Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, 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: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 3 of 18
Found at i:1469864 original size:57 final size:58
Alignment explanation
Indices: 1469776--1469928 Score: 209
Period size: 58 Copynumber: 2.7 Consensus size: 58
1469766 TAGATGTATG
* * **
1469776 CTCATGTTGTTGCCTTGTGGCTTGCTTATCATTTTCTTGTCTT-GCTTAAGCTAGTTA
1 CTCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTCTTAGCACAAGCTAGTTA
* * * * *
1469833 CTCATGTTGTTCCCTTATGGCTTACTCATCATTTTCTTGTTTTAGCACGAGCTAGTTG
1 CTCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTCTTAGCACAAGCTAGTTA
*
1469891 TTCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTT
1 CTCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTT
1469929 ATCCAGCTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
57 38 0.46
58 45 0.54
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (58 bp):
CTCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTCTTAGCACAAGCTAGTTA
Found at i:1469912 original size:58 final size:58
Alignment explanation
Indices: 1469777--1469958 Score: 224
Period size: 57 Copynumber: 3.2 Consensus size: 58
1469767 AGATGTATGC
* * * ** **
1469777 TCATGTTGTTGCCTTGTGGCTTGCTTATCATTTTCTTGTCTT-GCTTAAGCTAGTTAC
1 TCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTTTTAGCTCGAGCTAGTTGT
* * *
1469834 TCATGTTGTTCCCTTATGGCTTACTCATCATTTTCTTGTTTTAGCACGAGCTAGTTGT
1 TCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTTTTAGCTCGAGCTAGTTGT
* ** *
1469892 TCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTT-ATCCAGCTCGAGCTTGTTGT
1 TCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTTTTAGCTCGAGCTAGTTGT
1469949 TCATGTTGTT
1 TCATGTTGTT
1469959 ACCCTATGAC
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 62 0.58
58 45 0.42
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (58 bp):
TCATGTTGTTGCCTTGTGGCTTACTCATCATTTTCTTGTTTTAGCTCGAGCTAGTTGT
Found at i:1472589 original size:190 final size:186
Alignment explanation
Indices: 1472393--1472819 Score: 459
Period size: 186 Copynumber: 2.3 Consensus size: 186
1472383 ACTATTTTTT
** * * * *
1472393 AGGTTTTCTTCAGTTTTTTCCTTATTAGATTCTTTTCCTGGTGTTGAATCACCATTATTTGCCAC
1 AGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAATCACCAGTATCTGCCA-
* * *
1472458 TTTGGT-TATCTGTCGAGCACCATCACTTTCTAGGTTTTCTTCAAGCT-TGTCCTTATCAGATTC
65 TTT--TAAAT-TGTCAAGCACCATCACTTTCTAGGTTTCCTTCAA-CTCTGTCCTTATCAGATTC
* * * * *
1472521 GTTTACCGGATGTTGAATCACCAGTATTTGCCATTTTGGTCTATTGAGCATCGCCACATTCC
126 -TTTACCCGACGTTAAATCACCAATATTCGCCATTTTGGTCTATTGAGCATCGCCACATTCC
1472583 AGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAATCACCAGTATCTGCCAT
1 AGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAATCACCAGTATCTGCCAT
* * * * *
1472648 TTTAAATTGTCAAGCACCATCCCTTTCTAGGTTTCCTTTAACTCTTTCCTTATTAGATTCTTTTC
66 TTTAAATTGTCAAGCACCATCACTTTCTAGGTTTCCTTCAACTCTGTCCTTATCAGATTCTTTAC
* * * * * * *
1472713 CCTACGTTAAATCACCAATATTCGCCA-TTTGAGTTTATTCAGCACCATCC-CTTTTC
131 CCGACGTTAAATCACCAATATTCGCCATTTTG-GTCTATTGAGCATC-GCCACATTCC
* * * * * *
1472769 TGGTTTTCTTCAGCTTGTCCCCTAT-AAATTCTTTTCTTGGTGTTGAATCAC
1 AGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAATCAC
1472820 TAATATCCAC
Statistics
Matches: 201, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
185 28 0.14
186 63 0.31
187 47 0.23
188 2 0.01
189 3 0.01
190 58 0.29
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (186 bp):
AGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAATCACCAGTATCTGCCAT
TTTAAATTGTCAAGCACCATCACTTTCTAGGTTTCCTTCAACTCTGTCCTTATCAGATTCTTTAC
CCGACGTTAAATCACCAATATTCGCCATTTTGGTCTATTGAGCATCGCCACATTCC
Found at i:1472680 original size:93 final size:93
Alignment explanation
Indices: 1472191--1472826 Score: 366
Period size: 93 Copynumber: 6.8 Consensus size: 93
1472181 TGGGTTGTGG
* * * * * * * * * *
1472191 AGCACCATCACTCTCTGGGTTTTGTTTAGCTTTTCCCTTATCTGATCCTTTTAGC-AGTGTTGAA
1 AGCACCATCCCTTTCTAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTT-CCTGGTGTTGAA
* * * ** *
1472255 TCACTAGTATCTACCATTTTGGGCTATCGA
65 TCACCAATATCTGCCATTTTGATCTGTC-A
* * * * * * *
1472285 A-CACCATCACTTTTTGGGATTTT-TTGAGCTTTTCCCTTATCAAATTCTTTTCCTAGTGTTGAA
1 AGCACCATCCCTTTCTAGG-TTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAA
* * * * * **
1472348 TTACAAACATCTACCATTTTGGTAGGTCA
65 TCACCAATATCTGCCATTTTGATCTGTCA
* ** * ** * *
1472377 AGCATCA-CTATTTTTTAGGTTTTCTTCAGTTTTTTCCTTATTAGATTCTTTTCCTGGTGTTGAA
1 AGCACCATC-CCTTTCTAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAA
* * * *
1472441 TCACCATTATTTGCCACTTTGGTTATCTGTCG
65 TCACCAATATCTGCCA-TTT--TGATCTGTCA
* * *
1472473 AGCACCATCACTTTCTAGGTTTTCTTCAAGCTTGT-CCTTATCAGATTCGTTTACC-GGATGTTG
1 AGCACCATCCCTTTCTAGGTTTTCTTCAA-CTTTTCCCTTATCAGATTC-TTTTCCTGG-TGTTG
* * * * **
1472536 AATCACCAGTATTTGCCATTTTGGTCTATTG
63 AATCACCAATATCTGCCATTTTGATCTGTCA
* * * *
1472567 AGCATC-GCCACATTCCAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAA
1 AGCACCATCC-CTTTCTAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAA
* *
1472631 TCACCAGTATCTGCCATTTTAAAT-TGTCA
65 TCACCAATATCTGCCATTTT-GATCTGTCA
* * * ** *
1472660 AGCACCATCCCTTTCTAGGTTTCCTTTAACTCTTT-CCTTATTAGATTCTTTTCCCT-ACGTTAA
1 AGCACCATCCCTTTCTAGGTTTTCTTCAACT-TTTCCCTTATCAGATTCTTTT-CCTGGTGTTGA
* *
1472723 ATCACCAATAT-TCGCCA-TTTGAGTTTATTC-
64 ATCACCAATATCT-GCCATTTTGA-TCT-GTCA
* * * * *
1472753 AGCACCATCCCTTTTCT-GGTTTTCTTCAGCTTGTCCCCTAT-AAATTCTTTTCTTGGTGTTGAA
1 AGCACCATCCC-TTTCTAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAA
*
1472816 TCACTAATATC
65 TCACCAATATC
1472827 CACCATTTCA
Statistics
Matches: 430, Mismatches: 85, Indels: 55
0.75 0.15 0.10
Matches are distributed among these distances:
91 3 0.01
92 38 0.09
93 246 0.57
94 67 0.16
96 45 0.10
97 31 0.07
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (93 bp):
AGCACCATCCCTTTCTAGGTTTTCTTCAACTTTTCCCTTATCAGATTCTTTTCCTGGTGTTGAAT
CACCAATATCTGCCATTTTGATCTGTCA
Found at i:1476691 original size:2 final size:2
Alignment explanation
Indices: 1476684--1476716 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1476674 TTTGAAGCCT
1476684 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1476717 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1477202 original size:2 final size:2
Alignment explanation
Indices: 1477195--1477220 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1477185 CTTTGAAGCC
1477195 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
1477221 AATACATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1477395 original size:247 final size:240
Alignment explanation
Indices: 1476716--1477429 Score: 873
Period size: 245 Copynumber: 2.9 Consensus size: 240
1476706 ACACACACAC
* * *
1476716 ATATATATATATAAACACATGATGTAACTCTCATTCAAAAAGTTACAA-AAAAAGAAGCTAAAGC
1 ATATATATATATAAACACATGATGTAGCACTCATTCAAAAAGTTACAATAAAAA-AAGCAAAAGC
* * * *
1476780 TAAGTTATTATTTAGATAGCGTGCTCACCTCAGAATGTTCTCCATGTTGACATTGATCATTCTTA
65 TAAGTTATTAATCA-ATAGCATGCTCACCTCAGACTGTTCTCCATGTTGACATTGATCATTCTTA
* *
1476845 GCATCAGTACTAAAAGCCAATGTTACTTTCTCTAGAGGGTTTGCTTGGTCAAACTCAGAACTTAA
129 GCATCAGTACTAAAAGCCAATGTTATTTTCTCTAGA-GGTTTGCTTGGTCAAACTCAGAAC-TGA
* *
1476910 AGCTACTTGCTTCCTTTTTCTCCCACGTTTCTTTGAAGCCTATATATAT
192 AGCTACTTGCTTTCTTTTTCTCCCACGTCTCTTTGAAGCCTATATATAT
* * * *
1476959 ATATATATATATAAACACATGATGTAGCATTCATTCACAAAA-CTACAATAGAGAAA-CAAAAGC
1 ATATATATATATAAACACATGATGTAGCACTCATTCA-AAAAGTTACAATAAAAAAAGCAAAAGC
* * * *
1477022 TAAGTTATTATATCGATTGCATGCTCACCTTAGACTGTTCTCCATGTTGATATTGAATATCATTC
65 TAAGTTATTA-ATCAATAGCATGCTCACCTCAGACTGTTCTCCATGTTGACATTG---ATCATTC
*
1477087 TTAACATCAGTACTAAGAA-CCAATGTTATTTTCTCTAGAGAGTTTGCTTGGTCAAACTCAGAAC
126 TTAGCATCAGTACTAA-AAGCCAATGTTATTTTCTCTAGAG-GTTTGCTTGGTCAAACTCAGAAC
*
1477151 ATGAAGC-ACCTTGCTTTCTCTTTCTCCCACGTCTCTTTGAAGCCTATATATATATAT
189 -TGAAGCTA-CTTGCTTTCTTTTTCTCCCACGTCTCTTTGAAGCC----TATATATAT
* * * * *
1477208 ATATATATATATAAATACATGATGTAGCACGCATTTAGAAAGTTACAATAAAAAAAGCCAAAGCT
1 ATATATATATATAAACACATGATGTAGCACTCATTCAAAAAGTTACAATAAAAAAAGCAAAAGCT
* *
1477273 AAGTTATTACATCAATAACATGCTCACCTCAGACTGCTCTCTC-TGTTGACATTGATCATTCTTA
66 AAGTTATTA-ATCAATAGCATGCTCACCTCAGACTGTTCTC-CATGTTGACATTGATCATTCTTA
* * * * ** *
1477337 GCATCAGTATTAATAGCTAATATTATTTTCTCCGGACGGTTTACTTGGTCAAACTCAGAACTCGA
129 GCATCAGTACTAAAAGCCAATGTTATTTTCTCTAGA-GGTTTGCTTGGTCAAACTCAGAACT-GA
*
1477402 TGCTACTTGCTTTCTTTTTCTCCCACGT
192 AGCTACTTGCTTTCTTTTTCTCCCACGT
1477430 TTGTTTTTCA
Statistics
Matches: 403, Mismatches: 48, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
242 51 0.13
243 42 0.10
244 9 0.02
245 101 0.25
246 4 0.01
247 85 0.21
248 5 0.01
249 53 0.13
250 52 0.13
251 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (240 bp):
ATATATATATATAAACACATGATGTAGCACTCATTCAAAAAGTTACAATAAAAAAAGCAAAAGCT
