Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 22 of 31
Found at i:5186008 original size:2 final size:2
Alignment explanation
Indices: 5186001--5186098 Score: 196
Period size: 2 Copynumber: 49.0 Consensus size: 2
5185991 ATAAAATCGT
5186001 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5186043 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5186085 AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC
5186099 TCAATTTCTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 96 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5186229 original size:6 final size:6
Alignment explanation
Indices: 5186218--5186479 Score: 344
Period size: 6 Copynumber: 43.7 Consensus size: 6
5186208 ATAAAATCGT
5186218 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * *
5186266 ACACAC ACACAC ACACAC AGACAC AGACAC AGACAC AGACAC AGACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* *
5186314 AGACAC AGACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * * * *
5186362 ACGCAC ACGCAC ACGCGC ACACAC GCACAC ACACAC ACGCAC ACACGC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * * *
5186410 ACACAC GCACGC ACGCAC GCACGC ACGCAC ACACAC ACACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
5186458 ACACAC ACACAC ACACAC ACAC
1 ACACAC ACACAC ACACAC ACAC
5186480 TCAATTTCTT
Statistics
Matches: 232, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 232 1.00
ACGTcount: A:0.45, C:0.47, G:0.08, T:0.00
Consensus pattern (6 bp):
ACACAC
Found at i:5186231 original size:8 final size:8
Alignment explanation
Indices: 5186218--5186479 Score: 344
Period size: 8 Copynumber: 32.8 Consensus size: 8
5186208 ATAAAATCGT
5186218 ACACACAC
1 ACACACAC
5186226 ACACACAC
1 ACACACAC
5186234 ACACACAC
1 ACACACAC
5186242 ACACACAC
1 ACACACAC
5186250 ACACACAC
1 ACACACAC
5186258 ACACACAC
1 ACACACAC
5186266 ACACACAC
1 ACACACAC
5186274 ACACACAC
1 ACACACAC
*
5186282 ACAGACAC
1 ACACACAC
* *
5186290 AGACACAG
1 ACACACAC
*
5186298 ACACAGAC
1 ACACACAC
*
5186306 ACAGACAC
1 ACACACAC
* *
5186314 AGACACAG
1 ACACACAC
5186322 ACACACAC
1 ACACACAC
5186330 ACACACAC
1 ACACACAC
5186338 ACACACAC
1 ACACACAC
5186346 ACACACAC
1 ACACACAC
5186354 ACACACAC
1 ACACACAC
*
5186362 ACGCACAC
1 ACACACAC
* *
5186370 GCACACGC
1 ACACACAC
*
5186378 GCACACAC
1 ACACACAC
*
5186386 GCACACAC
1 ACACACAC
*
5186394 ACACACGC
1 ACACACAC
*
5186402 ACACACGC
1 ACACACAC
*
5186410 ACACACGC
1 ACACACAC
* *
5186418 ACGCACGC
1 ACACACAC
* *
5186426 ACGCACGC
1 ACACACAC
*
5186434 ACGCACAC
1 ACACACAC
5186442 ACACACAC
1 ACACACAC
5186450 ACACACAC
1 ACACACAC
5186458 ACACACAC
1 ACACACAC
5186466 ACACACAC
1 ACACACAC
5186474 ACACAC
1 ACACAC
5186480 TCAATTTCTT
Statistics
Matches: 230, Mismatches: 24, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 230 1.00
ACGTcount: A:0.45, C:0.47, G:0.08, T:0.00
Consensus pattern (8 bp):
ACACACAC
Found at i:5186257 original size:217 final size:217
Alignment explanation
Indices: 5185882--5186314 Score: 821
Period size: 217 Copynumber: 2.0 Consensus size: 217
5185872 TTTAAACATT
5185882 TCAATTTCTTTCTTAAACTATGATCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAA
1 TCAATTTCTTTCTTAAACTATGATCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAA
5185947 TTTCAACCCAAATTATACGTATATACTAATCACATCCCTTGTTAATAAAATCGTACACACACACA
66 TTTCAACCCAAATTATACGTATATACTAATCACATCCCTTGTTAATAAAATCGTACACACACACA
5186012 CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
131 CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
5186077 ACACACACACACACACACACAC
196 ACACACACACACACACACACAC
5186099 TCAATTTCTTTCTTAAACTATGATCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAA
1 TCAATTTCTTTCTTAAACTATGATCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAA
5186164 TTTCAACCCAAATTATACGTATATACTAATCACATCCCTTGTTAATAAAATCGTACACACACACA
66 TTTCAACCCAAATTATACGTATATACTAATCACATCCCTTGTTAATAAAATCGTACACACACACA
* *
5186229 CACACACACACACACACACACACACACACACACACACACACACACACACACACACAGACACAGAC
131 CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
* * *
5186294 ACAGACACAGACACAGACACA
196 ACACACACACACACACACACA
5186315 GACACAGACA
Statistics
Matches: 211, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 211 1.00
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.22
Consensus pattern (217 bp):
TCAATTTCTTTCTTAAACTATGATCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAA
TTTCAACCCAAATTATACGTATATACTAATCACATCCCTTGTTAATAAAATCGTACACACACACA
CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
ACACACACACACACACACACAC
Found at i:5186606 original size:2 final size:2
Alignment explanation
Indices: 5186599--5186643 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
5186589 ATAAAATCGT
5186599 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5186641 AC A
1 AC A
5186644 ATTTCTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5186618 original size:161 final size:161
Alignment explanation
Indices: 5186438--5186804 Score: 725
Period size: 161 Copynumber: 2.3 Consensus size: 161
5186428 GCACGCACGC
*
5186438 ACACACACACACACACACACACACACACACACACACACACACTCAATTTCTTTCTTAAACTATGA
1 ACACACACACACACACACACACACACACACACACACACACACACAATTTCTTTCTTAAACTATGA
5186503 TCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAATTTCAACCCAAATTATACGTATA
66 TCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAATTTCAACCCAAATTATACGTATA
5186568 TACTAATCACATCCCTTGTTAATAAAATCGT
131 TACTAATCACATCCCTTGTTAATAAAATCGT
5186599 ACACACACACACACACACACACACACACACACACACACACACACAATTTCTTTCTTAAACTATGA
1 ACACACACACACACACACACACACACACACACACACACACACACAATTTCTTTCTTAAACTATGA
5186664 TCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAATTTCAACCCAAATTATACGTATA
66 TCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAATTTCAACCCAAATTATACGTATA
5186729 TACTAATCACATCCCTTGTTAATAAAATCGT
131 TACTAATCACATCCCTTGTTAATAAAATCGT
5186760 ACACACACACACACACACACACACACACACACACACACACACACA
1 ACACACACACACACACACACACACACACACACACACACACACACA
5186805 CACACACACA
Statistics
Matches: 205, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 205 1.00
ACGTcount: A:0.41, C:0.30, G:0.03, T:0.26
Consensus pattern (161 bp):
ACACACACACACACACACACACACACACACACACACACACACACAATTTCTTTCTTAAACTATGA
TCTTTAGTCTAAATTGTTCTCAAAACTTTTTAAACAATTCAATTTCAACCCAAATTATACGTATA
TACTAATCACATCCCTTGTTAATAAAATCGT
Found at i:5186769 original size:4 final size:4
Alignment explanation
Indices: 5186760--5187345 Score: 494
Period size: 4 Copynumber: 147.2 Consensus size: 4
5186750 ATAAAATCGT
5186760 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * *
5186808 ACAC ACAC AGAC ACAG ACAC AGAC ACAG ACAC AGAC ACAG ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
*
5186856 ACAC ACAC -CAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACGC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * *
5186903 GCAC ACGC GCAC ACAC GCAC ACAC GCAC ACAC GCAC ACAC GCAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * * * *
5186951 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC ACAC GCAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * *
5186999 ACAC GCAC GCAC ACAC GCAC GCAC ACAC ACGC ACGC ACGC ACGC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * *
5187047 ACGC ACGC ACAC ACAC ACGC ACAC ACGC GCAC ACAC GCAC GCAC GCGC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * * * * *
5187095 GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC GCAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * * * * * * *
5187143 GCAC GCAC GCAC GCAC GCGC GCGC GCAC GCAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * *
5187191 ACAC ACAC ACAC ACAC CCAC ACAC ACAC ACAC AC-C ACAC -CCC CCCC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
* * * * *
5187237 CCCC CCCC CCAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
5187285 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
1 ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC ACAC
5187333 ACAC ACAC ACAC A
1 ACAC ACAC ACAC A
5187346 TATATTGTTA
Statistics
Matches: 522, Mismatches: 57, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
3 8 0.02
4 514 0.98
ACGTcount: A:0.38, C:0.51, G:0.11, T:0.00
