
GAATAATAGTGTCTGGTCACCCATTAAGGTTGAACCTACACAAATC
Found at i:44273665 original size:36 final size:36
Alignment explanation
Indices: 44273613--44273689 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 36
44273603 AATCCCAATA
*
44273613 AAAATCTAATAATAATTA-AAAATTAAAAATGTTAAT
1 AAAATCTAATAATAATTATAAAA-TAAAAACGTTAAT
* *
44273649 GAAAATCTCA-AATAATTATAAAATAATAACGTTAAT
1 -AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
44273685 AAAAT
1 AAAAT
44273690 TTTAAAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 5 0.14
36 19 0.53
37 12 0.33
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (36 bp):
AAAATCTAATAATAATTATAAAATAAAAACGTTAAT
Found at i:44274666 original size:22 final size:22
Alignment explanation
Indices: 44274641--44274684 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
44274631 CTTCTTTAAA
44274641 AAAGAAAAGATCTTTTCCAGAT
1 AAAGAAAAGATCTTTTCCAGAT
44274663 AAAGAAAAGATCTTTTCCAGAT
1 AAAGAAAAGATCTTTTCCAGAT
44274685 TTATTTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (22 bp):
AAAGAAAAGATCTTTTCCAGAT
Found at i:44287059 original size:86 final size:86
Alignment explanation
Indices: 44286969--44287149 Score: 355
Period size: 86 Copynumber: 2.1 Consensus size: 86
44286959 AATATAATTG
44286969 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
44287034 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
44287055 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
44287120 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
44287141 TAATT-TTAT
1 TAATTATTAT
44287150 GTGGAGAGAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.04
86 91 0.96
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (86 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
TGTTAAGTATTAATGTTGATA
Found at i:44287292 original size:51 final size:51
Alignment explanation
Indices: 44287223--44287432 Score: 278
Period size: 51 Copynumber: 3.9 Consensus size: 51
44287213 AAAAATTATT
44287223 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATAC
1 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATAC
*
44287274 ATACACCAACAATATTTTTTAGGGTAAATAACATTAAACTAACAATTAAACCAACAATTATAC
1 ATACACCAACAATGTTTTTTAGGG----------TAAA-TAAC-ATTAAACCAACAATTATAC
44287337 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATAC
1 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATAC
*
44287388 ATACACCAACAATGTTTTCTAGGG-ACAATAACATTAAACCAACAA
1 ATACACCAACAATGTTTTTTAGGGTA-AATAACATTAAACCAACAA
44287433 GTAATTTTAG
Statistics
Matches: 143, Mismatches: 3, Indels: 26
0.83 0.02 0.15
Matches are distributed among these distances:
50 1 0.01
51 84 0.59
52 4 0.03
53 4 0.03
61 4 0.03
62 4 0.03
63 42 0.29
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.28
Consensus pattern (51 bp):
ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATAC
Found at i:44287328 original size:63 final size:63
Alignment explanation
Indices: 44287247--44287384 Score: 244
Period size: 63 Copynumber: 2.2 Consensus size: 63
44287237 TTTTTTAGGG
44287247 TAAA-TAAC-ATTAAACCAACAATTATACATACACCAACAATATTTTTTAGGGTAAATAACAT
1 TAAACTAACAATTAAACCAACAATTATACATACACCAACAATATTTTTTAGGGTAAATAACAT
*
44287308 TAAACTAACAATTAAACCAACAATTATACATACACCAACAATGTTTTTTAGGGTAAATAACAT
1 TAAACTAACAATTAAACCAACAATTATACATACACCAACAATATTTTTTAGGGTAAATAACAT
*
44287371 TAAACCAACAATTA
1 TAAACTAACAATTA
44287385 TACATACACC
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
61 4 0.05
62 4 0.05
63 65 0.89
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.28
Consensus pattern (63 bp):
TAAACTAACAATTAAACCAACAATTATACATACACCAACAATATTTTTTAGGGTAAATAACAT
Found at i:44287355 original size:114 final size:114
Alignment explanation
Indices: 44287223--44287432 Score: 377
Period size: 114 Copynumber: 1.8 Consensus size: 114
44287213 AAAAATTATT
44287223 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATACATACACCAACAATA
1 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATACATACACCAACAATA
* *
44287288 TTTTTTAGGGTA-AATAACATTAAACTAACAATTAAACCAACAATTATAC
66 TTTTCTAGGG-ACAATAACATTAAACCAACAATTAAACCAACAATTATAC
*
44287337 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATACATACACCAACAATG
1 ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATACATACACCAACAATA
44287402 TTTTCTAGGGACAATAACATTAAACCAACAA
66 TTTTCTAGGGACAATAACATTAAACCAACAA
44287433 GTAATTTTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
113 1 0.01
114 91 0.99
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.28
Consensus pattern (114 bp):
ATACACCAACAATGTTTTTTAGGGTAAATAACATTAAACCAACAATTATACATACACCAACAATA
TTTTCTAGGGACAATAACATTAAACCAACAATTAAACCAACAATTATAC
Found at i:44287462 original size:33 final size:33
Alignment explanation
Indices: 44287379--44287488 Score: 129
Period size: 33 Copynumber: 3.3 Consensus size: 33
44287369 ATTAAACCAA
*
44287379 CAATTATACATACACCAACAATGT--TTTCTAGGGA
1 CAATTATACATACACCAACAA-GTAATTT-TA-GGT
*
44287413 CAA-TA-ACATTAAACCAACAAGTAATTTTAGGT
1 CAATTATACA-TACACCAACAAGTAATTTTAGGT
*
44287445 CAATTATACATACACCAACAATTAATTTTAGGT
1 CAATTATACATACACCAACAAGTAATTTTAGGT
44287478 CAATTATACAT
1 CAATTATACAT
44287489 GCTTTATAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
32 10 0.15
33 48 0.72
34 9 0.13
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (33 bp):
CAATTATACATACACCAACAAGTAATTTTAGGT
Found at i:44290576 original size:29 final size:28
Alignment explanation
Indices: 44290543--44290629 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
44290533 TCATAAGAAC
44290543 ATTTTATGAAATTATATTTAATAATAATT
1 ATTTTAT-AAATTATATTTAATAATAATT
* * *
44290572 A-TTT-TAAATTGTATTAAATCAT-A-T
1 ATTTTATAAATTATATTTAATAATAATT
* *
44290596 ATTTTAATTAAAATATATTTAATATTAATT
1 ATTTT-A-TAAATTATATTTAATAATAATT
44290626 ATTT
1 ATTT
44290630 CAAATTTTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
24 2 0.05
25 4 0.09
26 14 0.32
27 1 0.02
28 16 0.36
29 2 0.05
30 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTATAAATTATATTTAATAATAATT
Found at i:44290862 original size:18 final size:17
Alignment explanation
Indices: 44290834--44290868 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
44290824 AATTATAAGA
*
44290834 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
44290851 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
44290869 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:44290930 original size:136 final size:138
Alignment explanation
Indices: 44290686--44290943 Score: 403
Period size: 136 Copynumber: 1.9 Consensus size: 138
44290676 TAAGAATATG
* * * *
44290686 AATTATTAAGAATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTTTGTTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAACTATGTTTA
* * *
44290751 AATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATATGTAA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATGTAA
44290816 TTTCTGCT
131 TTTCTGCT
****
44290824 AATTA-TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACTAT-TTTA
1 AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAACTATGTTTA
44290887 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACA
66 AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACA
44290944 TTAACAATAA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
136 58 0.53
137 46 0.42
138 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (138 bp):
AATTATTAAGAATTTTATTAAATTATATACCAAAATTAAAATATATTTAATAATAACTATGTTTA
AATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATGTAA
TTTCTGCT
Found at i:44290978 original size:155 final size:155
Alignment explanation
Indices: 44290816--44291135 Score: 561
Period size: 155 Copynumber: 2.1 Consensus size: 155
44290806 CAATATGTAA
44290816 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACT
1 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACT
*
44290881 AT-TTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAT
66 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTT-TTAAAATTTAAATAACAA
44290945 TAACAATAATCATCTACCAAAACAAT
130 TAACAATAATCATCTACCAAAACAAT
* * *
44290971 TTTCTGCTAATTATAAGCATTTTATTAAATTATATATTTTAATTAAAATATATTTAATTATAATT
1 TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACT
*
44291036 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTTTTAAATTTAAATAACAAT
66 ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTTTAAAATTTAAATAACAAT
*
44291101 AACAATAATCATTTACCAAAACAAT
131 AACAATAATCATCTACCAAAACAAT
*
44291126 TTTATGCTAA
1 TTTCTGCTAA
44291136 GGGTATTCTA
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
155 114 0.73
156 43 0.27
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (155 bp):
TTTCTGCTAATTATAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACT
ATATTTAAATATGATTAAAATATTTATTACTGATAATAATAATCTTTTAAAATTTAAATAACAAT
AACAATAATCATCTACCAAAACAAT
Found at i:44290985 original size:136 final size:137
Alignment explanation
Indices: 44290696--44290973 Score: 339
Period size: 136 Copynumber: 2.0 Consensus size: 137
44290686 AATTATTAAG
**** * * * *
44290696 AATTTTATTAAATTATATACCAAAATTATAATGTATTTAATAATAATTTTGTTTAAATATGATTA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACTATGTTTAAATATGATTA
* * * ** *
44290761 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATATGTAATTTCTGCTAA
66 AAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATACAATATCTGCTAA
** * *
44290826 TTATAAG
131 CCAAAAC
44290833 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACTAT-TTTAAATATGATTA
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACTATGTTTAAATATGATTA
*
44290897 AAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACATTA-ACAATAATCAT-CT
66 AAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATACAAT-ATC-TGCT
44290960 -ACCAAAAC
129 AACCAAAAC
44290968 AATTTT
1 AATTTT
44290974 CTGCTAATTA
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
135 13 0.11
136 64 0.53
137 43 0.36
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (137 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAACTATGTTTAAATATGATTA
AAATATTTATTACTGATAATAATAATCTTATTAAAATTTAAATAACAATATACAATATCTGCTAA
CCAAAAC
Found at i:44291017 original size:18 final size:18
Alignment explanation
Indices: 44290989--44291039 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
44290979 AATTATAAGC
44290989 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
44291006 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
44291022 A-TTTAATTATAATTATAT
1 ATTTTAATTA-AATTATAT
44291040 TTAAATATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.27
16 7 0.23
17 5 0.17
18 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:44291023 original size:16 final size:16
Alignment explanation
Indices: 44290989--44291041 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
44290979 AATTATAAGC
44290989 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
44291006 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
44291022 A-TTTAATTATAATTAT
1 ATTTTAATTA-AAATAT
44291038 ATTT
1 ATTT
44291042 AAATATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 8 0.25
16 11 0.34
17 7 0.22
18 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:44291028 original size:15 final size:16
Alignment explanation
Indices: 44291002--44291043 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
44290992 TTATTAAATT
44291002 ATATATTTTAATTA-AA
1 ATATA-TTTAATTATAA
44291018 ATATATTTAATTATAA
1 ATATATTTAATTATAA
*
44291034 TTATATTTAA
1 ATATATTTAA
44291044 ATATGATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATTTAATTATAA
Found at i:44291052 original size:16 final size:16
Alignment explanation
Indices: 44291019--44291052 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44291009 TTAATTAAAA
*