AAGTTATTAATCAATAGCATGCTCACCTCAGACTGTTCTCCATGTTGACATTGATCATTCTTAGC
ATCAGTACTAAAAGCCAATGTTATTTTCTCTAGAGGTTTGCTTGGTCAAACTCAGAACTGAAGCT
ACTTGCTTTCTTTTTCTCCCACGTCTCTTTGAAGCCTATATATAT
Found at i:1477962 original size:57 final size:57
Alignment explanation
Indices: 1477874--1478120 Score: 291
Period size: 57 Copynumber: 4.3 Consensus size: 57
1477864 TGTGCTTATC
* * * *
1477874 TTGTTGCCTTATGGCTTGCTCATCATTTTCTTGACCAGCAAAAGCTAGTTGCTCATG
1 TTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAACAAGAGCTAGTTGCTCATG
* * ** *
1477931 TTGTT-CTTTTGTGGTTTGCTCATCATTTTCTTGTCCAACTTGAGTTAGTTGCTCATG
1 TTGTTGC-CTTGTGGCTTGCTCATCATTTTCTTGTCCAACAAGAGCTAGTTGCTCATG
* * * *
1477988 TTGTTGCCTTGTGACTTGCTCATCATTTTCTTGTCCAGCATGAGCTTGTTGCTCATG
1 TTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAACAAGAGCTAGTTGCTCATG
* * * *
1478045 TTGTTGCCTTATGGCTTGCTCATTC-TTTTCTTTTCCAACTAGAGCTAGTTGTTCATG
1 TTGTTGCCTTGTGGCTTGCTCA-TCATTTTCTTGTCCAACAAGAGCTAGTTGCTCATG
* *
1478102 TTGTTGCCCTGTGACTTGC
1 TTGTTGCCTTGTGGCTTGC
1478121 AGGTGCCTAA
Statistics
Matches: 160, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
56 1 0.01
57 156 0.98
58 3 0.02
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (57 bp):
TTGTTGCCTTGTGGCTTGCTCATCATTTTCTTGTCCAACAAGAGCTAGTTGCTCATG
Found at i:1478074 original size:114 final size:114
Alignment explanation
Indices: 1477874--1478120 Score: 336
Period size: 114 Copynumber: 2.2 Consensus size: 114
1477864 TGTGCTTATC
* * *
1477874 TTGTTGCCTTATGGCTTGCTCATCATTTTCTTGACCAGCAAAAGCTAGTTGCTCATGTTGTTCTT
1 TTGTTGCCTTGTGACTTGCTCATCATTTTCTTGACCAGCAAAAGCTAGTTGCTCATGTTGTTCTC
* * * *
1477939 TTGTGGTTTGCTCATCATTTTCTTGTCCAACTTGAGTTAGTTGCTCATG
66 TTATGGCTTGCTCATCATTTTCTTGTCCAACTAGAGCTAGTTGCTCATG
* ** *
1477988 TTGTTGCCTTGTGACTTGCTCATCATTTTCTTGTCCAGCATGAGCTTGTTGCTCATGTTGTTGC-
1 TTGTTGCCTTGTGACTTGCTCATCATTTTCTTGACCAGCAAAAGCTAGTTGCTCATGTTGTT-CT
* *
1478052 CTTATGGCTTGCTCATTC-TTTTCTTTTCCAACTAGAGCTAGTTGTTCATG
65 CTTATGGCTTGCTCA-TCATTTTCTTGTCCAACTAGAGCTAGTTGCTCATG
*
1478102 TTGTTGCCCTGTGACTTGC
1 TTGTTGCCTTGTGACTTGC
1478121 AGGTGCCTAA
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
114 114 0.97
115 3 0.03
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (114 bp):
TTGTTGCCTTGTGACTTGCTCATCATTTTCTTGACCAGCAAAAGCTAGTTGCTCATGTTGTTCTC
TTATGGCTTGCTCATCATTTTCTTGTCCAACTAGAGCTAGTTGCTCATG
Found at i:1480153 original size:22 final size:22
Alignment explanation
Indices: 1480128--1480170 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1480118 TGCATACTTC
1480128 TCAAAATCAGATAATAACTTTA
1 TCAAAATCAGATAATAACTTTA
* *
1480150 TCAAGATCAGATAATAGCTTT
1 TCAAAATCAGATAATAACTTT
1480171 TATTACGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (22 bp):
TCAAAATCAGATAATAACTTTA
Found at i:1481204 original size:93 final size:92
Alignment explanation
Indices: 1481035--1481487 Score: 437
Period size: 93 Copynumber: 4.8 Consensus size: 92
1481025 TTGGTTTCAT
* * * *
1481035 CCATTTTGGACTGTTGAGGACCATCACTTT-TCGGGTTTTCTAT-AGCTTTTCCCTTATCAGATT
1 CCATTTTGGGCTGTTGAGCACCATCACTTTCT-AGGTTTTCT-TCAGCTTTTTCCTTATCAGA-T
* * **
1481098 CTTTT-CGAGGTGTTGAATCACTAGTATCTG
63 CTTTTCCTA-GTGTTGAATCACCAGTATCCA
* * * * *
1481128 TCACTTTGGGCTGTCGAGAACCATCACTTTCTAGGTTTTCTTTAGCTTTTTCCTTATCAGATCCT
1 CCATTTTGGGCTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGAT-CT
1481193 TTTCCTAGTGTTGAATCACCAGTATCCA
65 TTTCCTAGTGTTGAATCACCAGTATCCA
* * *
1481221 CCATTTTGGTGATCTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCCTTGTCCTTATCAAAA
1 CCATTTTGG-G--CTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATC-AGA
* *
1481286 TCTTGTACC-AGTGTTGAATCTCCAGTATCCA
62 TCTT-TTCCTAGTGTTGAATCACCAGTATCCA
* * * * * * * * *
1481317 CCATTTTGGTCTGTCGAGCATCACCGCTTTCTTGGTTTTCTTCAACTTTTCCCTTATCAGATTTT
1 CCATTTTGGGCTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATCTT
* *
1481382 TTTCTTGATGTTGAATCACCAGTATCCA
66 TTCCTAG-TGTTGAATCACCAGTATCCA
* * * * * * *
1481410 CCATTTTGGTCTGTTGAGCACCATCCCTTTCCAAGTTTCCTTCATCTTTTTGCTTATCAGATTCT
1 CCATTTTGGGCTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGA-TCT
*
1481475 TTTCGTAGTGTTG
65 TTTCCTAGTGTTG
1481488 GGCGATCGAT
Statistics
Matches: 296, Mismatches: 52, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
91 2 0.01
92 8 0.03
93 193 0.65
94 11 0.04
96 76 0.26
97 6 0.02
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (92 bp):
CCATTTTGGGCTGTTGAGCACCATCACTTTCTAGGTTTTCTTCAGCTTTTTCCTTATCAGATCTT
TTCCTAGTGTTGAATCACCAGTATCCA
Found at i:1492633 original size:6 final size:6
Alignment explanation
Indices: 1492622--1492654 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1492612 GCATGATGTA
*
1492622 TGTGGG TGTGGG TGTGGG TGTGGG CGTGGG TGT
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGT
1492655 CATCTTTGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.64, T:0.33
Consensus pattern (6 bp):
TGTGGG
Found at i:1497423 original size:21 final size:20
Alignment explanation
Indices: 1497399--1497440 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1497389 GGTGAACAAT
* *
1497399 ATCATATTATCATGTTATTAA
1 ATCACATTATCAT-TTACTAA
1497420 ATCACATTATCATTTACTAA
1 ATCACATTATCATTTACTAA
1497440 A
1 A
1497441 ACACCAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (20 bp):
ATCACATTATCATTTACTAA
Found at i:1502059 original size:16 final size:17
Alignment explanation
Indices: 1502027--1502062 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1502017 ATTCTAGGGT
1502027 TTAAAACCCCAAAAAAA
1 TTAAAACCCCAAAAAAA
1502044 TTAAAA-CCCAATAAAAA
1 TTAAAACCCCAA-AAAAA
1502061 TT
1 TT
1502063 TCACAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (17 bp):
TTAAAACCCCAAAAAAA
Found at i:1511515 original size:13 final size:14
Alignment explanation
Indices: 1511489--1511517 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1511479 CCTTTTATGA
1511489 ATTAATTATAATTT
1 ATTAATTATAATTT
1511503 ATTAATT-TAATTT
1 ATTAATTATAATTT
1511516 AT
1 AT
1511518 ATTTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTAATTATAATTT
Found at i:1521291 original size:6 final size:6
Alignment explanation
Indices: 1521282--1521306 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1521272 GTAAACAAAA
1521282 AAAACC AAAACC AAAACC AAAACC A
1 AAAACC AAAACC AAAACC AAAACC A
1521307 GTTGGGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:1532936 original size:29 final size:29
Alignment explanation
Indices: 1532844--1532937 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
1532834 ATTTGAAACT
*
1532844 TTTAATAAATAACATAA--TCTTAGAAAAA
1 TTTAATAAATAACATAACTTC-TAAAAAAA
* **
1532872 TTTAATCAAATAATCAATATCGATTC--AAAACT
1 TTTAAT-AAATAA-C-ATAAC--TTCTAAAAAAA
1532904 TTTAATAAATAACATAACTTCTAAAAAAA
1 TTTAATAAATAACATAACTTCTAAAAAAA
1532933 TTTAA
1 TTTAA
1532938 CTTTTGAACC
Statistics
Matches: 50, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 19 0.38
30 2 0.04
31 9 0.18
32 9 0.18
35 2 0.04
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTAATAAATAACATAACTTCTAAAAAAA
Found at i:1542317 original size:2 final size:2
Alignment explanation
Indices: 1542310--1542341 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1542300 TTTACATGAA
1542310 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1542342 GGTAGTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1549226 original size:3 final size:3
Alignment explanation
Indices: 1549212--1549252 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
1549202 TCCAAAGAAA
* * *
1549212 AAC AAT AAC AAC AAC AAC AAC AAC AAC CAC AAC CAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1549253 TGTAGAGAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.34, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:1550108 original size:14 final size:16
Alignment explanation
Indices: 1550085--1550118 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1550075 AGAATTTAAT
1550085 TTTTAGAATTT-TTTA
1 TTTTAGAATTTATTTA
1550100 TTTTA-AATTTATTTA
1 TTTTAGAATTTATTTA
1550115 TTTT
1 TTTT
1550119 TTAACGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTAGAATTTATTTA
Found at i:1563653 original size:28 final size:27
Alignment explanation
Indices: 1563608--1563664 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1563598 TATAAGGATT
1563608 TTTTAAATAAAAAAATATGATATTA-AA
1 TTTTAAATAAAAAAATATGAT-TTATAA
* *
1563635 TTTTAATATTAAAATATATGATTTATAA
1 TTTTAA-ATAAAAAAATATGATTTATAA
1563663 TT
1 TT
1563665 AGATTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTTAAATAAAAAAATATGATTTATAA
Found at i:1563983 original size:2 final size:2
Alignment explanation
Indices: 1563976--1564003 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1563966 GCAAGAATGA
1563976 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
1564004 CATTAAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1571860 original size:2 final size:2