Consensus pattern (4 bp):
ACAC
Found at i:5187755 original size:213 final size:213
Alignment explanation
Indices: 5187388--5187814 Score: 854
Period size: 213 Copynumber: 2.0 Consensus size: 213
5187378 GAAACTGAAT
5187388 ACATATTTGGATGAATTTGGGGATAAAATTGGAAGATTCAAAAGTTTGGGAATCAATTTAGAATG
1 ACATATTTGGATGAATTTGGGGATAAAATTGGAAGATTCAAAAGTTTGGGAATCAATTTAGAATG
5187453 AGAGTCATAGTTTGGAGATAGAATTGAAATGTTCATAAGTTTAAGGATTAATTTAGAATGATATC
66 AGAGTCATAGTTTGGAGATAGAATTGAAATGTTCATAAGTTTAAGGATTAATTTAGAATGATATC
5187518 ATGGTATGGGGGTGAAATTGGAATGTTCAACAACTTAAAGACCAATTTGAAATGAGGGTCTTAGT
131 ATGGTATGGGGGTGAAATTGGAATGTTCAACAACTTAAAGACCAATTTGAAATGAGGGTCTTAGT
5187583 TTAAGGATATACGATGCA
196 TTAAGGATATACGATGCA
5187601 ACATATTTGGATGAATTTGGGGATAAAATTGGAAGATTCAAAAGTTTGGGAATCAATTTAGAATG
1 ACATATTTGGATGAATTTGGGGATAAAATTGGAAGATTCAAAAGTTTGGGAATCAATTTAGAATG
5187666 AGAGTCATAGTTTGGAGATAGAATTGAAATGTTCATAAGTTTAAGGATTAATTTAGAATGATATC
66 AGAGTCATAGTTTGGAGATAGAATTGAAATGTTCATAAGTTTAAGGATTAATTTAGAATGATATC
5187731 ATGGTATGGGGGTGAAATTGGAATGTTCAACAACTTAAAGACCAATTTGAAATGAGGGTCTTAGT
131 ATGGTATGGGGGTGAAATTGGAATGTTCAACAACTTAAAGACCAATTTGAAATGAGGGTCTTAGT
5187796 TTAAGGATATACGATGCA
196 TTAAGGATATACGATGCA
5187814 A
1 A
5187815 TTAACTCTAA
Statistics
Matches: 214, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 214 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (213 bp):
ACATATTTGGATGAATTTGGGGATAAAATTGGAAGATTCAAAAGTTTGGGAATCAATTTAGAATG
AGAGTCATAGTTTGGAGATAGAATTGAAATGTTCATAAGTTTAAGGATTAATTTAGAATGATATC
ATGGTATGGGGGTGAAATTGGAATGTTCAACAACTTAAAGACCAATTTGAAATGAGGGTCTTAGT
TTAAGGATATACGATGCA
Found at i:5196234 original size:40 final size:40
Alignment explanation
Indices: 5196190--5196270 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
5196180 TCTTCAAACA
5196190 ACTGGGGTTGTGCACCGTGTAACTTGTCCACACACCTCCG
1 ACTGGGGTTGTGCACCGTGTAACTTGTCCACACACCTCCG
5196230 ACTGGGGTTGTGCACCGTGTAACTTGTCCACACACCTCCG
1 ACTGGGGTTGTGCACCGTGTAACTTGTCCACACACCTCCG
5196270 A
1 A
5196271 GCAGAATGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.19, C:0.32, G:0.25, T:0.25
Consensus pattern (40 bp):
ACTGGGGTTGTGCACCGTGTAACTTGTCCACACACCTCCG
Found at i:5200816 original size:29 final size:30
Alignment explanation
Indices: 5200784--5200879 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 30
5200774 ACTTTTGAAT
5200784 ATTCTAATTTCA-CCCTAAATTATGATTTC
1 ATTCTAATTTCATCCCTAAATTATGATTTC
* ** * *
5200813 ATTCTAAATT-AGTCTTTAAACTTTTGA--AC
1 ATTCTAATTTCA-TCCCTAAA-TTATGATTTC
5200842 ATTCTAATTTCATCCCTAAATTATGATTCTC
1 ATTCTAATTTCATCCCTAAATTATGATT-TC
*
5200873 TTTCTAA
1 ATTCTAA
5200880 ATCAGTCCCC
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
28 6 0.12
29 25 0.51
30 6 0.12
31 12 0.24
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (30 bp):
ATTCTAATTTCATCCCTAAATTATGATTTC
Found at i:5200836 original size:58 final size:60
Alignment explanation
Indices: 5200774--5200886 Score: 185
Period size: 58 Copynumber: 1.9 Consensus size: 60
5200764 TAACCCTTAC
* *
5200774 ACTTTTGAATATTCTAATTTCA-CCCTAAATTATGATT-TCATTCTAAATTAGTCTTTAA
1 ACTTTTGAACATTCTAATTTCATCCCTAAATTATGATTCTCATTCTAAATCAGTCTTTAA
*
5200832 ACTTTTGAACATTCTAATTTCATCCCTAAATTATGATTCTCTTTCTAAATCAGTC
1 ACTTTTGAACATTCTAATTTCATCCCTAAATTATGATTCTCATTCTAAATCAGTC
5200887 CCCAAATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 21 0.42
59 15 0.30
60 14 0.28
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (60 bp):
ACTTTTGAACATTCTAATTTCATCCCTAAATTATGATTCTCATTCTAAATCAGTCTTTAA
Found at i:5200913 original size:60 final size:59
Alignment explanation
Indices: 5200774--5200923 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 59
5200764 TAACCCTTAC
* * * * ***
5200774 ACTTTTGAATATTCTAATTTCA-CCCTAAATTATGATTTCATTCTAAATTAGTCTTTAA
1 ACTTTTGAACACTCCAATTTCATCCCTAAATTATGATTTCATTCTAAATCAGTCCCCAA
* * *
5200832 ACTTTTGAACATTCTAATTTCATCCCTAAATTATGATTCTCTTTCTAAATCAGTCCCCAA
1 ACTTTTGAACACTCCAATTTCATCCCTAAATTATGATT-TCATTCTAAATCAGTCCCCAA
* * * *
5200892 ATTTTTTAATACTCCAATTTCATCCCCAAATT
1 ACTTTTGAACACTCCAATTTCATCCCTAAATT
5200924 CATCCAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 21 0.27
59 15 0.19
60 42 0.54
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.43
Consensus pattern (59 bp):
ACTTTTGAACACTCCAATTTCATCCCTAAATTATGATTTCATTCTAAATCAGTCCCCAA
Found at i:5203410 original size:64 final size:65
Alignment explanation
Indices: 5203283--5203412 Score: 201
Period size: 65 Copynumber: 2.0 Consensus size: 65
5203273 TGCCATCATT
5203283 ATTTAAAAATATTTTGTTCCTATAGAAAAAAGTAAAAAAAATTCATATGTACTAATTTAGGAAAC
1 ATTTAAAAATATTTTGTTCCTATAGAAAAAAGTAAAAAAAATTCATATGTACTAATTTAGGAAAC
* * * *
5203348 ATTTAAATATATTTTGTTTCTATAGAAAAAA-T-AATAAAATATCATATGTTCTAATTTAGGAAA
1 ATTTAAAAATATTTTGTTCCTATAGAAAAAAGTAAAAAAAAT-TCATATGTACTAATTTAGGAAA
5203411 C
65 C
5203412 A
1 A
5203413 ATTTGTTGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
63 7 0.12
64 24 0.40
65 29 0.48
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (65 bp):
ATTTAAAAATATTTTGTTCCTATAGAAAAAAGTAAAAAAAATTCATATGTACTAATTTAGGAAAC
Found at i:5205184 original size:51 final size:52
Alignment explanation
Indices: 5205114--5205300 Score: 216
Period size: 51 Copynumber: 3.6 Consensus size: 52
5205104 TCATATTATA
* * * *
5205114 AAAAAAATTGTAGCACTTAACATATACTTACACCGATGTAAGTGAATAAAAT
1 AAAAAAAGTATAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * **
5205166 ATAAAAA-TGTAGCACTTAACACATACTTACACCGGTGTGGGTGAATAAAAT
1 AAAAAAAGTATAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* * * * * *
5205217 -AGAAAATTATATCACTTAATACATACTCACACCGGTGTAAGTGAATAAAAA
1 AAAAAAAGTATAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
* *
5205268 AAAAAAAGTATATCACTTAACACATATTTACAC
1 AAAAAAAGTATAGCACTTAACACATACTTACAC
5205301 ATGTATAAGT
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
50 4 0.04
51 77 0.68
52 33 0.29
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (52 bp):
AAAAAAAGTATAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAAT
Found at i:5212695 original size:3 final size:3
Alignment explanation
Indices: 5212680--5212751 Score: 85
Period size: 3 Copynumber: 24.0 Consensus size: 3
5212670 TTTTATTTGT
* *
5212680 TTA TTA CTA TTA TTA TTA TTA -TA CTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
5212725 TTA -TA CTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA
5212752 GTAGTAGTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.07
3 51 0.84
4 6 0.10
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5212725 original size:27 final size:27
Alignment explanation
Indices: 5212687--5212751 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
5212677 TGTTTATTAC
5212687 TATTATTATTATTATACTATTATTTAT
1 TATTATTATTATTATACTATTATTTAT
5212714 TATTATTATTATTATACTATTATTTAT
1 TATTATTATTATTATACTATTATTTAT
5212741 TATTATTATTA
1 TATTATTATTA
5212752 GTAGTAGTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (27 bp):
TATTATTATTATTATACTATTATTTAT
Found at i:5215415 original size:15 final size:16
Alignment explanation
Indices: 5215385--5215421 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
5215375 TTCATAATAT
*
5215385 TTATTATATTTTTTTA
1 TTATTATATGTTTTTA
5215401 TTATTA-ATGTTTTTA
1 TTATTATATGTTTTTA
5215416 TT-TTAT
1 TTATTAT
5215422 TTTTAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTATTATATGTTTTTA
Found at i:5217027 original size:35 final size:34
Alignment explanation
Indices: 5216972--5217041 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
5216962 CAATCACATA
*
5216972 TTTACATTTGCATTTGCATTTTGCATTTTTGCATT
1 TTTACATTTGCATTTACATTTT-CATTTTTGCATT
* * *
5217007 TTTACGTTTGTATTTACATTTTTATTTTTGCATT
1 TTTACATTTGCATTTACATTTTCATTTTTGCATT
5217041 T
1 T
5217042 ACATCTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 12 0.39
35 19 0.61
ACGTcount: A:0.17, C:0.11, G:0.10, T:0.61
Consensus pattern (34 bp):
TTTACATTTGCATTTACATTTTCATTTTTGCATT
Found at i:5217028 original size:20 final size:20
Alignment explanation
Indices: 5217003--5217045 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
5216993 TGCATTTTTG
*
5217003 CATTTTTACGTTTGTATTTA
1 CATTTTTACGTTTGCATTTA