44291019 TATATTTAATTATAAT
1 TATATTTAAATATAAT
*
44291035 TATATTTAAATATGAT
1 TATATTTAAATATAAT
44291051 TA
1 TA
44291053 AAATATTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TATATTTAAATATAAT
Found at i:44291267 original size:45 final size:40
Alignment explanation
Indices: 44291168--44291277 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 40
44291158 TTTTCCATTA
*
44291168 TGCTATTACACCTCTATTCCATT-CAACCAAACACAATAT
1 TGCTATTACACCTCTATTCCATTACAACCAAAAACAATAT
* **
44291207 TACTATTACACCTCTATTCCATTACATTCAACCAAACAATGAAT
1 TGCTATTACACCTCTATTCCATTACAACCAA--AAACAAT--AT
* *
44291251 TGGCTATTACACCTCTAATCCAATACA
1 T-GCTATTACACCTCTATTCCATTACA
44291278 CCTTTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 22 0.38
40 5 0.09
42 6 0.10
44 3 0.05
45 22 0.38
ACGTcount: A:0.36, C:0.29, G:0.04, T:0.31
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCATTACAACCAAAAACAATAT
Found at i:44291279 original size:16 final size:16
Alignment explanation
Indices: 44291258--44291293 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
44291248 AATTGGCTAT
44291258 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
44291274 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
44291290 TACA
1 TACA
44291294 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:44292324 original size:18 final size:18
Alignment explanation
Indices: 44292298--44292335 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
44292288 AAATAATTTT
*
44292298 AATATTAAATAATTAATG
1 AATAGTAAATAATTAATG
44292316 AATAGTAAATAATTAATG
1 AATAGTAAATAATTAATG
44292334 AA
1 AA
44292336 AAACATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (18 bp):
AATAGTAAATAATTAATG
Found at i:44296065 original size:5 final size:5
Alignment explanation
Indices: 44296057--44296085 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
44296047 CATATCATCA
44296057 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
44296086 AGCTGTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:44304967 original size:15 final size:15
Alignment explanation
Indices: 44304947--44304978 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
44304937 CATTTCACTA
*
44304947 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
44304962 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
44304977 TT
1 TT
44304979 TGCATGCATA
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:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:44306109 original size:15 final size:14
Alignment explanation
Indices: 44306081--44306107 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44306071 GAATTTTCTT
44306081 GAAAAATTAATTTG
1 GAAAAATTAATTTG
44306095 GAAAAATTAATTT
1 GAAAAATTAATTT
44306108 TGATCAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
GAAAAATTAATTTG
Found at i:44306746 original size:59 final size:61
Alignment explanation
Indices: 44306632--44306748 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
44306622 AATAATTATA
* * *
44306632 TTAATATTAAATTTAATTTAATGTTTACCTATAAGATAAACATTATATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTACCTAT-AGATAAACATTATATTAATTTAATAAGAT
* * *
44306694 TTAATATTAAATTTAATCTGATATTTATCT-T-GATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTACCTATAGATAAACATTATATTAATTTAATA
44306749 TTAAAGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 22 0.45
61 1 0.02
62 26 0.53
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (61 bp):
TTAATATTAAATTTAATCTAATATTTACCTATAGATAAACATTATATTAATTTAATAAGAT
Found at i:44308956 original size:22 final size:21
Alignment explanation
Indices: 44308907--44308960 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
44308897 ACTAATAATT
* *
44308907 TTTTTTCATTTTTTAAAAATTA
1 TTTTTT-ATTTTTAAAAAATCA
*
44308929 TCTTTTATTTTTAAAAAATACA
1 TTTTTTATTTTTAAAAAAT-CA
44308951 TTTTTTATTT
1 TTTTTTATTT
44308961 CTCAAGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTTATTTTTAAAAAATCA
Found at i:44311542 original size:2 final size:2
Alignment explanation
Indices: 44311535--44311565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44311525 TCGCAAATCA
44311535 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
44311566 TGACGATGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44317336 original size:12 final size:12
Alignment explanation
Indices: 44317319--44317349 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
44317309 ATAATTTCTT
44317319 TTTTATTTTAAA
1 TTTTATTTTAAA
44317331 TTTTATTTTAAA
1 TTTTATTTTAAA
*
44317343 ATTTATT
1 TTTTATT
44317350 ATTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATTTTAAA
Found at i:44317344 original size:13 final size:13
Alignment explanation
Indices: 44317319--44317360 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 13
44317309 ATAATTTCTT
44317319 TTTTATTTT-AAA
1 TTTTATTTTAAAA
44317331 TTTTATTTTAAAA
1 TTTTATTTTAAAA
*
44317344 TTTATTATTATAAAA
1 -TT-TTATTTTAAAA
44317359 TT
1 TT
44317361 GGTTAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 9 0.35
13 3 0.12
14 4 0.15
15 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTATTTTAAAA
Found at i:44328035 original size:45 final size:44
Alignment explanation
Indices: 44327969--44328123 Score: 211
Period size: 45 Copynumber: 3.4 Consensus size: 44
44327959 AGTATACAGT
* * *
44327969 AATCAGTAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
* * *
44328014 AATCTGTAACAGTAACGGTAACGGTATTCGACACACAAAGTGCCG
1 AATC-GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
44328059 AATCGATAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
1 AATCG-TAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
*
44328104 AATCAGTAATAGTAACAGTA
1 AATC-GTAACAGTAACAGTA
44328124 GTCGGCACAT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
44 1 0.01
45 95 0.98
46 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (44 bp):
AATCGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCTG
Found at i:44328111 original size:39 final size:40
Alignment explanation
Indices: 44327984--44328150 Score: 144
Period size: 45 Copynumber: 4.0 Consensus size: 40
44327974 GTAACGGTAG
* *
44327984 CAGTAACAGTATTCAACACACAAAGTG-CTGAATCTGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCTGAATCAGTAA
*
44328023 CAGTAACGGTAACGGTATTCGACACACAAAGTGCCGAATCGATAACAGTAA
1 CAGTAAC----A--GTATTCGACACACAAAGTGCC---T-GA-ATCAGTAA
44328074 CAGTAACAGTATTCGACACACAAAGTG-CTGAATCAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCTGAATCAGTAA
* * * *
44328113 TAGTAACAGTAGTCGGCACA-TAAGTGCCT-AATCAGTAA
1 CAGTAACAGTATTCGACACACAAAGTGCCTGAATCAGTAA
44328151 GCCGGCAAAT
Statistics
Matches: 107, Mismatches: 8, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
38 14 0.13
39 33 0.31
40 2 0.02
41 1 0.01
43 1 0.01
44 1 0.01
45 37 0.35
46 1 0.01
47 1 0.01
49 1 0.01
50 2 0.02
51 13 0.12
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (40 bp):
CAGTAACAGTATTCGACACACAAAGTGCCTGAATCAGTAA
Found at i:44329662 original size:18 final size:18
Alignment explanation
Indices: 44329641--44329677 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
44329631 AAAGGAAGAC
44329641 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
44329659 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
44329677 A
1 A
44329678 AGAGCAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:44331484 original size:33 final size:35
Alignment explanation
Indices: 44331447--44331518 Score: 114
Period size: 33 Copynumber: 2.1 Consensus size: 35
44331437 GAGTTAGTTT
44331447 ATTAAATTTT-GTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
*
44331480 ATT-AATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
44331514 ATTAA
1 ATTAA
44331519 TTTGTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 6 0.17
33 24 0.69
34 4 0.11