Alignment explanation
Indices: 1571853--1571881 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1571843 TTGTGAGTGA
1571853 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1571882 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:1574335 original size:2 final size:2
Alignment explanation
Indices: 1574330--1574357 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1574320 GCTCTCTTGC
1574330 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
1574358 TTTGCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1577358 original size:14 final size:14
Alignment explanation
Indices: 1577339--1577378 Score: 59
Period size: 12 Copynumber: 3.1 Consensus size: 14
1577329 GGAAGGCCAT
1577339 TTATATATACTATA
1 TTATATATACTATA
1577353 TTATATAT-CTAT-
1 TTATATATACTATA
1577365 TTATATATA-TATA
1 TTATATATACTATA
1577378 T
1 T
1577379 AATTAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.46
13 5 0.21
14 8 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATATACTATA
Found at i:1587491 original size:15 final size:15
Alignment explanation
Indices: 1587471--1587499 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1587461 TATATATATT
1587471 GTTAATAAAAAATAG
1 GTTAATAAAAAATAG
1587486 GTTAATAAAAAATA
1 GTTAATAAAAAATA
1587500 AATTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
GTTAATAAAAAATAG
Found at i:1587505 original size:15 final size:15
Alignment explanation
Indices: 1587472--1587505 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1587462 ATATATATTG
**
1587472 TTAATAAAAAATAGG
1 TTAATAAAAAATAAA
1587487 TTAATAAAAAATAAA
1 TTAATAAAAAATAAA
1587502 TTAA
1 TTAA
1587506 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
TTAATAAAAAATAAA
Found at i:1597104 original size:3 final size:3
Alignment explanation
Indices: 1597089--1597126 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
1597079 GTGATTGATT
1597089 TGA TGA T-A GTGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA -TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1597127 GTGTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:1604780 original size:29 final size:29
Alignment explanation
Indices: 1604748--1604832 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
1604738 TTAATTAATT
1604748 ATAAATTATAAAAATTTATTAAATTTAAA
1 ATAAATTATAAAAATTTATTAAATTTAAA
* ** *
1604777 ATAAAAATATAAAAATTTTATTAAACATAAT
1 AT-AAATTATAAAAA-TTTATTAAATTTAAA
*
1604808 A-AAATAATAAAAATTTATTTAAATT
1 ATAAATTATAAAAATTTA-TTAAATT
1604833 GTTTTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.09
29 17 0.38
30 11 0.24
31 13 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
ATAAATTATAAAAATTTATTAAATTTAAA
Found at i:1606616 original size:23 final size:22
Alignment explanation
Indices: 1606588--1606633 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
1606578 GTTTGTTACT
*
1606588 AAATTAAAAATATTATAATAATA
1 AAATTAAAAATATTA-AAAAATA
* *
1606611 AAATTACACATATTAAAAAATA
1 AAATTAAAAATATTAAAAAATA
1606633 A
1 A
1606634 TAAATTTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
AAATTAAAAATATTAAAAAATA
Found at i:1630546 original size:29 final size:29
Alignment explanation
Indices: 1630487--1630571 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
1630477 AATTTTTTAA
* * * *
1630487 TTATTAAAAAATATTTAAATTTTTTTGTTT
1 TTATTATAAATTAATTAAATTTTTAT-TTT
*
1630517 TTATTAT-ATTTAATTAAA-TTTTATATTT
1 TTATTATAAATTAATTAAATTTTTAT-TTT
* *
1630545 TTATTTTAAATTAAATAAATTTTTATT
1 TTATTATAAATTAATTAAATTTTTATT
1630572 AGTAATGACC
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 14 0.32
29 18 0.41
30 12 0.27
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
TTATTATAAATTAATTAAATTTTTATTTT
Found at i:1630571 original size:28 final size:27
Alignment explanation
Indices: 1630508--1630571 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
1630498 TATTTAAATT
* * *
1630508 TTTTTGTTTTTATTATATTTAATTAAA
1 TTTTTATTTTTATTATAATTAAATAAA
*
1630535 TTTTATATTTTTATTTTAAATTAAATAAA
1 TTTT-TATTTTTATTAT-AATTAAATAAA
1630564 TTTTTATT
1 TTTTTATT
1630572 AGTAATGACC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 14 0.45
29 13 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTTATTTTTATTATAATTAAATAAA
Found at i:1630853 original size:30 final size:31
Alignment explanation
Indices: 1630793--1630863 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
1630783 AATAATAAGA
*
1630793 ATTTATTTGATTCAAAATAAAAAGTATAAAG
1 ATTTATTTAATTCAAAATAAAAAGTATAAAG
1630824 ATTTATTTAACTT-AAAATAAAAA-TATAAAG
1 ATTTATTTAA-TTCAAAATAAAAAGTATAAAG
1630854 ATTTATTTAA
1 ATTTATTTAA
1630864 ATTTTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 17 0.45
31 19 0.50
32 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (31 bp):
ATTTATTTAATTCAAAATAAAAAGTATAAAG
Found at i:1635100 original size:23 final size:23
Alignment explanation
Indices: 1635066--1635119 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1635056 AATAAGTCAG
*
1635066 TAATTTTTTACAAAAAATTTCAA
1 TAATTTTCTACAAAAAATTTCAA
1635089 TAATTTTCTACAAAAAATTTCAA
1 TAATTTTCTACAAAAAATTTCAA
1635112 TAATTTTC
1 TAATTTTC
1635120 ATTGATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATTTTCTACAAAAAATTTCAA
Found at i:1637003 original size:34 final size:33
Alignment explanation
Indices: 1636960--1637031 Score: 117
Period size: 34 Copynumber: 2.2 Consensus size: 33
1636950 TATTGTTCAG
*
1636960 CGGTTTCCGATGACGAACTCAAGGCACCAGGAGA
1 CGGTTTCCGATGACGAACTCAAGGCA-CAAGAGA
*
1636994 CGGTTTCCGATGCCGAACTCAAGGCACAAGAGA
1 CGGTTTCCGATGACGAACTCAAGGCACAAGAGA
1637027 CGGTT
1 CGGTT
1637032 AATCGAGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 11 0.31
34 25 0.69
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (33 bp):
CGGTTTCCGATGACGAACTCAAGGCACAAGAGA
Found at i:1638624 original size:27 final size:27
Alignment explanation
Indices: 1638586--1638638 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1638576 TAACGAATCT
*
1638586 AACCACCATGAGTATTGTGATCAAGCC
1 AACCACCATGAGTATTGTGATAAAGCC
*
1638613 AACCACCATGAGTATTTTGATAAAGC
1 AACCACCATGAGTATTGTGATAAAGC
1638639 TGATAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (27 bp):
AACCACCATGAGTATTGTGATAAAGCC
Found at i:1643133 original size:17 final size:18
Alignment explanation
Indices: 1643111--1643148 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1643101 TTAAATATTG
1643111 TTAGAGAAATGATTA-AA
1 TTAGAGAAATGATTATAA
* *
1643128 TTAGAGTAATTATTATAA
1 TTAGAGAAATGATTATAA
1643146 TTA
1 TTA
1643149 AAAACTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.39
Consensus pattern (18 bp):
TTAGAGAAATGATTATAA
Found at i:1654444 original size:58 final size:58
Alignment explanation
Indices: 1654354--1654522 Score: 248
Period size: 58 Copynumber: 2.9 Consensus size: 58
1654344 CGTTAATTAA
* * ** * *
1654354 TTGTCAATAATAAAAAAATGACTTGTCATTTTATGCACACGTGATCTTCATATGTGAC
1 TTGTCAATAGTTAAAATGTGACTTATTATTTTATGCACACGTGATCTTCATATGTGAC
*
1654412 TTGTCAATAGTTAAAATGTGACTTATTATTTTATGCAAACGTGATCTTCATATGTGAC
1 TTGTCAATAGTTAAAATGTGACTTATTATTTTATGCACACGTGATCTTCATATGTGAC
* * *
1654470 TTGTTAATAGTTAAAATGTGACTTATTATTTTATCCACACGTGATCTTGATAT
1 TTGTCAATAGTTAAAATGTGACTTATTATTTTATGCACACGTGATCTTCATAT
1654523 AACATTGAAA
Statistics
Matches: 100, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 100 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (58 bp):
TTGTCAATAGTTAAAATGTGACTTATTATTTTATGCACACGTGATCTTCATATGTGAC
Found at i:1655265 original size:16 final size:17
Alignment explanation
Indices: 1655239--1655270 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1655229 GTAAACTTTA
1655239 TTTATATTTTTTGTATT
1 TTTATATTTTTTGTATT
1655256 TTTA-ATTTTTTGTAT
1 TTTATATTTTTTGTAT
1655271 GATATTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTATATTTTTTGTATT
Found at i:1657222 original size:29 final size:30
Alignment explanation
Indices: 1657191--1657294 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
1657181 TTAAAAAATT
* **
1657191 TTAAATAAATTTTTATATTTTTATTAT-GT
1 TTAAATAAATTTTTATATTTTTATTTTAAA
*
1657220 TTAATTAAA-TTTTATATTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTTTAAA
* *
1657249 TTAAATAAATATTTGTATTTTTATTTTAAA
1 TTAAATAAATTTTTATATTTTTATTTTAAA
1657279 TTAAATAAATTTTTAT
1 TTAAATAAATTTTTAT
1657295 CGTTAATTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 16 0.25
29 16 0.25
30 32 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
TTAAATAAATTTTTATATTTTTATTTTAAA
Found at i:1657592 original size:28 final size:29
Alignment explanation
Indices: 1657519--1657592 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
1657509 ATCATTTATC
**
1657519 ATAAAAATTTATTTGATTCAAAATAAAAAT
1 ATAAAAATTTATTT-AAACAAAATAAAAAT
* * *
1657549 ATAAAAACTTAATTAAACACAATAAAAA-
1 ATAAAAATTTATTTAAACAAAATAAAAAT
1657577 ATAAAAATTTATTTAA