**
5217023 CATTTTTATTTTTGCATTTA
1 CATTTTTACGTTTGCATTTA
5217043 CAT
1 CAT
5217046 CTTTGCATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (20 bp):
CATTTTTACGTTTGCATTTA
Found at i:5217336 original size:42 final size:43
Alignment explanation
Indices: 5217267--5217351 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 43
5217257 GAGATGATTG
* * *
5217267 ATCAAGTAAAAAAAGTTCCAGGGTGATTC-AAATGAACAAATGA
1 ATCAAGCAAAAAAAGTTCCAAGATGATTCAAAAT-AACAAATGA
5217310 ATCAAGCAAAAAAA-TTCCAAGATGATTCAAAATAACAAATGA
1 ATCAAGCAAAAAAAGTTCCAAGATGATTCAAAATAACAAATGA
5217352 CAAAACTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 21 0.55
43 17 0.45
ACGTcount: A:0.53, C:0.13, G:0.14, T:0.20
Consensus pattern (43 bp):
ATCAAGCAAAAAAAGTTCCAAGATGATTCAAAATAACAAATGA
Found at i:5227244 original size:20 final size:20
Alignment explanation
Indices: 5227215--5227252 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5227205 TTTAAAAGTG
5227215 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
5227235 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
5227253 TTATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:5227321 original size:45 final size:45
Alignment explanation
Indices: 5227271--5227369 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 45
5227261 CAAACATCGA
* * *
5227271 ATGCATTTTATGCATCGATGC-CCATACCATGCATCGATGTACTC
1 ATGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
**
5227315 AGTGCATTAGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 A-TGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
*
5227361 ATGCTTTTT
1 ATGCATTTT
5227370 TAAAACATCG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
44 1 0.02
45 23 0.51
46 21 0.47
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (45 bp):
ATGCATTTTATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:5227419 original size:110 final size:110
Alignment explanation
Indices: 5227214--5227428 Score: 267
Period size: 110 Copynumber: 2.0 Consensus size: 110
5227204 TTTTAAAAGT
* * *
5227214 GATGCACCGATGCACCAATCCATGCATCGATGCACCAATTTATTTTTCAAACATCGAATGCATTT
1 GATGCACCGATGCACCAAACCATGCATCGATGCACCAATCTATTTTTAAAACATCGAATGCATTT
* * * *
5227279 TATGCATCGATGCCCATACCATGCATCGATGTACTCAGTGCATTA
66 TATGCATCGATGCACATACCATGCACCGATGCACTAAGTGCATTA
*
5227324 GATGCATCGATGCA-CAAGACCATGCATCGATGCACTC-ATGCT-TTTTTAAAACATCGAATGCA
1 GATGCACCGATGCACCAA-ACCATGCATCGATGCAC-CAAT-CTATTTTTAAAACATCGAATGCA
***
5227386 TTTTATGCATCGATGCACACT-TGGTGCACCGATGCACTAAGTG
63 TTTTATGCATCGATGCACA-TACCATGCACCGATGCACTAAGTG
5227429 TTCCAATGGT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
109 3 0.03
110 84 0.93
111 3 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (110 bp):
GATGCACCGATGCACCAAACCATGCATCGATGCACCAATCTATTTTTAAAACATCGAATGCATTT
TATGCATCGATGCACATACCATGCACCGATGCACTAAGTGCATTA
Found at i:5229518 original size:21 final size:21
Alignment explanation
Indices: 5229492--5229535 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5229482 ATTCTGGGCT
* *
5229492 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
5229513 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
5229534 AG
1 AG
5229536 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:5229605 original size:23 final size:22
Alignment explanation
Indices: 5229561--5229605 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5229551 AATGTCATGG
*
5229561 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
5229583 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
5229606 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:5231197 original size:103 final size:103
Alignment explanation
Indices: 5230972--5231189 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
5230962 GTCGAGGGTC
5230972 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
5231037 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
5231075 TATGTGGTCCTTCGGGACATATTTGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
5231140 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
5231178 TATGTGGTCCTT
1 TATGTGGTCCTT
5231190 ATGGACATTA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:5231255 original size:23 final size:23
Alignment explanation
Indices: 5231201--5231273 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
5231191 TGGACATTAT
*
5231201 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
5231224 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
5231247 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
5231268 TATATG
1 TATATG
5231274 AGCTGTGGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 33 0.79
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:5232449 original size:123 final size:121
Alignment explanation
Indices: 5232230--5232599 Score: 614
Period size: 123 Copynumber: 3.0 Consensus size: 121
5232220 AAGTTCTTCT
*
5232230 AAAAAAAAGTCATATATTCAAAGCATGACTTTGATAGGATATTTGGCAGTTCGGTGTTTGCTCCA
1 AAAAAAAAGTCATATATTCAAAGCATGACCTTGATAGGATATTTGGCAGTTC-GTGTTTGCTCCA
5232295 TTGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
65 TTGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
*
5232352 AAAAAAATAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCAGTGTTTGCTCC
1 AAAAAAA-AGTCATATATTCAAAGCATGACCTTGATAGGATATTTGGCAGTTC-GTGTTTGCTCC
*
5232417 ACTGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
64 ATTGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
*
5232475 AAAAAAAGAGTCATATATTCAAAGCATGACCTTGATTGGATATTTGGCAGTTCGATGTTTGCTCC
1 AAAAAAA-AGTCATATATTCAAAGCATGACCTTGATAGGATATTTGGCAGTTCG-TGTTTGCTCC
* * ** *
5232540 ATTGTGATTGTCAAGTCGAAGACATTGTAATGAGTTGAACTGTTTAATTAGTCCAATG
64 ATTGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
5232598 AA
1 AA
5232600 GGCTAATGTC
Statistics
Matches: 234, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
122 8 0.03
123 226 0.97
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (121 bp):
AAAAAAAAGTCATATATTCAAAGCATGACCTTGATAGGATATTTGGCAGTTCGTGTTTGCTCCAT
TGTGATTGTCAAGTCAAAGACATTGTTATGAGTTGAACCCTTTATTTAGTCCAATG
Found at i:5236592 original size:54 final size:55
Alignment explanation
Indices: 5236521--5236654 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 55
5236511 CACAGAAAAG
* * * *
5236521 GATGAATGTGTTATCAAATATTTTACT-AGCATCTGAGAAGAAACCACATGAGAT
1 GATGAATGTGTTGTCAAATATTTTACTGAACATCTGAGAAGAAACCACAAGAAAT
* * * * *
5236575 GGTGAACGTGTTGTCAAATATTTTA-TGAACATCTGGGCAGAAGCCACAAGAAAT
1 GATGAATGTGTTGTCAAATATTTTACTGAACATCTGAGAAGAAACCACAAGAAAT
*
5236629 GATGAATGTGTTGTCAAATGTTTTAC
1 GATGAATGTGTTGTCAAATATTTTAC
5236655 AAACCAGTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.02
54 65 0.98
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (55 bp):
GATGAATGTGTTGTCAAATATTTTACTGAACATCTGAGAAGAAACCACAAGAAAT
Found at i:5237068 original size:20 final size:22
Alignment explanation
Indices: 5237022--5237076 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
5237012 TACATCTACA
5237022 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
5237044 CTCTTCAAAGATGATATATTCT
1 CTCTTCAAAGATGATAGATTCT
*
5237066 CTTTTCAAAGA
1 CTCTTCAAAGA
5237077 CGAAAGCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:5237923 original size:123 final size:120
Alignment explanation
Indices: 5237754--5238190 Score: 535
Period size: 123 Copynumber: 3.7 Consensus size: 120
5237744 GGATCAACAT
* *
5237754 TTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAG
1 TTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAG
5237819 AGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAGTA
65 AGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCA-TA
*
5237876 TTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCGTAATGAGAA
1 TT-CCAGG-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
* ** *** *
5237941 GAGCTTGTTCAACCTTATGCTCGA----ATC-CATCACCCGATGGATC-A-A-CAT-
64 GAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCATA
* * * **
5237989 TTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTAAATAATGAGAAG
1 TTCCAG-GAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAG
*
5238054 AGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAACA
65 AGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATC-ATA
* *
5238111 TTTCCAAAGAGAGTTCATAATGAGAAGAACTAATCT------GAAGAAGAAGTTCATAATGAGAA
1 -TTCC-AGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAA
5238170 GAGCTTGTTCAACCTTTTGCT
64 GAGCTTGTTCAACCTTTTGCT
5238191 AGATTTCATC
Statistics
Matches: 270, Mismatches: 30, Indels: 35
0.81 0.09 0.10
Matches are distributed among these distances:
112 78 0.29
113 2 0.01
114 1 0.00
115 2 0.01
116 4 0.01
117 53 0.20
118 11 0.04
119 4 0.01
120 1 0.00
121 1 0.00
122 3 0.01
123 109 0.40
124 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (120 bp):
TTCCAGGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
GCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCATA
Found at i:5237945 original size:235 final size:234
Alignment explanation
Indices: 5237526--5238190 Score: 947
Period size: 235 Copynumber: 2.9 Consensus size: 234
5237516 TTTTTCTTAA
* * *
5237526 AACATTTCCATAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAATGA
1 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
* * * * **
5237591 GAAGAACTTGTTCAACCTTTTGCTCGA--AT-TCATC------A-CTCGAT--GGATCAGCATTG
66 GAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCA-CAGAAGGAGATAGATCAACATCAGCATTG
*
5237644 CCATGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
130 CCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
*
5237709 CTTGTTCAACATTTTGCTCGAATCCATCACCC-ATTGGATC
195 CTTGTTCAACCTTTTGCTCGAATCCATCACCCGA-TGGATC
*
5237749 AACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATA
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
5237814 AGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAGTATTG
65 AGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAGCATTG
* *
5237879 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCGTAATGAGAAGAG
130 CCAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAG
*
5237944 CTTGTTCAACCTTATGCTCGAATCCATCACCCGATGGATC
195 CTTGTTCAACCTTTTGCTCGAATCCATCACCCGATGGATC
* **
5237984 AACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTAAATAATG
1 AACATTTCCAG-AAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* *
5238049 AGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAACATTT
65 AGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAGCATTG
*
5238114 CCAAAG-AGAGTTCATAATGAGAAGAACTAATCT------GAAGAAGAAGTTCATAATGAGAAGA
130 CC-AAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGA
5238172 GCTTGTTCAACCTTTTGCT
194 GCTTGTTCAACCTTTTGCT
5238191 AGATTTCATC
Statistics
Matches: 400, Mismatches: 26, Indels: 26
0.88 0.06 0.06
Matches are distributed among these distances:
223 11 0.03
224 76 0.19
226 2 0.00
227 3 0.01
229 42 0.10
232 1 0.00
233 4 0.01
235 257 0.64
236 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (234 bp):
AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
GAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATCAGCATTGC
CAAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGC
TTGTTCAACCTTTTGCTCGAATCCATCACCCGATGGATC
Found at i:5238085 original size:112 final size:112
Alignment explanation
Indices: 5237526--5238190 Score: 724
Period size: 112 Copynumber: 5.8 Consensus size: 112
5237516 TTTTTCTTAA
* *
5237526 AACATTTCCA-TAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAATAAGTTCATAATG
1 AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * *
5237590 AGAAGAACTTGTTCAACCTTTTGCTCGAA-TTCATCACTCGATGGATC
66 AGAAGAGCTTGTTCAACCTTTTGCTCGAAGCT-ATCACCCGATGGATC
* * *
5237637 AGCATTGCCATG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 AACATTTCCA-GAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * *
5237701 GAGAAGAGCTTGTTCAACATTTTGCTCGAATCCATCACCC-ATTGGATC
65 GAGAAGAGCTTGTTCAACCTTTTGCTCGAAGCTATCACCCGA-TGGATC
5237749 AACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
* * ** *
5237813 AAGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATC
65 GAGAAGAGCTTGTTCAACCTTTTGCTCGAAGCTATCAC-----CCGATGGATC
**
5237866 AACATCAGTATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTC
1 -A-A-CA-T-TT-CCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTC
* * * *
5237931 GTAATGAGAAGAGCTTGTTCAACCTTATGCTCGAATCCATCACCCGATGGATC
60 ATAATGAGAAGAGCTTGTTCAACCTTTTGCTCGAAGCTATCACCCGATGGATC
* * **
5237984 AACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTAAATAATG
1 AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* ** *
5238049 AGAAGAGCTTGTTCAACCTTTTGCTCGACGCTATCACAGAAGGAGATAGATCAACATC
66 AGAAGAGCTTGTTCAACCTTTTGCTCGAAGCTATCAC-----CCGAT-G-----GATC
*
5238107 AACATTTCCA-AAGAGAGTTCATAATGAGAAGAACTAATCT------GAAGAAGAAGTTCATAAT
1 AACATTTCCAGAA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
5238165 GAGAAGAGCTTGTTCAACCTTTTGCT
65 GAGAAGAGCTTGTTCAACCTTTTGCT
5238191 AGATTTCATC
Statistics
Matches: 474, Mismatches: 49, Indels: 56
0.82 0.08 0.10
Matches are distributed among these distances:
111 10 0.02
112 264 0.56
113 3 0.01
114 1 0.00
115 2 0.00
116 1 0.00
117 51 0.11
118 10 0.02
119 1 0.00
120 2 0.00
121 1 0.00
122 5 0.01
123 123 0.26
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (112 bp):
AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCAACCTTTTGCTCGAAGCTATCACCCGATGGATC
Found at i:5238421 original size:21 final size:21
Alignment explanation
Indices: 5238394--5238436 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5238384 GAAGACACTA
*
5238394 GTTTTTTTTTCATTTTGTTTTT
1 GTTTTTGTTTCA-TTTGTTTTT
*
5238416 GTTTTTGTTTTATTTGTTTTT
1 GTTTTTGTTTCATTTGTTTTT
5238437 TACTATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.05, C:0.02, G:0.12, T:0.81
Consensus pattern (21 bp):
GTTTTTGTTTCATTTGTTTTT
Found at i:5238437 original size:22 final size:22
Alignment explanation
Indices: 5238394--5238436 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5238384 GAAGACACTA
5238394 GTTTTTTTTTCATTTTGTTTTT
1 GTTTTTTTTTCATTTTGTTTTT
5238416 GTTTTTGTTTT-A-TTTGTTTTT
1 GTTTTT-TTTTCATTTTGTTTTT
5238437 TACTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.05, C:0.02, G:0.12, T:0.81
Consensus pattern (22 bp):
GTTTTTTTTTCATTTTGTTTTT
Found at i:5244134 original size:21 final size:21
Alignment explanation
Indices: 5244108--5244152 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5244098 CCATTGCAAG
5244108 AAACGTGCCCAGCATGAAACA
1 AAACGTGCCCAGCATGAAACA
5244129 AAACGTGCCCAGCATGAAACA
1 AAACGTGCCCAGCATGAAACA
5244150 AAA
1 AAA
5244153 ATCAGTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (21 bp):
AAACGTGCCCAGCATGAAACA
Found at i:5247254 original size:21 final size:21
Alignment explanation
Indices: 5247230--5247273 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5247220 TTTTTGTAAT
5247230 CTTCCCGAGGGATTTCGAAAC
1 CTTCCCGAGGGATTTCGAAAC
* *
5247251 CTTCCCTAGGGGTTTCGAAAC
1 CTTCCCGAGGGATTTCGAAAC
5247272 CT
1 CT
5247274 CCAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (21 bp):
CTTCCCGAGGGATTTCGAAAC
Found at i:5256117 original size:15 final size:12
Alignment explanation
Indices: 5256080--5256110 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5256070 TGAAATGGGT
5256080 GACGACGGTAGG
1 GACGACGGTAGG
5256092 GACGACGGTAGG
1 GACGACGGTAGG
5256104 GACGACG
1 GACGACG
5256111 ATAGTAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.48, T:0.06
Consensus pattern (12 bp):
GACGACGGTAGG
Found at i:5256386 original size:3 final size:3
Alignment explanation
Indices: 5256378--5256427 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5256368 ATTTTAAAAT
5256378 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5256426 AT
1 AT
5256428 TAAAACCCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5257582 original size:18 final size:19
Alignment explanation
Indices: 5257543--5257583 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5257533 CATCATGCTC
*
5257543 GAAGACTTACTGATAATTTA
1 GAAGACTTACTCAT-ATTTA
5257563 GAAGACTTACTCAT-TTTA
1 GAAGACTTACTCATATTTA
5257581 GAA
1 GAA
5257584 ATATTCTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
20 13 0.65
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (19 bp):
GAAGACTTACTCATATTTA
Found at i:5258645 original size:43 final size:41