35 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.42
Consensus pattern (35 bp):
ATTAAATTTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:44342745 original size:41 final size:42
Alignment explanation
Indices: 44342650--44342765 Score: 155
Period size: 41 Copynumber: 2.8 Consensus size: 42
44342640 AGCCCGTACA
* * *
44342650 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCTAGACAG-GGTCTTACATG-AATCAAATATCG
*
44342693 ATGCCACTGTCCTAGACAGGGTCTTACATGAATCAAATA-CG
1 ATGCCAATGTCCTAGACAGGGTCTTACATGAATCAAATATCG
*
44342734 ATGCCAATGTCCTAGACATGGTCTTACATGAA
1 ATGCCAATGTCCTAGACAGGGTCTTACATGAA
44342766 AACACATATC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.48
42 8 0.12
43 25 0.38
44 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCTAGACAGGGTCTTACATGAATCAAATATCG
Found at i:44343712 original size:15 final size:14
Alignment explanation
Indices: 44343675--44343718 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
44343665 TTTTATTATA
44343675 ATAACTTTATAATAT
1 ATAACTTTATAAT-T
*
44343690 ATAA-TTTATTATT
1 ATAACTTTATAATT
44343703 ATAACCTTTATAATT
1 ATAA-CTTTATAATT
44343718 A
1 A
44343719 ATATAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 13 0.52
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAACTTTATAATT
Found at i:44357993 original size:40 final size:40
Alignment explanation
Indices: 44357897--44358014 Score: 116
Period size: 40 Copynumber: 3.0 Consensus size: 40
44357887 AGATGCATAA
* *
44357897 CAGAGGCATCGAAGTGCGAACAGAGGCA-CGAATGTGCAGG
1 CAGAGGCATCGAAGTGCGAATAGAGACACCGAA-GTGCAGG
* * * * *
44357937 TAGAGGCA-CCATAGTGCGATTAGAGACACCGAAGTGTATG
1 CAGAGGCATCGA-AGTGCGAATAGAGACACCGAAGTGCAGG
*
44357977 CAGAGGCATCGAAGTGCAAATAGAGGA-ACCGAAGTGCA
1 CAGAGGCATCGAAGTGCGAATAGA-GACACCGAAGTGCA
44358015 AACCCGTACA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
39 2 0.03
40 52 0.84
41 8 0.13
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.14
Consensus pattern (40 bp):
CAGAGGCATCGAAGTGCGAATAGAGACACCGAAGTGCAGG
Found at i:44358001 original size:20 final size:19
Alignment explanation
Indices: 44357898--44358016 Score: 67
Period size: 20 Copynumber: 5.9 Consensus size: 19
44357888 GATGCATAAC
* *
44357898 AGAGGCATCGAAGTGCGAAC
1 AGAGGCA-CGAAGTGCAAAT
**
44357918 AGAGGCACGAATGTGCAGGT
1 AGAGGCACGAA-GTGCAAAT
* * *
44357938 AGAGGCACCATAGTGCGATT
1 AGAGGCACGA-AGTGCAAAT
* * ***
44357958 AGAGACACCGAAGTGTATGC
1 AGAGGCA-CGAAGTGCAAAT
44357978 AGAGGCATCGAAGTGCAAAT
1 AGAGGCA-CGAAGTGCAAAT
*
44357998 AGAGGAACCGAAGTGCAAA
1 AGAGGCA-CGAAGTGCAAA
44358017 CCCGTACAAG
Statistics
Matches: 73, Mismatches: 23, Indels: 6
0.72 0.23 0.06
Matches are distributed among these distances:
19 4 0.05
20 66 0.90
21 3 0.04
ACGTcount: A:0.36, C:0.18, G:0.33, T:0.13
Consensus pattern (19 bp):
AGAGGCACGAAGTGCAAAT
Found at i:44369575 original size:23 final size:21
Alignment explanation
Indices: 44369534--44369575 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
44369524 TCAAACACTA
44369534 TTATAATTATGGTAATTATAT
1 TTATAATTATGGTAATTATAT
*
44369555 TTATAATATTTGGTTAATTAT
1 TTATAAT-TATGG-TAATTAT
44369576 TAAAATATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TTATAATTATGGTAATTATAT
Found at i:44372326 original size:43 final size:43
Alignment explanation
Indices: 44372224--44372340 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
44372214 TGTCATGGAG
* * *
44372224 TCTTTCATCCATGGTCTTACTCATTATACTTGGTTACCATAGCA
1 TCTTTCATCCATGGTCTTACTCCTTATAC-CGGGTACCATAGCA
** *
44372268 TCACTCATCTATGGTCTTACTCCTTATACCGGGTAGCCAT-GCA
1 TCTTTCATCCATGGTCTTACTCCTTATACCGGGTA-CCATAGCA
* *
44372311 TCTTTCATCCATGGTCTTACGCCATATACC
1 TCTTTCATCCATGGTCTTACTCCTTATACC
44372341 TTTACCTTGT
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 32 0.52
44 29 0.48
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.37
Consensus pattern (43 bp):
TCTTTCATCCATGGTCTTACTCCTTATACCGGGTACCATAGCA
Done.