1 ATAAAAATTTATTTAA
1657593 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 14 0.38
29 11 0.30
30 12 0.32
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (29 bp):
ATAAAAATTTATTTAAACAAAATAAAAAT
Found at i:1659899 original size:64 final size:66
Alignment explanation
Indices: 1659822--1659952 Score: 221
Period size: 67 Copynumber: 2.0 Consensus size: 66
1659812 AAGGTCTACA
*
1659822 ACTTGATTTTGAATGAATAATTTC-TTT-AAGGGTATTATGACTTGATCTTGACCTCAAAGATCT
1 ACTTGATTCTGAATGAATAATTTCTTTTCAAGGGTATTATGACTTGATCTTGACCTCAAAGATCT
1659885 T
66 T
*
1659886 ACTTGATTCTGAATGAATATTTTCTTTTTCAAGGGTATTATGACTTGATCTTGACCTCAAAGATC
1 ACTTGATTCTGAATGAATAATTTC-TTTTCAAGGGTATTATGACTTGATCTTGACCTCAAAGATC
1659951 TT
65 TT
1659953 CATGACTTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
64 22 0.35
66 3 0.05
67 37 0.60
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (66 bp):
ACTTGATTCTGAATGAATAATTTCTTTTCAAGGGTATTATGACTTGATCTTGACCTCAAAGATCT
T
Found at i:1663454 original size:26 final size:27
Alignment explanation
Indices: 1663417--1663468 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1663407 GAAGAATTGA
1663417 GAAATGTGGGTGCTTTTGTTATTCTCG
1 GAAATGTGGGTGCTTTTGTTATTCTCG
*
1663444 GAAA-GTGGGTGCTTTTGTTGTTCTC
1 GAAATGTGGGTGCTTTTGTTATTCTC
1663469 AACTGTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.13, C:0.12, G:0.31, T:0.44
Consensus pattern (27 bp):
GAAATGTGGGTGCTTTTGTTATTCTCG
Found at i:1667947 original size:27 final size:28
Alignment explanation
Indices: 1667912--1667969 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
1667902 TATTAAAAAA
1667912 ATTAATTTAAGTT-AATTTTTAT-TTTTT
1 ATTAATTTAA-TTAAATTTTTATATTTTT
*
1667939 ATTATTTTAATTAAATTTTTATATTTTT
1 ATTAATTTAATTAAATTTTTATATTTTT
1667967 ATT
1 ATT
1667970 TTTAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 2 0.07
27 18 0.64
28 8 0.29
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (28 bp):
ATTAATTTAATTAAATTTTTATATTTTT
Found at i:1667980 original size:26 final size:27
Alignment explanation
Indices: 1667925--1667980 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
1667915 AATTTAAGTT
*
1667925 AATTTTTATTTTTTATTATTTTAATTA
1 AATTTTTATTTTTTATTATTTTAATCA
1667952 AATTTTTATATTTTTA-T-TTTTAATCA
1 AATTTTTAT-TTTTTATTATTTTAATCA
1667978 AAT
1 AAT
1667981 AAGTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.41
27 10 0.37
28 6 0.22
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
AATTTTTATTTTTTATTATTTTAATCA
Found at i:1668946 original size:32 final size:32
Alignment explanation
Indices: 1668873--1668946 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
1668863 TAAAAAATTT
1668873 AATATTTTTTATTGTTTGCATAAACTGTCAAA
1 AATATTTTTTATTGTTTGCATAAACTGTCAAA
* * * * *
1668905 AACATTTTTTATTGTTTGGATGATATTGTGAAA
1 AATATTTTTTATTGTTTGCAT-AAACTGTCAAA
1668938 AATATTTTT
1 AATATTTTT
1668947 CACCATCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 19 0.54
33 16 0.46
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.50
Consensus pattern (32 bp):
AATATTTTTTATTGTTTGCATAAACTGTCAAA
Found at i:1669440 original size:14 final size:14
Alignment explanation
Indices: 1669377--1669440 Score: 58
Period size: 14 Copynumber: 4.4 Consensus size: 14
1669367 TTTAAATATG
1669377 AATATTTTAAGTTA
1 AATATTTTAAGTTA
1669391 AAT-TTTTAAGGTTA
1 AATATTTTAA-GTTA
* ** *
1669405 AATATTAATATTTTTT
1 AATATT-TTA-AGTTA
1669421 AATATTTTAAGTTA
1 AATATTTTAAGTTA
1669435 AATATT
1 AATATT
1669441 AGGGTAAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
13 6 0.16
14 18 0.47
15 4 0.11
16 10 0.26
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
AATATTTTAAGTTA
Found at i:1669606 original size:19 final size:21
Alignment explanation
Indices: 1669582--1669621 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1669572 CTTTTCTATT
1669582 TTATTA-A-TTTAAAAAATTA
1 TTATTATATTTTAAAAAATTA
1669601 TTATTATATTTTAAAAAATTA
1 TTATTATATTTTAAAAAATTA
1669622 AAAAAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTATTATATTTTAAAAAATTA
Found at i:1670488 original size:79 final size:80
Alignment explanation
Indices: 1670357--1670508 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 80
1670347 CAGATTGTCG
*
1670357 GATGGTATGACCAGATTCTTAAGCAGGTAGTATGATCCGATGGCTCATGATG-TTAATTGATGAT
1 GATGGTATGACCAGATTCTTAAGCAGGTAGTATGAACCGATGGCTCATGATGTTTAA-TGATGAT
1670421 CAT-AAAAATCCGTCA
65 CATCAAAAATCCGTCA
* * * * * * * *
1670436 GATGGTGTGACCAGTTTGTTAAGTATGTAGTCTGAACGGATGGCTCCTGATGTTTAATGATGATC
1 GATGGTATGACCAGATTCTTAAGCAGGTAGTATGAACCGATGGCTCATGATGTTTAATGATGATC
1670501 ATCAAAAA
66 ATCAAAAA
1670509 AGTTTCAGCA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
79 53 0.85
80 9 0.15
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (80 bp):
GATGGTATGACCAGATTCTTAAGCAGGTAGTATGAACCGATGGCTCATGATGTTTAATGATGATC
ATCAAAAATCCGTCA
Found at i:1680178 original size:16 final size:16
Alignment explanation
Indices: 1680157--1680187 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1680147 CCATTTTAAA
1680157 AGTATAATACCTCACG
1 AGTATAATACCTCACG
1680173 AGTATAATACCTCAC
1 AGTATAATACCTCAC
1680188 ATGAGTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.10, T:0.26
Consensus pattern (16 bp):
AGTATAATACCTCACG
Found at i:1682625 original size:7 final size:7
Alignment explanation
Indices: 1682613--1682637 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1682603 TAAATTAAAT
1682613 AATTCAA
1 AATTCAA
1682620 AATTCAA
1 AATTCAA
1682627 AATTCAA
1 AATTCAA
1682634 AATT
1 AATT
1682638 TCTCTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTCAA
Found at i:1683775 original size:21 final size:23
Alignment explanation
Indices: 1683749--1683799 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
1683739 ATGTTTTAGT
*
1683749 TTAATTTTAA-TTAAA-AAATAA
1 TTAATTTAAATTTAAATAAATAA
*
1683770 TTAATTTAAATTTAAATTAAATTA
1 TTAATTTAAATTTAAA-TAAATAA
1683794 TTAATT
1 TTAATT
1683800 CGATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 5 0.20
24 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTTAAATTTAAATAAATAA
Found at i:1695622 original size:35 final size:35
Alignment explanation
Indices: 1695569--1695652 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 35
1695559 TTTAAGCTGT
*
1695569 TATTTGA-ATATTTATTTTTAGTTATTTAAATTGA
1 TATTTGATATATTTATTTTTAATTATTTAAATTGA
*
1695603 TATTTGATATATTTATTTTTAATTATTTAAATTTA
1 TATTTGATATATTTATTTTTAATTATTTAAATTGA
* *
1695638 AATTTTAT-TATTTAT
1 TATTTGATATATTTAT
1695653 ATATTTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 14 0.31
35 31 0.69
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (35 bp):
TATTTGATATATTTATTTTTAATTATTTAAATTGA
Found at i:1699879 original size:25 final size:25
Alignment explanation
Indices: 1699803--1699880 Score: 61
Period size: 25 Copynumber: 3.0 Consensus size: 25
1699793 TTATTTAAAA
1699803 AAATTTAAAT-AACTTTTTATTCTTATATT
1 AAATTTAAATAAAC-TTTTA---TTAT-TT
* * *
1699832 ATATTTAATTAAACTTTTTTTATTT
1 AAATTTAAATAAACTTTTATTATTT
1699857 AAATTTAAATAAA-TATTTATTATT
1 AAATTTAAATAAACT-TTTATTATT
1699881 ATTTGTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
24 1 0.02
25 21 0.51
26 4 0.10
29 12 0.29
30 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
AAATTTAAATAAACTTTTATTATTT
Found at i:1700109 original size:30 final size:29
Alignment explanation
Indices: 1700044--1700113 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
1700034 TTTGAGTAAG
* * * *
1700044 TCAAAATAAAATATAATAACTTATTTTAT
1 TCAAAATAAAAAATAAAAACTTATTTAAC
* *
1700073 TTAAAATATAAAAATAAAAATTTATTTAAC
1 TCAAAATA-AAAAATAAAAACTTATTTAAC
1700103 TCAAAATAAAA
1 TCAAAATAAAA
1700114 GTAGAAGAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.36
Consensus pattern (29 bp):
TCAAAATAAAAAATAAAAACTTATTTAAC
Found at i:1700908 original size:3 final size:3
Alignment explanation
Indices: 1700900--1700940 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1700890 AAAACACCTA
* *
1700900 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT GTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1700941 GAATGAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1702679 original size:34 final size:34
Alignment explanation
Indices: 1702633--1702702 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
1702623 TATTAATTAA
* ** *
1702633 AATGTCAGTTATTATTTCATGTTGTGGTGGACCC
1 AATGTCAATTATTATTTCATGCAGCGGTGGACCC
1702667 AATGTCAATTATTATTTCATGCAGCGGTGGACCC
1 AATGTCAATTATTATTTCATGCAGCGGTGGACCC
1702701 AA
1 AA
1702703 AAGTTTATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (34 bp):
AATGTCAATTATTATTTCATGCAGCGGTGGACCC
Found at i:1702961 original size:17 final size:18
Alignment explanation
Indices: 1702934--1702968 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1702924 TCATAAAAAT
*
1702934 ATCATTAAAAAATTTAAA
1 ATCATTAAAAAATATAAA
1702952 ATCA-TAAAAAATATAAA