Alignment explanation
Indices: 5258597--5258976 Score: 219
Period size: 43 Copynumber: 8.7 Consensus size: 41
5258587 TCAATTTTAT
*
5258597 TTTTTACATCTATAATTGAGGCCCCTAATTTTTGTAATCCTAC
1 TTTTTAC-TTTATAATTGAGGCCCCTAATTTTT-TAATCCTAC
* * * * *
5258640 TTTTTATCTTTACAATTAAGGCCCTTAATTTTTCAATCCCAC
1 TTTTTA-CTTTATAATTGAGGCCCCTAATTTTTTAATCCTAC
* * * *
5258682 TTTTTAATATTTATAATTGATGACCCTAAATTTTTCAATCCTAC
1 TTTTT-A-CTTTATAATTGAGGCCCCT-AATTTTTTAATCCTAC
* ** *
5258726 TTTGTATCTTTATAATTG-CTCTCCTAATTCTTTTCAAT-CTCAC
1 TTTTTA-CTTTATAATTGAGGCCCCTAATT-TTTT-AATCCT-AC
* * ** * *
5258769 TTTCTACTTTAAAAATTGAAACTCCTAATTTTTTAA-GCTCAC
1 TTTTTACTTT-ATAATTGAGGCCCCTAATTTTTTAATCCT-AC
* * * *
5258811 TTTTTTCGTTTATAACTGAGGCCCCTAATTTTTTCAATCCCATT
1 TTTTTAC-TTTATAATTGAGGCCCCTAATTTTTT-AATCCTA-C
*
5258855 TTTTTACTTATATAATTTAGGCCCCTAATTTTTTTCAATCTCT-C
1 TTTTTACTT-TATAATTGAGGCCCCTAA-TTTTTT-AATC-CTAC
* * *
5258899 TTTTTTACCTTTAAAATTGAGGTCCCTAATTTTTTTTCAATCATAC
1 -TTTTTA-CTTTATAATTGAGGCCCCTAA--TTTTTT-AATCCTAC
* * *
5258945 TTTTTTACTTTCATAGTTTAAGCCCCTAATTT
1 -TTTTTACTTT-ATAATTGAGGCCCCTAATTT
5258977 AATCATTTTT
Statistics
Matches: 268, Mismatches: 48, Indels: 41
0.75 0.13 0.11
Matches are distributed among these distances:
41 4 0.01
42 54 0.20
43 82 0.31
44 55 0.21
45 37 0.14
46 36 0.13
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (41 bp):
TTTTTACTTTATAATTGAGGCCCCTAATTTTTTAATCCTAC
Found at i:5258697 original size:86 final size:86
Alignment explanation
Indices: 5258607--5258933 Score: 274
Period size: 86 Copynumber: 3.8 Consensus size: 86
5258597 TTTTTACATC
* * *
5258607 TATAATTGAGGCCCCTAATTTTTGTAATCCTACTTTTTATCTTTACAATTAAGGCCCTTAA-TTT
1 TATAATTGAGGCCCCTAATTTTT-TAATCCTACTTTTTATCTTTATAATTGAGGCCCCTAATTTT
5258671 TTCAATCCCACTTTTTAATATT
65 TTCAATCCCACTTTTTAATATT
* * * * ** *
5258693 TATAATTGATGACCCTAAATTTTTCAATCCTACTTTGTATCTTTATAATTG-CTCTCCTAATTCT
1 TATAATTGAGGCCCCT-AATTTTTTAATCCTACTTTTTATCTTTATAATTGAGGCCCCTAATT-T
* * *
5258757 TTTCAATCTCACTTTCTACT-TT
64 TTTCAATCCCACTTTTTAATATT
* * ** * * *
5258779 AAAAATTGAAACTCCTAATTTTTTAA-GCTCACTTTTT-TCGTTTATAACTGAGGCCCCTAATTT
1 TATAATTGAGGCCCCTAATTTTTTAATCCT-ACTTTTTATC-TTTATAATTGAGGCCCCTAATTT
*
5258842 TTTCAATCCCA-TTTTT-TTACTT
64 TTTCAATCCCACTTTTTAATA-TT
* * * *
5258864 ATATAATTTAGGCCCCTAATTTTTTTCAATCTCT-CTTTTTTACCTTTAAAATTGAGGTCCCTAA
1 -TATAATTGAGGCCCCTAA-TTTTTT-AATC-CTAC-TTTTTATCTTTATAATTGAGGCCCCTAA
5258928 TTTTTT
61 TTTTTT
5258934 TTCAATCATA
Statistics
Matches: 186, Mismatches: 40, Indels: 27
0.74 0.16 0.11
Matches are distributed among these distances:
83 1 0.01
84 8 0.04
85 42 0.23
86 70 0.38
87 31 0.17
88 3 0.02
89 28 0.15
90 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (86 bp):
TATAATTGAGGCCCCTAATTTTTTAATCCTACTTTTTATCTTTATAATTGAGGCCCCTAATTTTT
TCAATCCCACTTTTTAATATT
Found at i:5258894 original size:45 final size:44
Alignment explanation
Indices: 5258811--5258976 Score: 158
Period size: 45 Copynumber: 3.7 Consensus size: 44
5258801 TTAAGCTCAC
* * *
5258811 TTTTTT-CGTTTATAACTGAGGCCCCTAA-TTTTTTCAATCCCAT
1 TTTTTTAC-TTTATAATTTAGGCCCCTAATTTTTTTCAATCACAT
*
5258854 TTTTTTACTTATATAATTTAGGCCCCTAATTTTTTTCAATCTC-T
1 TTTTTTACTT-TATAATTTAGGCCCCTAATTTTTTTCAATCACAT
* * * * *
5258898 CTTTTTTACCTTTAAAATTGAGGTCCCTAATTTTTTTTCAATCATAC
1 -TTTTTTA-CTTTATAATTTAGGCCCCTAA-TTTTTTTCAATCACAT
* *
5258945 TTTTTTACTTTCATAGTTTAAGCCCCTAATTT
1 TTTTTTACTTT-ATAATTTAGGCCCCTAATTT
5258977 AATCATTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
43 8 0.08
44 18 0.18
45 41 0.41
46 34 0.34
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.51
Consensus pattern (44 bp):
TTTTTTACTTTATAATTTAGGCCCCTAATTTTTTTCAATCACAT
Found at i:5260836 original size:32 final size:32
Alignment explanation
Indices: 5260791--5260852 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
5260781 TTCTCCCCGG
*
5260791 GCGGATAAGAACGTCCCCACCATCTATTTCCC
1 GCGGATAAAAACGTCCCCACCATCTATTTCCC
5260823 GCGGATAAAAACGTCCCCACCATCTATTTC
1 GCGGATAAAAACGTCCCCACCATCTATTTC
5260853 ATGCCCTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (32 bp):
GCGGATAAAAACGTCCCCACCATCTATTTCCC
Found at i:5261434 original size:29 final size:29
Alignment explanation
Indices: 5261401--5261485 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
5261391 AGCAGGGGAT
* * **
5261401 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* * *
5261430 GTCGCCGGGCGTACATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
5261459 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
5261486 GCAACTGTTG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.14, C:0.29, G:0.39, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:5262449 original size:28 final size:27
Alignment explanation
Indices: 5262418--5262471 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
5262408 AATGTTTTTT
5262418 TTATCTGAAT-AAAGATAATTTTTATTAG
1 TTATCTGAATCAAA-ATAA-TTTTATTAG
* *
5262446 TTATTTTAATCAAAATAATTTTATTA
1 TTATCTGAATCAAAATAATTTTATTA
5262472 ACAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 8 0.35
28 12 0.52
29 3 0.13
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.50
Consensus pattern (27 bp):
TTATCTGAATCAAAATAATTTTATTAG
Found at i:5263073 original size:16 final size:15
Alignment explanation
Indices: 5263034--5263075 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 15
5263024 GACATATTAA
5263034 AAAT-TAAAAAA-AT
1 AAATATAAAAAAGAT
5263047 AAATA-AAAAAAGAT
1 AAATATAAAAAAGAT
5263061 ACAATATAAAAAAGA
1 A-AATATAAAAAAGA
5263076 AAAGACAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 4 0.16
16 8 0.32
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (15 bp):
AAATATAAAAAAGAT
Found at i:5263590 original size:3 final size:3
Alignment explanation
Indices: 5263576--5263644 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
5263566 AAATCATTTG
* * *
5263576 TTA TTCA TTA TTA TTA TTG TTA TT- TTAA TTA TTA TCA CTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* *
5263622 TTAA TT- TTT TTA TTA CTA TTA TT
1 TT-A TTA TTA TTA TTA TTA TTA TT
5263645 TTTAGGTTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
2 4 0.08
3 40 0.77
4 8 0.15
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5267269 original size:6 final size:6
Alignment explanation
Indices: 5267252--5267323 Score: 135
Period size: 6 Copynumber: 12.0 Consensus size: 6
5267242 ACACTTTTTG
*
5267252 GCATTT GTATTT GCATTT GCATTT GCATTT GCATTT GCATTT GCATTT
1 GCATTT GCATTT GCATTT GCATTT GCATTT GCATTT GCATTT GCATTT
5267300 GCATTT GCATTT GCATTT GCATTT
1 GCATTT GCATTT GCATTT GCATTT
5267324 TTCACCTGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (6 bp):
GCATTT
Found at i:5268842 original size:15 final size:14
Alignment explanation
Indices: 5268811--5268856 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
5268801 GGAAAAAAAC
*
5268811 AAAGAAAGAAATAA
1 AAAGAAAGAAAGAA
5268825 AAAGCAAAGATAAGAA
1 AAAG-AAAGA-AAGAA
5268841 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
5268855 AA
1 AA
5268857 TGAATCAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.38
15 10 0.34
16 8 0.28
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:5269748 original size:25 final size:24
Alignment explanation
Indices: 5269711--5269775 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
5269701 ATGGACAATA
* * *
5269711 ATTTTTTATAATTTTTTTATTAAAC
1 ATTTTTCAAAATTTTTTAATT-AAC
*
5269736 ATTTTTCAAAATTCTTTTAATTAAG
1 ATTTTTCAAAATT-TTTTAATTAAC
*
5269761 GTTTTTC-AAATTTTT
1 ATTTTTCAAAATTTTT
5269776 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 3 0.09
24 5 0.15
25 19 0.56
26 7 0.21
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (24 bp):
ATTTTTCAAAATTTTTTAATTAAC
Found at i:5271793 original size:66 final size:66
Alignment explanation
Indices: 5271679--5271843 Score: 235
Period size: 66 Copynumber: 2.5 Consensus size: 66
5271669 TTGACCTCAC
*
5271679 TTGAGATTGTTTTTCTCAAAA-AAACTTTGTCTCACTTGAGACAGTCTTCCATAAGAAACAAACA
1 TTGATATTGTTTTTCTCAAAACAAACTTTGTCTCACTTGAGACAGTCTTCCATAAGAAACAAACA
5271743 T
66 T
* * * *
5271744 TTGATATTATTTTTCTTCAAAACAAA-TTTGTCTCACTTGAGACAGTCTTCCTTAAGACACGAAC