1 ATCATTAAAAAATATAAA
1702969 TGAAGGTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
ATCATTAAAAAATATAAA
Found at i:1703998 original size:164 final size:162
Alignment explanation
Indices: 1703727--1704540 Score: 506
Period size: 145 Copynumber: 5.2 Consensus size: 162
1703717 TAATGTATGG
* * * *
1703727 ATCATATCAAAACTCGATTATTAATACATGCAAGACTTTAAACTCGACTATTCAATAATATAAGA
1 ATCATATCCAAACTCGATTATTAATACATGTAAAAC-TTAAACTCGACTATTTAATAATATAAGA
* **
1703792 TATTAGTAAATTTCGAGATATCTGAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATTG
65 TATTAGTAAATTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATTG
* * * *
1703857 GAGCTTGAGTAAAATTTAAATACCTAATACATGA
130 GAACTTCACTAAAAATT-AATACCTAATACATGA
** * * *
1703891 ATCATATCCATGCTCGATTATTAATACATGTAAAATCTTAAACTTGACTATTTAATGATATAAGT
1 ATCATATCCAAACTCGATTATTAATACATGTAAAA-CTTAAACTCGACTATTTAATAATATAAGA
* * * * * **
1703956 TATTTGTAAATTTTAAGCTCTCCCAATATGAACTTAACTAAAATTAAATTATTCATATTTTATTG
65 TATTAGTAAATTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATTG
*
1704021 GAACTTCACTAAAAATTAATACCTAATATATGA
130 GAACTTCACTAAAAATTAATACCTAATACATGA
* * *
1704054 ATCATATCCAAACTCGATTACTT-ATACTTGTAAAACCTTGAACTCGGCTA-TT--T-A-AT---
1 ATCATATCCAAACTCGATTA-TTAATACATGTAAAA-CTTAAACTCGACTATTTAATAATATAAG
* * * * *
1704110 A-A-TA--AAA--T----ATATCCAAATATGAACTTAATTAAAAATAAATTATTCATATCTTATT
64 ATATTAGTAAATTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATT
* * * **
1704165 GGAACTTCATTAACAATTAATACCTACTTTATGA
129 GGAACTTCACTAAAAATTAATACCTAATACATGA
* * ** * *
1704199 ATCATAT-TAAAGCTTGATTACCAATACATGTAAAACCTTGAACCCGACTATTTAATAATATAAG
1 ATCATATCCAAA-CTCGATTATTAATACATGTAAAA-CTTAAACTCGACTATTTAATAATATAAG
* * * *
1704263 ------GT--A-TTC-----AT----ATATGAACTTAATTAAAATTAAATTATTCATATCTTATC
64 ATATTAGTAAATTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATT
* ** * * * * *
1704310 AGAGGTTGATTAAAAATTAATACTTAATATACGA
129 GGAACTTCACTAAAAATTAATACCTAATACATGA
** * * * * * * * *
1704344 ATCATATTAAAATTTGATTAGTAATACATGTAAAATTTTGAACTCGACTATATAAGAATATAAAA
1 ATCATATCCAAACTCGATTATTAATACATGTAAAA-CTTAAACTCGACTATTTAATAATATAAGA
* *** * * *
1704409 TATTTA-TAAATTTTGAA-ATATGTGAATATGAACTTAATTAAAAATAAATTATTCATAT-CT-T
65 TA-TTAGTAAA-TTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTAT
* * * *
1704470 TAGGAACTTGAGTAAAAAGTAATACCTAATATATGA
128 T-GGAACTTCACTAAAAATTAATACCTAATACATGA
* * * * *
1704506 ACCATATCTAAACTGGAATATTAATGCATGTAAAA
1 ATCATATCCAAACTCGATTATTAATACATGTAAAA
1704541 TTTTCAACTC
Statistics
Matches: 523, Mismatches: 90, Indels: 76
0.76 0.13 0.11
Matches are distributed among these distances:
144 3 0.01
145 221 0.42
146 5 0.01
148 1 0.00
149 5 0.01
150 3 0.01
151 4 0.01
153 2 0.00
154 1 0.00
155 2 0.00
158 2 0.00
159 3 0.01
160 1 0.00
161 1 0.00
162 57 0.11
163 87 0.17
164 124 0.24
165 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (162 bp):
ATCATATCCAAACTCGATTATTAATACATGTAAAACTTAAACTCGACTATTTAATAATATAAGAT
ATTAGTAAATTTCAAGATATCCCAATATGAACTTAACTAAAATTAAAGTATTCATATCCTATTGG
AACTTCACTAAAAATTAATACCTAATACATGA
Found at i:1704250 original size:145 final size:143
Alignment explanation
Indices: 1703980--1704411 Score: 531
Period size: 145 Copynumber: 3.0 Consensus size: 143
1703970 AAGCTCTCCC
* * *
1703980 AATATGAACTTAACTAAAATTAAATTATTCATATTTTATTGGAACTTCACTAAAAATTAATACCT
1 AATATGAACTTAATTAAAATTAAATTATTCATATCTTATTGGAACTTCATTAAAAATTAATACCT
* * * * *
1704045 AATATATGAATCATATCCAAACTCGATTACTTATACTTGTAAAACCTTGAACTCGGCTATTTAAT
66 AATATATGAATCATAT-TAAACTTGATTACTAATACATGTAAAACCTTGAACTCGACTATTTAAT
1704110 AATAAAATATATCCA
130 AATAAAA-ATATCCA
* *
1704125 AATATGAACTTAATTAAAAATAAATTATTCATATCTTATTGGAACTTCATTAACAATTAATACCT
1 AATATGAACTTAATTAAAATTAAATTATTCATATCTTATTGGAACTTCATTAAAAATTAATACCT
* * * *
1704190 ACTTTATGAATCATATTAAAGCTTGATTACCAATACATGTAAAACCTTGAACCCGACTATTTAAT
66 AATATATGAATCATATTAAA-CTTGATTACTAATACATGTAAAACCTTGAACTCGACTATTTAAT
** *
1704255 AATATAAGGTATTCA
130 AATA-AAAATATCCA
* ** ** * *
1704270 TATATGAACTTAATTAAAATTAAATTATTCATATCTTATCAGAGGTTGATTAAAAATTAATACTT
1 AATATGAACTTAATTAAAATTAAATTATTCATATCTTATTGGAACTTCATTAAAAATTAATACCT
* * * ** * *
1704335 AATATACGAATCATATTAAAATTTGATTAGTAATACATGTAAAATTTTGAACTCGACTATATAAG
66 AATATATGAATCATATT-AAACTTGATTACTAATACATGTAAAACCTTGAACTCGACTATTTAAT
1704400 AATATAAAATAT
130 AATA-AAAATAT
1704412 TTATAAATTT
Statistics
Matches: 245, Mismatches: 39, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
144 3 0.01
145 237 0.97
146 5 0.02
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (143 bp):
AATATGAACTTAATTAAAATTAAATTATTCATATCTTATTGGAACTTCATTAAAAATTAATACCT
AATATATGAATCATATTAAACTTGATTACTAATACATGTAAAACCTTGAACTCGACTATTTAATA
ATAAAAATATCCA
Found at i:1708029 original size:109 final size:110
Alignment explanation
Indices: 1707817--1708033 Score: 339
Period size: 110 Copynumber: 2.0 Consensus size: 110
1707807 TCTCGAAGGT
* ** *
1707817 AAAGCGATCTCAAGTTTTTTGGTGACTTCTATTTCTATTACCTGCTTGTTTCAACTTTTTAAAAT
1 AAAGCGATCTCAAGTTTTTTGGTGACTTATATTTAAATTACCTGCGTGTTTCAACTTTTTAAAAT
1707882 GTTTTCTTCAGTATCCTTATCTGATGACAGGTTTCATTGAATCCA
66 GTTTTCTTCAGTATCCTTATCTGATGACAGGTTTCATTGAATCCA
** *
1707927 AAAGCGATCTTGAGTTTTTTGGTGACTTATATTTAAATTGCCTGCGTGTTTCAA-TTTTTAAAAT
1 AAAGCGATCTCAAGTTTTTTGGTGACTTATATTTAAATTACCTGCGTGTTTCAACTTTTTAAAAT
*
1707991 ATTTTTCTTCA-TATCCTTATCTGATGACAGGTTTCATTGAATC
66 -GTTTTCTTCAGTATCCTTATCTGATGACAGGTTTCATTGAATC
1708034 GATTCTTGGG
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
109 42 0.43
110 56 0.57
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.45
Consensus pattern (110 bp):
AAAGCGATCTCAAGTTTTTTGGTGACTTATATTTAAATTACCTGCGTGTTTCAACTTTTTAAAAT
GTTTTCTTCAGTATCCTTATCTGATGACAGGTTTCATTGAATCCA
Found at i:1718181 original size:30 final size:29
Alignment explanation
Indices: 1718079--1718174 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 29
1718069 AATGCATTCG
* * *
1718079 AATAAATCTTTATATTTTTATTGTATTCA
1 AATAAATCCTTATATTTTTATTTTATTTA
* * *
1718108 ATTAAATTCTTATATTTTT-TTTGTAAATTA
1 AATAAATCCTTATATTTTTATTT-T-ATTTA
*
1718138 AATAAACCCTTATATTTTTATTTTATGTTA
1 AATAAATCCTTATATTTTTATTTTAT-TTA
1718168 AATAAAT
1 AATAAAT
1718175 TTTTATAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
28 2 0.04
29 18 0.35
30 29 0.56
31 3 0.06
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.54
Consensus pattern (29 bp):
AATAAATCCTTATATTTTTATTTTATTTA
Found at i:1719085 original size:2 final size:2
Alignment explanation
Indices: 1719078--1719102 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1719068 CGAACATAGA
1719078 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1719103 AAAATAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1733069 original size:81 final size:80
Alignment explanation
Indices: 1732830--1733069 Score: 214
Period size: 81 Copynumber: 3.0 Consensus size: 80
1732820 CTATGATGTC
* * **
1732830 CTATATCTATCAGACATGAAAAGAACATGATGGCATATCA-G-ACACGCTTCTATTGCCAATTGC
1 CTATAACTATCAGACATGAAAA-AACATGATGGCATATCAGGCACAC-CTAC-ATTGCCAATACC
* *
1732893 AGCTTGAAAAATGTAGTG
63 AGCTTGAAAAAGGTTGTG
* * * ** * * * * *
1732911 CTATAACTGTTAGGCATGAAATAAACATGATGATACATCAGCCACGCCTCCATTGCCGATACCAG
1 CTATAACTATCAGACATGAAA-AAACATGATGGCATATCAGGCACACCTACATTGCCAATACCAG
* *
1732976 TTTAAAAAAGGTTGTG
65 CTTGAAAAAGGTTGTG
** * *
1732992 CTATAGTTATCAGACATGAAACAAACATGATGGCATAGCAGGCACACCTACATTGGCAATACCAG
1 CTATAACTATCAGACATGAAA-AAACATGATGGCATATCAGGCACACCTACATTGCCAATACCAG
*
1733057 CATGAAAAAGGTT
65 CTTGAAAAAGGTT
1733070 CAATTACCAT
Statistics
Matches: 121, Mismatches: 35, Indels: 6
0.75 0.22 0.04
Matches are distributed among these distances:
81 114 0.94
82 4 0.03
83 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (80 bp):
CTATAACTATCAGACATGAAAAAACATGATGGCATATCAGGCACACCTACATTGCCAATACCAGC
TTGAAAAAGGTTGTG
Found at i:1735589 original size:2 final size:2
Alignment explanation
Indices: 1735582--1735607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1735572 AATTGACACA
1735582 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
1735608 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1741837 original size:30 final size:30
Alignment explanation
Indices: 1741803--1741879 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
1741793 GATAATTAGT
* **
1741803 TGTAAAAATTTATTTGACTTAAAATAAATG
1 TGTAAAAATTTATTTAACTTAAAATAAAAA
* *
1741833 TGTAAAAACTTATTTAATTTAAAATAAAAA
1 TGTAAAAATTTATTTAACTTAAAATAAAAA
* *
1741863 TATAAAAATTTAATTAA
1 TGTAAAAATTTATTTAA
1741880 ATATATTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (30 bp):
TGTAAAAATTTATTTAACTTAAAATAAAAA
Found at i:1741923 original size:30 final size:30
Alignment explanation
Indices: 1741857--1741937 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 30
1741847 TAATTTAAAA
* *
1741857 TAAAAAT-ATAAAAATTTAATTAAATATAT
1 TAAAAATAATAAAAATTTATTTTAATATAT
* *
1741886 T-AAAATAATAAAAATTTATTTTAATTTTT
1 TAAAAATAATAAAAATTTATTTTAATATAT
*
1741915 TAAAAATAATATAAATTT-TTTTA
1 TAAAAATAATAAAAATTTATTTTA
1741938 TTTAAATACT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 5 0.11
29 25 0.56
30 15 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TAAAAATAATAAAAATTTATTTTAATATAT
Found at i:1741944 original size:23 final size:24
Alignment explanation
Indices: 1741918--1741964 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
1741908 AATTTTTTAA
1741918 AAATA-ATATAAATTTTTTTATTT
1 AAATACATATAAATTTTTTTATTT
1741941 AAATACTATATAAATTTTTTTATT
1 AAATAC-ATATAAATTTTTTTATT
1741965 GATACTTCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
25 17 0.77
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
AAATACATATAAATTTTTTTATTT
Found at i:1743335 original size:14 final size:16
Alignment explanation
Indices: 1743298--1743337 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1743288 TTAATGGAAC
1743298 ATTTTTAAAAATAACTT
1 ATTTTTAAAAATAAC-T
1743315 ATTTTTAAAAATAA-T
1 ATTTTTAAAAATAACT
1743330 -TTTTTAAA
1 ATTTTTAAA
1743338 TAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
17 14 0.61
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTTAAAAATAACT
Found at i:1744219 original size:20 final size:21
Alignment explanation
Indices: 1744174--1744220 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1744164 GAATTATTAT
1744174 TTTA-AAAAATTAATTAAACA
1 TTTATAAAAATTAATTAAACA
* *
1744194 -TAATAAAAATTATTTAAA-A
1 TTTATAAAAATTAATTAAACA
1744213 TTTATAAA
1 TTTATAAA
1744221 TAAAAACCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TTTATAAAAATTAATTAAACA
Found at i:1749169 original size:39 final size:39
Alignment explanation
Indices: 1749125--1749200 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
1749115 AATCTGGTAC
*
1749125 ATTGATTCTCTTGGTCCTTTGTTAATGCGAAATCATCGG
1 ATTGATTCTCTTGGTACTTTGTTAATGCGAAATCATCGG
1749164 ATTGATTCTCTTGGTACTTTGTTAATGCGAAATCATC
1 ATTGATTCTCTTGGTACTTTGTTAATGCGAAATCATC
1749201 TGAATATATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (39 bp):
ATTGATTCTCTTGGTACTTTGTTAATGCGAAATCATCGG
Found at i:1769882 original size:19 final size:19
Alignment explanation
Indices: 1769858--1769898 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
1769848 TAATATTTTA
1769858 TTTG-TAATATTATTAAAAT
1 TTTGATAATATTA-TAAAAT
1769877 TTTGTATAATATTATAAAAT
1 TTTG-ATAATATTATAAAAT
1769897 TT
1 TT
1769899 ACAGAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTGATAATATTATAAAAT
Found at i:1775620 original size:68 final size:69
Alignment explanation
Indices: 1775537--1775667 Score: 228
Period size: 68 Copynumber: 1.9 Consensus size: 69
1775527 ATATTGGTAT
1775537 TAAATGTGAAAAAAATATAATTAAAAACTTAAACTGTTGTA-TTTTGTAAGATTTTACTATGTTG
1 TAAATGTGAAAAAAATATAATTAAAAACTTAAACTGTTGTAGTTTTGTAAGATTTTACTATGTTG
1775601 TTGC
66 TTGC
* * *
1775605 TAAATGTGAATAAAATATAATTAAAAACTTAAACTGTTGTAGTTTTTTAAGATTTTTCTATGT
1 TAAATGTGAAAAAAATATAATTAAAAACTTAAACTGTTGTAGTTTTGTAAGATTTTACTATGT
1775668 AAAAAAATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 40 0.68
69 19 0.32
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (69 bp):
TAAATGTGAAAAAAATATAATTAAAAACTTAAACTGTTGTAGTTTTGTAAGATTTTACTATGTTG
TTGC
Found at i:1776030 original size:15 final size:15
Alignment explanation
Indices: 1776010--1776038 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1776000 AATGATGCTT
1776010 ACTACTCGTGCATGA
1 ACTACTCGTGCATGA
1776025 ACTACTCGTGCATG
1 ACTACTCGTGCATG
1776039 CAAGGTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (15 bp):
ACTACTCGTGCATGA
Found at i:1783412 original size:2 final size:2
Alignment explanation
Indices: 1783405--1783432 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1783395 TACAAAGAAG
1783405 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
1783433 GTCAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1786236 original size:30 final size:29
Alignment explanation
Indices: 1786199--1786269 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1786189 AAAAGTTAAT
*
1786199 AATAAATATTTAATTAATTTAAAATAAAAA
1 AATAAATATTTAATTAA-ATAAAATAAAAA
* * *
1786229 TATAAATACTTAATTAAATATAATAAAAA
1 AATAAATATTTAATTAAATAAAATAAAAA
*
1786258 AATAAAAATTTA
1 AATAAATATTTA
1786270 TATAAAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 19 0.56
30 15 0.44
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
AATAAATATTTAATTAAATAAAATAAAAA
Found at i:1793971 original size:2 final size:2
Alignment explanation
Indices: 1793964--1793990 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1793954 TTAATGCCAA
1793964 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1793991 CATCCATACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1806412 original size:18 final size:18
Alignment explanation
Indices: 1806374--1806412 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1806364 TTAGAATATC
*
1806374 AATTAATCTGTTCTAATT
1 AATTAATCTGCTCTAATT
1806392 AATTAATCTGCT-TAATGT
1 AATTAATCTGCTCTAAT-T
1806410 AAT
1 AAT
1806413 GGTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (18 bp):
AATTAATCTGCTCTAATT
Found at i:1818889 original size:30 final size:30
Alignment explanation
Indices: 1818855--1818919 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
1818845 ATTCGTCACT
*
1818855 ATTTTTATCATTATATTTTAAATTTTATTA
1 ATTTTTATCACTATATTTTAAATTTTATTA
* * * *
1818885 ATTTTTGTCACTATATTTTTAATTTTGTTG
1 ATTTTTATCACTATATTTTAAATTTTATTA
1818915 ATTTT
1 ATTTT
1818920 GTGTATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (30 bp):
ATTTTTATCACTATATTTTAAATTTTATTA
Found at i:1820455 original size:70 final size:70
Alignment explanation
Indices: 1820305--1820436 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
1820295 TTGGATACTG
1820305 AACTTGTTATGGAAATCCTAGAATGAAATTATTTTGTCATGCCAAACACCTCGAATATTCTTGAA
1 AACTTGTTATGGAAATCCTAGAATGAAATTATTTTGTCATGCCAAACACCTCGAATATTCTTGAA
1820370 TATTT
66 TATTT
* * *
1820375 AACTTGTTATGGAAATCTTAGAATGAAATTATTTTGTCATGCCAAACACGTTG-ATATTCTTG
1 AACTTGTTATGGAAATCCTAGAATGAAATTATTTTGTCATGCCAAACACCTCGAATATTCTTG
1820437 CATCATTCCC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
69 9 0.15
70 50 0.85
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (70 bp):
AACTTGTTATGGAAATCCTAGAATGAAATTATTTTGTCATGCCAAACACCTCGAATATTCTTGAA
TATTT
Found at i:1837384 original size:2 final size:2
Alignment explanation
Indices: 1837377--1837416 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1837367 TTTGATGGAA
1837377 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
1837417 TCCATTCATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1842642 original size:52 final size:52
Alignment explanation
Indices: 1842559--1842667 Score: 164
Period size: 52 Copynumber: 2.1 Consensus size: 52
1842549 TCCATTCTTA
* * *
1842559 GTTTCCATTGTGTGTGATTCTATATATTCTATCTAATCCTAGTTTTGTTTAT
1 GTTTTCATTGTCTGTGATTCTATATATTCTATCTAATCCTAGTTTCGTTTAT
* **
1842611 GTTTTCATTGTCTGTGATTCTATCTATTCTATCTAATTTTAGTTTCGTTTAT
1 GTTTTCATTGTCTGTGATTCTATATATTCTATCTAATCCTAGTTTCGTTTAT
1842663 GTTTT
1 GTTTT
1842668 TAGGGCTTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (52 bp):
GTTTTCATTGTCTGTGATTCTATATATTCTATCTAATCCTAGTTTCGTTTAT
Found at i:1844967 original size:16 final size:15
Alignment explanation
Indices: 1844941--1844970 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1844931 GAAATTCGAA
1844941 AAACAAAAAGAATTC
1 AAACAAAAAGAATTC
1844956 AAACACAAAAGAATT
1 AAACA-AAAAGAATT
1844971 TTATCACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (15 bp):
AAACAAAAAGAATTC
Found at i:1845823 original size:22 final size:23
Alignment explanation
Indices: 1845784--1845829 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1845774 GGACATTGTG
* *
1845784 ATTAATTTTTAAGGTATTGCGTA
1 ATTAATTTTTAAGATATTACGTA
1845807 ATTAATTTTTAA-ATATTACGTA
1 ATTAATTTTTAAGATATTACGTA
1845829 A
1 A
1845830 CTGGTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (23 bp):
ATTAATTTTTAAGATATTACGTA
Found at i:1846071 original size:19 final size:20
Alignment explanation
Indices: 1846037--1846074 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1846027 AGTCATATAA
*
1846037 AAAATTAGTTAAAAATAATT
1 AAAATTAGTAAAAAATAATT
1846057 AAAATTA-TAAAAAATAAT
1 AAAATTAGTAAAAAATAAT
1846075 ATTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATTAGTAAAAAATAATT
Found at i:1847227 original size:117 final size:117
Alignment explanation
Indices: 1846901--1847228 Score: 512
Period size: 117 Copynumber: 2.8 Consensus size: 117
1846891 ACTCTGGTCT
** * * * *
1846901 TGATGATGGCCCGGGCCCTAATGAAATAGAAAGGTTGAGTAGTTTTTCATGGTCTTCTTCACCAT
1 TGATGATGGCCCTCGCCCTAATGAAAGAGAAAGGTCGACTAGTTCTTCATGGTCTTCTTCACCAT
*
1846966 CAAAGCTCAGGGAAAACAGACGTTTTTGATAAGTAGAAGGTAAGCCAGACGA
66 CAAAGCTCAGGGAAAACAGACGTTTTTTATAAGTAGAAGGTAAGCCAGACGA