1 TTGATATTGTTTTTC-TCAAAACAAACTTTGTCTCACTTGAGACAGTCTTCCATAAGAAACAAAC
5271808 AT
65 AT
* *
5271810 TTGATATTGTTTTTCCCCAAAACAAATTTTGTCT
1 TTGATATTGTTTTT-CTCAAAACAAACTTTGTCT
5271844 TGCTTAAGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
65 13 0.15
66 65 0.73
67 11 0.12
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (66 bp):
TTGATATTGTTTTTCTCAAAACAAACTTTGTCTCACTTGAGACAGTCTTCCATAAGAAACAAACA
T
Found at i:5271944 original size:102 final size:102
Alignment explanation
Indices: 5271828--5272128 Score: 422
Period size: 102 Copynumber: 2.9 Consensus size: 102
5271818 GTTTTTCCCC
** * *
5271828 AAAACAAATTTTGTCTTGCTTAAGATAATTCTCATTCGAAACACAAATTTTGAATTTGTTTCACT
1 AAAACAAAACTTGTCTCGCTTGAGATAATTCTCATTCGAAACACAAATTTTGAATTTGTTTCACT
5271893 TGAAACAAAATTAATCTCACTTTATATTGTTATCCTA
66 TGAAACAAAATTAATCTCACTTTATATTGTTATCCTA
5271930 AAAACAAAACTTGTCTCGCTTGAGATAATTCTCATTCGAAACACAAATTTTGAATTTGTTTCACT
1 AAAACAAAACTTGTCTCGCTTGAGATAATTCTCATTCGAAACACAAATTTTGAATTTGTTTCACT
*
5271995 TGAAACAAAATTAATCTCACTTGATATTGTTATCCTA
66 TGAAACAAAATTAATCTCACTTTATATTGTTATCCTA
* * * *** * * * *
5272032 AAAACAAAACTTGTCTCACTTGAGACAATTTTCCCACAAAACACAAAATTTGGAAATTGTTTTAC
1 AAAACAAAACTTGTCTCGCTTGAGATAATTCTCATTCGAAACAC-AAATTTTGAATTTGTTTCAC
* ** *
5272097 TTGAAACAAAATTGATAACACTTTAGATTGTT
65 TTGAAACAAAATTAATCTCACTTTATATTGTT
5272129 TTTCTTAAAA
Statistics
Matches: 178, Mismatches: 20, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
102 134 0.75
103 44 0.25
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (102 bp):
AAAACAAAACTTGTCTCGCTTGAGATAATTCTCATTCGAAACACAAATTTTGAATTTGTTTCACT
TGAAACAAAATTAATCTCACTTTATATTGTTATCCTA
Found at i:5272837 original size:139 final size:139
Alignment explanation
Indices: 5272618--5272869 Score: 353
Period size: 139 Copynumber: 1.8 Consensus size: 139
5272608 AGACGTCCTT
* * * *
5272618 AACACAAAGGAACAATGTCGTCTACCGACCAGATCTCCTCAATGTGAAGGAGCAGCATAATCCTC
1 AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAAGAGCAGCATAATCCTC
* * *
5272683 AGACAATCAGACTTCCTCAACGCG-ATGAATCCATGTTATCTCTAAATTTTCTCCAAAGATGGTT
66 AGACAACCAGACTTCCTAAACGCGAAGGAAT-CATGTTATCTCTAAATTTTCTCCAAAGATGGTT
5272747 AAATGTTATC
130 AAATGTTATC
* * * * *
5272757 AACACGAAGGAACAATGTCGTCCACCGACTAGATCTCCTCAACGCGAAAGAGCATCGTCATCCTC
1 AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAAGAGCAGCATAATCCTC
* * *
5272822 AGATAACCAGACTTCCTAAACGCGAAGGAATCGTGTTATCTTTAAATT
66 AGACAACCAGACTTCCTAAACGCGAAGGAATCATGTTATCTCTAAATT
5272870 AATCAAATTG
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
139 92 0.95
140 5 0.05
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (139 bp):
AACACAAAGGAACAATGTCGTCCACCGACCAGATCTCCTCAACGCGAAAGAGCAGCATAATCCTC
AGACAACCAGACTTCCTAAACGCGAAGGAATCATGTTATCTCTAAATTTTCTCCAAAGATGGTTA
AATGTTATC
Found at i:5273157 original size:122 final size:122
Alignment explanation
Indices: 5272931--5273199 Score: 333
Period size: 122 Copynumber: 2.2 Consensus size: 122
5272921 CGGCCAAAAC
* * * *
5272931 TCTTCAACATGGATGAGCAGTGTCATCTTCAACACCATATTATCTCTAGATTGACCTGATTTCCT
1 TCTTCAATATGGATGAGCAGTGTCATCTTCAACACCATATTATATCTAGATTAACCCGATTTCCT
* * * *
5272996 CAACGAGAAGGAACAACATCAGCTTTAGCAAATAATTTATCTGAAAGCTACAAGATA
66 CAACGAGAAGGAACAACATCAGCTTTAACAAACAATTTATCTAAAAGCGACAAGATA
* * *
5273053 TCTTCAATATGGATGAGCAGTTTCGTCTTCAACACCATATTATATCTGGATTAACCCGATTTCCT
1 TCTTCAATATGGATGAGCAGTGTCATCTTCAACACCATATTATATCTAGATTAACCCGATTTCCT
* * * * * * *
5273118 CAACGAGAAGGAACAACGTCA-TTTTCAACAAACATTTTATTTAAAAGCGGCCAGATC
66 CAACGAGAAGGAACAACATCAGCTTT-AACAAACAATTTATCTAAAAGCGACAAGATA
* * *
5273175 TCATCAATATGGAAGAGCAGCGTCA
1 TCTTCAATATGGATGAGCAGTGTCA
5273200 CCTTTAACTT
Statistics
Matches: 123, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
121 3 0.02
122 120 0.98
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (122 bp):
TCTTCAATATGGATGAGCAGTGTCATCTTCAACACCATATTATATCTAGATTAACCCGATTTCCT
CAACGAGAAGGAACAACATCAGCTTTAACAAACAATTTATCTAAAAGCGACAAGATA
Found at i:5273358 original size:3 final size:3
Alignment explanation
Indices: 5273343--5273412 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
5273333 CTAATCGTTC
* * *
5273343 ATT ATT CATT ATT ATT ATT GTT ATT -TT AATT ATT ATC ACT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
*
5273389 ATT AATT -TT ATT ATT ACT ATT ATT
1 ATT -ATT ATT ATT ATT ATT ATT ATT
5273413 TTTAGGTTAC
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.07
3 42 0.78
4 8 0.15
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5281618 original size:21 final size:21
Alignment explanation
Indices: 5281571--5281610 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5281561 GACTTTGGAA
5281571 CTTTTCCTGGGATGCAACTAG
1 CTTTTCCTGGGATGCAACTAG
*
5281592 CTTTTCCTGGGATGTAACT
1 CTTTTCCTGGGATGCAACT
5281611 GGTTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (21 bp):
CTTTTCCTGGGATGCAACTAG
Found at i:5282574 original size:31 final size:31
Alignment explanation
Indices: 5282451--5282575 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
5282441 CCCGAAGGAC
* * *
5282451 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
5282482 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5282513 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5282544 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5282575 C
1 C
5282576 CCTTGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5285668 original size:12 final size:12
Alignment explanation
Indices: 5285651--5285675 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5285641 AAAGATAAAG
5285651 ATTAAATAAATA
1 ATTAAATAAATA
5285663 ATTAAATAAATA
1 ATTAAATAAATA
5285675 A
1 A
5285676 AAGAGATTGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAATA
Found at i:5287676 original size:7 final size:8
Alignment explanation
Indices: 5287659--5287684 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5287649 AAAATAGTGA
5287659 TTTTTATT
1 TTTTTATT
5287667 TTTTTATT
1 TTTTTATT
5287675 TTTTTATT
1 TTTTTATT
5287683 TT
1 TT
5287685 CATGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTATT
Found at i:5292863 original size:5 final size:5
Alignment explanation
Indices: 5292853--5292885 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
5292843 TGATAGAGAA
5292853 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
5292886 TAATTCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5304191 original size:11 final size:11
Alignment explanation
Indices: 5304175--5304213 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5304165 TTAGCCTACA
5304175 TTTTTTTTCTT
1 TTTTTTTTCTT
5304186 TTTTTTTTCTT
1 TTTTTTTTCTT
* *
5304197 GTTTTCTTCTGT
1 TTTTTTTTCT-T
5304209 TTTTT
1 TTTTT
5304214 CAAAGATGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:5309450 original size:133 final size:133
Alignment explanation
Indices: 5309242--5309497 Score: 300
Period size: 133 Copynumber: 1.9 Consensus size: 133
5309232 AATATTGTAC
* * * * * *
5309242 TGATCACTTGTTACTGACTCGTATACCTTTGTAGTGCATGAGGTGGAGTGATAAGTGGATATCAT
1 TGATCACTTGTTACTGACTCGTATAACTTTGTAGTACAAGAGGAGGAGTGATAAGTGGACACCAT
* * * *** *
5309307 ACTGATCACTCAATACTGATTCGTGTACCTTAGTGGTGCATGAGGTGGAGTG-ATCTGGGTACCT
66 ACTGAACACTCAATACTGACTCGCGTACCTTAGTGAAACACGAGGTGGAGTGTATCTGGGTACCT
5309371 TAA
131 TAA
* ** *
5309374 TGATCACTTCGTTACTGACTCGTGTAACTTTGTAGTACAAGAGGAGGAGTGA-ATTTTGGGCACC
1 TGATCACTT-GTTACTGACTCGTATAACTTTGTAGTACAAGAGGAGGAGTGATA-AGTGGACACC
** *
5309438 ATACTGAACACTCGTTACTGACTCGCGTATCTTAGTGAAACACGAGGTGGAGTGTATCTG
64 ATACTGAACACTCAATACTGACTCGCGTACCTTAGTGAAACACGAGGTGGAGTGTATCTG
5309498 ATACCTTCAG
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
132 10 0.10
133 86 0.85
134 5 0.05
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (133 bp):
TGATCACTTGTTACTGACTCGTATAACTTTGTAGTACAAGAGGAGGAGTGATAAGTGGACACCAT
ACTGAACACTCAATACTGACTCGCGTACCTTAGTGAAACACGAGGTGGAGTGTATCTGGGTACCT
TAA
Found at i:5309462 original size:67 final size:66
Alignment explanation
Indices: 5309210--5309462 Score: 238
Period size: 67 Copynumber: 3.8 Consensus size: 66
5309200 AGTCAGTGAC
** *** * *
5309210 GCATGAGGTGGAGTGATTACTGAATATTGTACTGATCACTTGTTACTGACTCGTATACCTTTGTA