*
1847018 TGATGATGGCCCTCGCCCTAGTGAAAGAGAAAGGTCGACTAGTTCTTCATGGTCTTCTTCACCAT
1 TGATGATGGCCCTCGCCCTAATGAAAGAGAAAGGTCGACTAGTTCTTCATGGTCTTCTTCACCAT
* *
1847083 CAAAGCTCCGGGAAAGCAGACGTTTTTTATAAGTAGAAGGTAAGCCAGACGA
66 CAAAGCTCAGGGAAAACAGACGTTTTTTATAAGTAGAAGGTAAGCCAGACGA
* * * * *
1847135 TGATGATGGCCCTCGCCCTATTGAAAGAGAAAAGTCGATTACTTCTTCATGTTCTTCTTCACCAT
1 TGATGATGGCCCTCGCCCTAATGAAAGAGAAAGGTCGACTAGTTCTTCATGGTCTTCTTCACCAT
*
1847200 CAAAGCTCTGGGAAAACAGACGTTTTTTA
66 CAAAGCTCAGGGAAAACAGACGTTTTTTA
1847229 GGGTTAGGGC
Statistics
Matches: 194, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
117 194 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (117 bp):
TGATGATGGCCCTCGCCCTAATGAAAGAGAAAGGTCGACTAGTTCTTCATGGTCTTCTTCACCAT
CAAAGCTCAGGGAAAACAGACGTTTTTTATAAGTAGAAGGTAAGCCAGACGA
Found at i:1848280 original size:29 final size:29
Alignment explanation
Indices: 1848223--1848302 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
1848213 AATGAGTAAA
* * *
1848223 AAATAAATAATAATTTTTTTA-GATATTT
1 AAATAAATATTTATTTTTTTATTATATTT
*
1848251 AAATAAATATTTATTTTTTTATTATGTTT
1 AAATAAATATTTATTTTTTTATTATATTT
* * *
1848280 AATTAAATTTTTATATTTTTATT
1 AAATAAATATTTATTTTTTTATT
1848303 TTGAATCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 19 0.43
29 25 0.57
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (29 bp):
AAATAAATATTTATTTTTTTATTATATTT
Found at i:1848317 original size:30 final size:29
Alignment explanation
Indices: 1848251--1848323 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
1848241 TTAGATATTT
* * *
1848251 AAATAAATATTTATTTTTTTATTATGTTT
1 AAATAAATATTTATATTTTTATTATGATC
* * *
1848280 AATTAAATTTTTATATTTTTATTTTGAATC
1 AAATAAATATTTATATTTTTATTATG-ATC
*
1848310 AAATAAATCTTTAT
1 AAATAAATATTTAT
1848324 TACTTATTAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (29 bp):
AAATAAATATTTATATTTTTATTATGATC
Found at i:1848692 original size:2 final size:2
Alignment explanation
Indices: 1848687--1848725 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1848677 TGTGTTTGTG
1848687 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1848726 TTCAAGATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1868249 original size:18 final size:17
Alignment explanation
Indices: 1868214--1868251 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1868204 ATTTTAATTT
1868214 TTTAATTTTTTATTATA
1 TTTAATTTTTTATTATA
1868231 TTTAATTATATTT-TTATA
1 TTTAATT-T-TTTATTATA
1868249 TTT
1 TTT
1868252 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 9 0.47
19 3 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATTTTTTATTATA
Found at i:1869122 original size:31 final size:30
Alignment explanation
Indices: 1869062--1869143 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 30
1869052 ACTCGTTTTC
* *
1869062 TTTT-AAAATTTTATAATTTT-TTTTTATT
1 TTTTAAAAAATTTATAATTTTATCTTTATT
1869090 TTTTAAAAAAGTTTATAATTTTATCTTTATT
1 TTTTAAAAAA-TTTATAATTTTATCTTTATT
*
1869121 TTTTAAAAAAATTATAATTTTAT
1 TTTTAAAAAATTTATAATTTTAT
1869144 TTCTACAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
28 4 0.08
29 4 0.08
30 23 0.48
31 17 0.35
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTAAAAAATTTATAATTTTATCTTTATT
Found at i:1871829 original size:31 final size:30
Alignment explanation
Indices: 1871794--1871878 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
1871784 AATTATAAAT
1871794 ATTTATTTGACTCAAAATAAAAAATACAAAA
1 ATTTATTTGACTCAAAAT-AAAAATACAAAA
* *
1871825 ATTTATTTGACTCTAAATAAAAATATAAAA
1 ATTTATTTGACTCAAAATAAAAATACAAAA
* * **
1871855 ACTTAATT-AAACAAAATAAAAATA
1 ATTTATTTGACTCAAAATAAAAATA
1871879 TAAAGATCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 13 0.28
30 17 0.36
31 17 0.36
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (30 bp):
ATTTATTTGACTCAAAATAAAAATACAAAA
Found at i:1871849 original size:30 final size:31
Alignment explanation
Indices: 1871794--1871855 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1871784 AATTATAAAT
1871794 ATTTATTTGACTCAAAATAAAAAATACAAAA
1 ATTTATTTGACTCAAAATAAAAAATACAAAA
* *
1871825 ATTTATTTGACTCTAAAT-AAAAATATAAAA
1 ATTTATTTGACTCAAAATAAAAAATACAAAA
1871855 A
1 A
1871856 CTTAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.32
Consensus pattern (31 bp):
ATTTATTTGACTCAAAATAAAAAATACAAAA
Found at i:1875641 original size:2 final size:2
Alignment explanation
Indices: 1875636--1875665 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1875626 AGAAAGCTAC
1875636 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
1875666 GTTGAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1878823 original size:165 final size:165
Alignment explanation
Indices: 1878551--1878880 Score: 570
Period size: 165 Copynumber: 2.0 Consensus size: 165
1878541 ACTCTTATCA
1878551 ATTCAAAACTTGTCACCTAACCAACAAAAGAAGCTTCCCTAATCAAGTTCAACTTAAATCGACTA
1 ATTCAAAACTTGTCACCTAACCAACAAAAGAAGCTTCCCTAATCAAGTTCAACTTAAATCGACTA
* *
1878616 AAATTCAAAGTCCTCTGTCTAAAGTCTAAACTTTCTCCCAAAACACTTATAAAAAGGGAAAACCA
66 AAATTCAAAGCCCTCTGTCTAAAGTCTAAACTTTCTCCCAAAACACTCATAAAAAGGGAAAACCA
1878681 ACGTTTAATCTGAAATTCCAACAATCTAGCTAAAT
131 ACGTTTAATCTGAAATTCCAACAATCTAGCTAAAT
*
1878716 ATTCAAAACTTGTTACCTAACCAACAAAAGAAGCTTCCCTAATCAAGTTCAACTTAAATCGACTA
1 ATTCAAAACTTGTCACCTAACCAACAAAAGAAGCTTCCCTAATCAAGTTCAACTTAAATCGACTA
* *
1878781 AAATTCAAAGCCCTCTGTCTAAAGTCTCAACTTTCTCCCAAAACACTCATAAAAAGGGAAAACCC
66 AAATTCAAAGCCCTCTGTCTAAAGTCTAAACTTTCTCCCAAAACACTCATAAAAAGGGAAAACCA
* * * * *
1878846 ATGTTTAATTTGATATTCGAACAATCTATCTAAAT
131 ACGTTTAATCTGAAATTCCAACAATCTAGCTAAAT
1878881 GAGGCTTCAA
Statistics
Matches: 155, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
165 155 1.00
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.27
Consensus pattern (165 bp):
ATTCAAAACTTGTCACCTAACCAACAAAAGAAGCTTCCCTAATCAAGTTCAACTTAAATCGACTA
AAATTCAAAGCCCTCTGTCTAAAGTCTAAACTTTCTCCCAAAACACTCATAAAAAGGGAAAACCA
ACGTTTAATCTGAAATTCCAACAATCTAGCTAAAT
Found at i:1880689 original size:27 final size:27
Alignment explanation
Indices: 1880651--1880736 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
1880641 GGTTCTATCA
* * *
1880651 AATTCGGGGAAGGCTTTAATGGCGTCC
1 AATTCAGGGAAGGCTTTAGTGGTGTCC
*
1880678 AATTCAGGGAAGGCTTTAGTGGTATCC
1 AATTCAGGGAAGGCTTTAGTGGTGTCC
* **
1880705 AATTCAGGAAAGGCCCTAGTGGTGTCC
1 AATTCAGGGAAGGCTTTAGTGGTGTCC
1880732 AATTC
1 AATTC
1880737 TGGCAAGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.27
Consensus pattern (27 bp):
AATTCAGGGAAGGCTTTAGTGGTGTCC
Found at i:1906220 original size:31 final size:32
Alignment explanation
Indices: 1906170--1906245 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 32
1906160 TTATTTTTAT
*
1906170 ATTTTTATTATATTTTTATTTTAAATTAAATAA
1 ATTTTTA-TATATTTTTATTTTAAATCAAATAA
* *
1906203 ATTTTTATAT-TTTTTATTTTGAGTCAAATAA
1 ATTTTTATATATTTTTATTTTAAATCAAATAA
*
1906234 ATTCTTAT-TATT
1 ATTTTTATATATT
1906246 AATGATTGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 27 0.71
32 3 0.08
33 7 0.18
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (32 bp):
ATTTTTATATATTTTTATTTTAAATCAAATAA
Found at i:1906335 original size:33 final size:33
Alignment explanation
Indices: 1906298--1906364 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1906288 CATGACGTTA
* * *
1906298 ATGTAATATATTAAAATATTATAATTAATTATG
1 ATGTAACATATTAAAATATCATAATTAATGATG
* *
1906331 ATGTAACATATTGACATATCATAATTAATGATG
1 ATGTAACATATTAAAATATCATAATTAATGATG
1906364 A
1 A
1906365 CATATCATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.40
Consensus pattern (33 bp):
ATGTAACATATTAAAATATCATAATTAATGATG
Found at i:1906374 original size:33 final size:33
Alignment explanation
Indices: 1906313--1906375 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1906303 ATATATTAAA
* * **
1906313 ATATTATAATTAATTATGATGTAACATATTGAC
1 ATATCATAATTAATGATGACATAACATATTGAC
*
1906346 ATATCATAATTAATGATGACATATCATATT
1 ATATCATAATTAATGATGACATAACATATT
1906376 AATTTGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (33 bp):
ATATCATAATTAATGATGACATAACATATTGAC
Found at i:1906536 original size:30 final size:29
Alignment explanation
Indices: 1906502--1906573 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 29
1906492 CATTAGTTAT
*
1906502 AAAATTTTATTTAACTTAAATAAAAATACA
1 AAAATTTTATTTAACTT-AATAAAAAAACA
* * *
1906532 AAAATTTGATTGAACTTAATAAAAAAATA
1 AAAATTTTATTTAACTTAATAAAAAAACA
1906561 AAAA-TTTATTTAA
1 AAAATTTTATTTAA
1906574 ATATTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 7 0.19
29 14 0.39
30 15 0.42
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTTTATTTAACTTAATAAAAAAACA
Found at i:1906553 original size:29 final size:30
Alignment explanation
Indices: 1906502--1906567 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1906492 CATTAGTTAT
* * *
1906502 AAAATTTTATTTAACTTAAATAAAAATACA
1 AAAATTTGATTGAACTTAAATAAAAAAACA
*
1906532 AAAATTTGATTGAACTT-AATAAAAAAATA
1 AAAATTTGATTGAACTTAAATAAAAAAACA
1906561 AAAATTT
1 AAAATTT
1906568 ATTTAAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTTGATTGAACTTAAATAAAAAAACA
Found at i:1907248 original size:2 final size:2
Alignment explanation
Indices: 1907241--1907278 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1907231 TAATGTGGTA
1907241 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
1907279 GTTTTTGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 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:1916224 original size:22 final size:23
Alignment explanation
Indices: 1916180--1916224 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1916170 ATTTAATTTA
* **
1916180 AAATATAAATATAAAATTTAATT
1 AAATATAAATAAAAAATAAAATT
1916203 AAATAT-AATAAAAAATAAAATT
1 AAATATAAATAAAAAATAAAATT
1916225 TATTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAATAAAAAATAAAATT
Found at i:1927419 original size:60 final size:60
Alignment explanation
Indices: 1927305--1927419 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 60
1927295 AGACACCAAC
* * * *
1927305 CACTAATTTACTATCAACTTAAAAATCAAGATGACTAAACATAGACGATCACGCATCGAT
1 CACTAATTTACTATCAACTGAAAAATCAAAATGACTAAACATAGACAATAACGCATCGAT
** * * * * *
1927365 CACTAATTTTTTATTAACTGAAATATCAAAATGACTAAACGTGGATAATAACGCA
1 CACTAATTTACTATCAACTGAAAAATCAAAATGACTAAACATAGACAATAACGCA
1927420 CCAACTATTA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (60 bp):
CACTAATTTACTATCAACTGAAAAATCAAAATGACTAAACATAGACAATAACGCATCGAT
Found at i:1931778 original size:24 final size:24
Alignment explanation
Indices: 1931740--1931794 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1931730 AGAATTGTTT
*
1931740 TAATTATATTTTTCTCTGGTGAAC
1 TAATTGTATTTTTCTCTGGTGAAC
*
1931764 TGATTGTATTTTTCTCTGGTGAAC
1 TAATTGTATTTTTCTCTGGTGAAC
1931788 TAATTGT
1 TAATTGT
1931795 GCTAGTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.51
Consensus pattern (24 bp):
TAATTGTATTTTTCTCTGGTGAAC
Found at i:1933028 original size:15 final size:15
Alignment explanation
Indices: 1933008--1933036 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1932998 GATGGTTTGG
1933008 GCCACAAAGGACTAA
1 GCCACAAAGGACTAA
1933023 GCCACAAAGGACTA
1 GCCACAAAGGACTA
1933037 GCTAAACTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.07
Consensus pattern (15 bp):
GCCACAAAGGACTAA
Found at i:1940558 original size:2 final size:2
Alignment explanation
Indices: 1940551--1940581 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1940541 CTTCCCACAG
1940551 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1940582 TCCCCTTAAC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1948810 original size:20 final size:20
Alignment explanation
Indices: 1948781--1948819 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1948771 TTCGTTAATT
1948781 AAAAAAATATAAAA-ATTTG
1 AAAAAAATATAAAATATTTG
1948800 AAAATAAATATAAAATATTT
1 AAAA-AAATATAAAATATTT
1948820 TAATCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAAAAATATAAAATATTTG
Found at i:1951340 original size:2 final size:2
Alignment explanation
Indices: 1951333--1951367 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1951323 NNNNNNNNNN
1951333 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1951368 AATGCAACTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1959057 original size:22 final size:22
Alignment explanation
Indices: 1959020--1959061 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1959010 AGAAAAGTTC
1959020 AAATGAATATGAAAAATTTATA
1 AAATGAATATGAAAAATTTATA
1959042 AAATGGAATATG-AAAATTTA
1 AAAT-GAATATGAAAAATTTA
1959062 GTTTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (22 bp):
AAATGAATATGAAAAATTTATA
Found at i:1959487 original size:30 final size:29
Alignment explanation
Indices: 1959430--1959487 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1959420 TGTTGAATTA
* *
1959430 AACTTTTATATTTTATTTCGAACCAAATC
1 AACTATTATATTTTATTTCAAACCAAATC
* *
1959459 AACTATTATAATTTTATTTTAAATCAAAT
1 AACTATTAT-ATTTTATTTCAAACCAAAT
1959488 TTATCTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (29 bp):
AACTATTATATTTTATTTCAAACCAAATC
Found at i:1959630 original size:33 final size:33
Alignment explanation
Indices: 1959554--1959633 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
1959544 TGTGACACTA
* *
1959554 ACGTGATATACTAACATATTATAATTGATGATG
1 ACGTGACATACTAACATATCATAATTGATGATG
** * *
1959587 ATATTG-CATACTTATATATCATAATTGATGATG
1 A-CGTGACATACTAACATATCATAATTGATGATG
1959620 ACGTGACATACTAA
1 ACGTGACATACTAA
1959634 TTTGATATTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
32 2 0.06
33 32 0.89
34 2 0.06
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (33 bp):
ACGTGACATACTAACATATCATAATTGATGATG
Found at i:1963229 original size:14 final size:14
Alignment explanation
Indices: 1963210--1963239 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1963200 TCATGTTAGG
1963210 TTTTGTATTTTTCT
1 TTTTGTATTTTTCT
*
1963224 TTTTGTCTTTTTCT
1 TTTTGTATTTTTCT
1963238 TT
1 TT
1963240 CTAATGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.10, G:0.07, T:0.80
Consensus pattern (14 bp):
TTTTGTATTTTTCT
Found at i:1963482 original size:23 final size:21
Alignment explanation
Indices: 1963450--1963491 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1963440 TAAAAAGTTC
1963450 AAATGAATATAAAAAATTTATA
1 AAATGAATAT-AAAAATTTATA
*
1963472 AAATGGAATATGAAAATTTA
1 AAAT-GAATATAAAAATTTA
1963492 GTTTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAATATAAAAATTTATA
Found at i:1963826 original size:20 final size:20
Alignment explanation
Indices: 1963798--1963836 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1963788 TAAGATATAA
1963798 TATTAAAAA-AACTTTTAAAT
1 TATTAAAAAGAA-TTTTAAAT
*
1963818 TATTTAAAAGAATTTTAAA
1 TATTAAAAAGAATTTTAAA
1963837 AAATTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TATTAAAAAGAATTTTAAAT
Found at i:1963842 original size:20 final size:21
Alignment explanation
Indices: 1963800--1963842 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1963790 AGATATAATA
**
1963800 TTAAAAAAACTTTTAAATTAT
1 TTAAAAAAACTTTTAAAAAAT
*
1963821 TTAAAAGAA-TTTTAAAAAAT
1 TTAAAAAAACTTTTAAAAAAT
1963841 TT
1 TT
1963843 GTATATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAAAAAAACTTTTAAAAAAT
Found at i:1964047 original size:22 final size:22
Alignment explanation
Indices: 1964022--1964067 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1964012 ATAAAAGTTT
1964022 ATTTGATTTAAA-A-AATATAAAA
1 ATTTGA-TTAAACATAATA-AAAA
1964044 ATTTGATTAAACATAATAAAAA
1 ATTTGATTAAACATAATAAAAA
1964066 AT
1 AT
1964068 AAAAATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
ATTTGATTAAACATAATAAAAA
Found at i:1971824 original size:116 final size:116
Alignment explanation
Indices: 1971611--1971826 Score: 276
Period size: 116 Copynumber: 1.9 Consensus size: 116
1971601 TTTTTATGAG
* * * *
1971611 TTATTTTATGAATATATTGTTTGATTATTTGATTTTTGAATTTAACTTTATATAGTTTGTGGATG
1 TTATTTTATGAATATATTATTTGATTATTTAATTTTTGAATTTAACTTTATATAGTCTGTGAATG
* *
1971676 CTTATACTTAGTTTTAATTAATAAATAAAAATTTGTTATGAGTTTATTTAT
66 CTTATACTTAGTTCTAATCAATAAATAAAAATTTGTTATGAGTTTATTTAT
* *
1971727 TTATTTTAT-AGATGTATTATTTGATTATTTAATTATTTGTATTTAACTTTAT-T-GATCTGTGA
1 TTATTTTATGA-ATATATTATTTGATTATTTAATT-TTTGAATTTAACTTTATATAG-TCTGTGA
* * * *
1971789 ATGCTTATACTTAGTTCTGATCCATGAATAGAAATTTG
63 ATGCTTATACTTAGTTCTAATCAATAAATAAAAATTTG
1971827 GATCATATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
115 2 0.02
116 67 0.79
117 16 0.19
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (116 bp):
TTATTTTATGAATATATTATTTGATTATTTAATTTTTGAATTTAACTTTATATAGTCTGTGAATG
CTTATACTTAGTTCTAATCAATAAATAAAAATTTGTTATGAGTTTATTTAT
Found at i:1985884 original size:22 final size:22
Alignment explanation
Indices: 1985859--1985900 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1985849 TAGCACACAT
1985859 ATGCATACAAACATGCAAACAA
1 ATGCATACAAACATGCAAACAA
* * *
1985881 ATGCATGCAAGCCTGCAAAC
1 ATGCATACAAACATGCAAAC
1985901 GAGCACACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.14
Consensus pattern (22 bp):
ATGCATACAAACATGCAAACAA
Found at i:1986602 original size:27 final size:27
Alignment explanation
Indices: 1986572--1986670 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
1986562 AAAAAAATAA
1986572 ATTATTTAAATAAATTTTTATATTTTT
1 ATTATTTAAATAAATTTTTATATTTTT
* *
1986599 ATTATATT-TATAAATTATTATATTTTT
1 ATTAT-TTAAATAAATTTTTATATTTTT
* *
1986626 ATTTTAAATTAAATAAAATTTTATATTTTT
1 A--TT-ATTTAAATAAATTTTTATATTTTT
* *
1986656 ATTTTTTAATTAAAT
1 ATTATTTAAATAAAT
1986671 AAAATTTAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 31 0.54
28 4 0.07
29 4 0.07
30 18 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
ATTATTTAAATAAATTTTTATATTTTT
Done.