1 GCATGAGGTGGAGTGATT-CTGGGTACCATACTGATCACTCGTTACTGACTCGTGTACCTTTGTA
5309275 GT
65 GT
** * * ** * * *
5309277 GCATGAGGTGGAGTGATAAGTGGATATCATACTGATCACTCAATACTGATTCGTGTACCTTAGTG
1 GCATGAGGTGGAGTGAT-TCTGGGTACCATACTGATCACTCGTTACTGACTCGTGTACCTTTGTA
5309342 GT
65 GT
* * *
5309344 GCATGAGGTGGAGTGA-TCTGGGTACCTTAATGATCACTTCGTTACTGACTCGTGTAACTTTGTA
1 GCATGAGGTGGAGTGATTCTGGGTACCATACTGATCAC-TCGTTACTGACTCGTGTACCTTTGTA
5309408 GT
65 GT
* * * * * *
5309410 ACAAGAGGAGGAGTGAATTTTGGGCACCATACTGAACACTCGTTACTGACTCG
1 GCATGAGGTGGAGTG-ATTCTGGGTACCATACTGATCACTCGTTACTGACTCG
5309463 CGTATCTTAG
Statistics
Matches: 150, Mismatches: 32, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
65 15 0.10
66 34 0.23
67 85 0.57
68 16 0.11
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (66 bp):
GCATGAGGTGGAGTGATTCTGGGTACCATACTGATCACTCGTTACTGACTCGTGTACCTTTGTAG
T
Found at i:5309490 original size:67 final size:66
Alignment explanation
Indices: 5309348--5309497 Score: 151
Period size: 67 Copynumber: 2.2 Consensus size: 66
5309338 AGTGGTGCAT
* * * * * *
5309348 GAGGTGGAGTGATCTGGGTACCTTAATGATCACTTCGTTACTGACTCGTGTAACTTTGTAGTACA
1 GAGGTGGAGTGATCTGGGCACCATAATGAACACTTCGTTACTGACTCGCGTAACTTAGTAGAACA
5309413 A
66 A
* * * *
5309414 GAGGAGGAGTGAATTTTGGGCACCATACTGAACAC-TCGTTACTGACTCGCGTATCTTAGT-GAA
1 GAGGTGGAGTG-A-TCTGGGCACCATAATGAACACTTCGTTACTGACTCGCGTAACTTAGTAG-A
*
5309477 ACAC
63 ACAA
5309481 GAGGTGGAGTGTATCTG
1 GAGGTGGAGTG-ATCTG
5309498 ATACCTTCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
66 14 0.21
67 37 0.55
68 16 0.24
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (66 bp):
GAGGTGGAGTGATCTGGGCACCATAATGAACACTTCGTTACTGACTCGCGTAACTTAGTAGAACA
A
Found at i:5309732 original size:17 final size:18
Alignment explanation
Indices: 5309710--5309757 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
5309700 AAAGATAGTC
5309710 CAATATAGAAAAAAG-AA
1 CAATATAGAAAAAAGTAA
**
5309727 CAATATAG-TGAAAGTAA
1 CAATATAGAAAAAAGTAA
5309744 CAATATAAGAAAAA
1 CAATAT-AGAAAAA
5309758 GGAAAAGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.17
17 16 0.67
18 2 0.08
19 2 0.08
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (18 bp):
CAATATAGAAAAAAGTAA
Found at i:5309785 original size:16 final size:17
Alignment explanation
Indices: 5309766--5309798 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5309756 AAGGAAAAGT
*
5309766 ACATAA-AATAGAAACA
1 ACATAAGAAAAGAAACA
5309782 ACATAAGAAAAGAAACA
1 ACATAAGAAAAGAAACA
5309799 GTAGAGAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.12, G:0.09, T:0.09
Consensus pattern (17 bp):
ACATAAGAAAAGAAACA
Found at i:5312585 original size:6 final size:6
Alignment explanation
Indices: 5312574--5312607 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
5312564 AGAAAATTAA
* *
5312574 TATAAT TATAAT TGTAAT TGTAAT TATAAT TATA
1 TATAAT TATAAT TATAAT TATAAT TATAAT TATA
5312608 GAAATGCAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:5314975 original size:5 final size:5
Alignment explanation
Indices: 5314965--5314998 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
5314955 AGAGATATCT
5314965 TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA TTCA
1 TTCAA TTCAA TTCAA TTCAA TTCAA TTCAA TTCA
5314999 TAATTAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (5 bp):
TTCAA
Found at i:5316377 original size:23 final size:23
Alignment explanation
Indices: 5316335--5316378 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5316325 ATAATTTTTT
*
5316335 TAAATTTAAAATATTCAAAAAAA
1 TAAATTTAAAATACTCAAAAAAA
5316358 TAAATTTAAAAATACT-AAAAA
1 TAAATTT-AAAATACTCAAAAA
5316379 TAAAAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATTTAAAATACTCAAAAAAA
Found at i:5319696 original size:2 final size:2
Alignment explanation
Indices: 5319689--5319750 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
5319679 TAAACAACGC
5319689 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5319731 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
5319751 AGTGAATATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5335918 original size:24 final size:24
Alignment explanation
Indices: 5335872--5335918 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5335862 TATTTTCATA
5335872 AGTATTAAGAATTTCTAGAATTTG
1 AGTATTAAGAATTTCTAGAATTTG
* *
5335896 AGTATTTAAGCATTT-TAGGATTT
1 AGTA-TTAAGAATTTCTAGAATTT
5335919 ATATTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (24 bp):
AGTATTAAGAATTTCTAGAATTTG
Found at i:5337503 original size:32 final size:32
Alignment explanation
Indices: 5337411--5337510 Score: 112
Period size: 32 Copynumber: 3.1 Consensus size: 32
5337401 GTTGAGTCAC
* *
5337411 ATTTGGATAATGC-CTAGTCGAGTTAGAGTTGG
1 ATTTGGATAATGCTC-AGTTGAGTTAGAGTTGT
* * *
5337443 ATTTGGATTATACTTAGTTGAGTTAGAGTTGT
1 ATTTGGATAATGCTCAGTTGAGTTAGAGTTGT
* * *
5337475 ATTTGGATAATGCTCAGTTAAGTCAGAGTCGT
1 ATTTGGATAATGCTCAGTTGAGTTAGAGTTGT
5337507 ATTT
1 ATTT
5337511 AGACAATGTA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (32 bp):
ATTTGGATAATGCTCAGTTGAGTTAGAGTTGT
Found at i:5340584 original size:32 final size:32
Alignment explanation
Indices: 5340541--5340686 Score: 143
Period size: 32 Copynumber: 4.6 Consensus size: 32
5340531 GATGTATGTT
* * ** *
5340541 GAGTTTCATTTGGATAATACCTAGTTTAGTTA
1 GAGTTGCATTTGGATAATGCCTAGTCGAGTCA
*
5340573 GAGTTGTATTTGGATAATGCCTAGTCGAGTCA
1 GAGTTGCATTTGGATAATGCCTAGTCGAGTCA
*
5340605 GAGTTGCATTTAGATAATGCCTAGTCGAGAT-A
1 GAGTTGCATTTGGATAATGCCTAGTCGAG-TCA
* * * * *
5340637 GAGTTACCTTTGGATAAT-TCTCCGTCGAGTTA
1 GAGTTGCATTTGGATAATGCCT-AGTCGAGTCA
*
5340669 GAGTTGCATTTAGATAAT
1 GAGTTGCATTTGGATAAT
5340687 ACAAAGCAAT
Statistics
Matches: 95, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.03
32 91 0.96
33 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (32 bp):
GAGTTGCATTTGGATAATGCCTAGTCGAGTCA
Found at i:5353062 original size:2 final size:2
Alignment explanation
Indices: 5353045--5353099 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
5353035 ATCCCAAAGG
* *
5353045 TA TA CA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5353087 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
5353100 CACTTTATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5354012 original size:20 final size:20
Alignment explanation
Indices: 5353959--5354038 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
5353949 CATCTTAAAA
* *
5353959 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACTACCCTC
*
5353979 TTGGTATCGATACTACCCTC
1 ATGGTATCGATACTACCCTC
* * **
5353999 ATAGTATCGATACTATCACAA
1 ATGGTATCGATACTA-CCCTC
5354020 ATGGTATCGATACTACCCT
1 ATGGTATCGATACTACCCT
5354039 TAATAATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGGTATCGATACTACCCTC
Found at i:5354201 original size:22 final size:22
Alignment explanation
Indices: 5354173--5354216 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5354163 CTTTCCTTAA
5354173 GCCTTTAAACTAAACTTCTTTC
1 GCCTTTAAACTAAACTTCTTTC
*
5354195 GCCTTTAAATTAAACTTCTTTC
1 GCCTTTAAACTAAACTTCTTTC
5354217 ATTCAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.25, G:0.05, T:0.43
Consensus pattern (22 bp):
GCCTTTAAACTAAACTTCTTTC
Found at i:5360172 original size:23 final size:23
Alignment explanation
Indices: 5360138--5360198 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
5360128 CATAATTATC
* * *
5360138 CCGAAGGACCACATAGGTTTGTA
1 CCGAAGGGCCACATAGGGTTGCA
*
5360161 CTGAAGGGCCACATAGGGTTGCA
1 CCGAAGGGCCACATAGGGTTGCA
*
5360184 CCGAAGTGCCACATA
1 CCGAAGGGCCACATA
5360199 TTTATCCCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.18
Consensus pattern (23 bp):
CCGAAGGGCCACATAGGGTTGCA
Found at i:5371254 original size:19 final size:21
Alignment explanation
Indices: 5371211--5371262 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5371201 GAAACCCCTT
5371211 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5371232 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5371251 TGAAGATACATG
1 TGAAAATACATG
5371263 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5374478 original size:17 final size:16
Alignment explanation
Indices: 5374450--5374503 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 16
5374440 TTGAATTTTC
5374450 TTTT-TCTTTTCTTCT
1 TTTTGTCTTTTCTTCT
5374465 TTTCTGAT-TTTTCTTCT
1 TTT-TG-TCTTTTCTTCT
5374482 TTTTGTCTTTTCTTTCT
1 TTTTGTCTTTTC-TTCT
5374499 TTTTG
1 TTTTG
5374504 CACTCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.12
16 8 0.24
17 21 0.62
18 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTGTCTTTTCTTCT
Found at i:5374490 original size:28 final size:27
Alignment explanation
Indices: 5374435--5374490 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
5374425 GCTTGCTTTC
*
5374435 TCTTTTTGAATTTTCTTTTTCTTTTCT
1 TCTTTTTGAATTTTCTTTTTCTTGTCT
*
5374462 TCTTTTCTGATTTTTCTTCTTT-TTGTCT
1 TCTTTT-TGAATTTTCTT-TTTCTTGTCT
5374490 T
1 T
5374491 TTCTTTCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 16 0.64
29 3 0.12
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.73
Consensus pattern (27 bp):
TCTTTTTGAATTTTCTTTTTCTTGTCT
Found at i:5375249 original size:19 final size:21
Alignment explanation
Indices: 5375206--5375257 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
5375196 GAAACCCCTT
5375206 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
5375227 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
5375246 TGAAGATACATG
1 TGAAAATACATG
5375258 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:5386206 original size:71 final size:71
Alignment explanation
Indices: 5386090--5386232 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
5386080 ATTCCCAAAC
*
5386090 GACCATGGGAAGGTGTTTCCATGGACTTCATAGTTGGATTACCAAATATTGATGGGCTTTAAAGC
1 GACCATGAGAAGGTGTTTCCATGGACTTCATAGTTGGATTACCAAATATTGATGGGCTTTAAAGC
5386155 ATCATG
66 ATCATG
5386161 GACCATGAGAAGGTGTTTCCATGGACTTCATAGTTGGATTACCAAATATTGATGGGCTTTAAAGC
1 GACCATGAGAAGGTGTTTCCATGGACTTCATAGTTGGATTACCAAATATTGATGGGCTTTAAAGC
5386226 ATCATG
66 ATCATG
5386232 G
1 G
5386233 TTGTGGTGGA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (71 bp):
GACCATGAGAAGGTGTTTCCATGGACTTCATAGTTGGATTACCAAATATTGATGGGCTTTAAAGC
ATCATG
Found at i:5387459 original size:17 final size:17
Alignment explanation
Indices: 5387419--5387460 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5387409 ATAATATATT
* *
5387419 TAAAAAAATAATATTAT
1 TAAAAATATAATATTAA
*
5387436 TATAAATATAATATTAA
1 TAAAAATATAATATTAA
5387453 TAAAAATA
1 TAAAAATA
5387461 CATTAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATATAATATTAA
Found at i:5387470 original size:32 final size:29
Alignment explanation
Indices: 5387411--5387470 Score: 68
Period size: 32 Copynumber: 2.0 Consensus size: 29
5387401 TTATTAAGAT
*
5387411 AATATATTTAAAAAAATAATATTATTATA
1 AATATATTTAAAAAAATAATATAATTATA
5387440 AATATAATATTAATAAAAATACAT-TAATTAT
1 AATAT-AT-TTAA-AAAAATA-ATATAATTAT
5387471 TAAAGAACTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 5 0.19
30 2 0.08
31 4 0.15
32 13 0.50
33 2 0.08
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
AATATATTTAAAAAAATAATATAATTATA
Found at i:5391172 original size:2 final size:2
Alignment explanation
Indices: 5391165--5391211 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
5391155 AAACGTGTTA
5391165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5391207 AT AT A
1 AT AT A
5391212 CGATATAAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5393897 original size:23 final size:23
Alignment explanation
Indices: 5393871--5393930 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
5393861 TAAAATAATT
*
5393871 AATAAAGTAGTAATTGATCATAA
1 AATAATGTAGTAATTGATCATAA
* *
5393894 AATAATGGAGTAATTGATTATAA
1 AATAATGTAGTAATTGATCATAA
5393917 AATAATGTA-TAATT
1 AATAATGTAGTAATT
5393931 TAAGCACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 5 0.15
23 28 0.85
ACGTcount: A:0.50, C:0.02, G:0.13, T:0.35
Consensus pattern (23 bp):
AATAATGTAGTAATTGATCATAA
Found at i:5394481 original size:6 final size:6
Alignment explanation
Indices: 5394470--5394517 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
5394460 CTCTCGAAAT
*
5394470 TTTTTA TTTTTA TTTAT- TTTTTA TTTTT- TTATTT- TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
5394516 TT
1 TT
5394518 GATAATTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
5 9 0.24
6 28 0.76
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:5394490 original size:17 final size:18
Alignment explanation
Indices: 5394468--5394517 Score: 77
Period size: 17 Copynumber: 2.9 Consensus size: 18
5394458 TACTCTCGAA
5394468 ATTTTTTATTTTTATT-T
1 ATTTTTTATTTTTATTAT
5394485 ATTTTTTATTTTT-TTAT
1 ATTTTTTATTTTTATTAT
*
5394502 TTTTTTTATTTTTATT
1 ATTTTTTATTTTTATT
5394518 GATAATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 2 0.07
17 26 0.87
18 2 0.07
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (18 bp):
ATTTTTTATTTTTATTAT
Found at i:5395372 original size:4 final size:4
Alignment explanation
Indices: 5395359--5395398 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
5395349 ATTGATTAAC
* *
5395359 ATAA AT-A ATAA ATAA ATAA ACAA ACAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
5395399 GACGATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:5399401 original size:25 final size:28
Alignment explanation
Indices: 5399367--5399421 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 28
5399357 AAAAAAAAGG
* *
5399367 TTATTCTTTC-CTTT-TTCA-TCTTCTT
1 TTATTATTTCTCTTTCTTCATTCTTATT
5399392 TTATTATTTCTCTTTCTTCATTCTTATT
1 TTATTATTTCTCTTTCTTCATTCTTATT
5399420 TT
1 TT
5399422 TCTCTCCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
26 4 0.16
27 4 0.16
28 8 0.32
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (28 bp):
TTATTATTTCTCTTTCTTCATTCTTATT
Found at i:5401446 original size:2 final size:2
Alignment explanation
Indices: 5401439--5401478 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5401429 ATGCATTTAT
*
5401439 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5401479 GCGCGCGCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:5401505 original size:4 final size:4
Alignment explanation
Indices: 5401498--5401705 Score: 380
Period size: 4 Copynumber: 52.0 Consensus size: 4
5401488 CGCACTCATG
5401498 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
5401546 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
5401594 CATA CATA CATA TATA CATA CATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5401642 CATA CATA CATA TATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
5401690 CATA CATA TATA CATA
1 CATA CATA CATA CATA
5401706 TGAGAAATAT
Statistics
Matches: 196, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 196 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
CATA
Found at i:5401785 original size:22 final size:22
Alignment explanation
Indices: 5401760--5401802 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5401750 GTATCTGTTT
* *
5401760 TAATGCGCTTTTATATTAGTGC
1 TAATGCACTTTCATATTAGTGC
5401782 TAATGCACTTTCATATTAGTG
1 TAATGCACTTTCATATTAGTG
5401803 TTAAGGCATA
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:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (22 bp):
TAATGCACTTTCATATTAGTGC
Found at i:5407655 original size:21 final size:21
Alignment explanation
Indices: 5407631--5407676 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5407621 ACTTAGCCTA
*
5407631 ACCAACCATGCATGGCTTACT
1 ACCAACCATGCATGGCTCACT
*
5407652 ACCAACCGTGCATGGCTCACT
1 ACCAACCATGCATGGCTCACT
5407673 ACCA
1 ACCA
5407677 CTCCCTTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.37, G:0.15, T:0.20
Consensus pattern (21 bp):
ACCAACCATGCATGGCTCACT
Found at i:5410837 original size:2 final size:2
Alignment explanation
Indices: 5410832--5410863 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5410822 ACACACACGC
5410832 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
5410864 CAATCTCGGG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5411496 original size:72 final size:72
Alignment explanation
Indices: 5411405--5411543 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
5411395 CGTGGACGCG
*
5411405 CACACACAAAGCATGCTATTTCTTGTAGTGGATATATTAATTTATATGTTTTAAAACTTAAAAGC
1 CACACACAAAGCATGCTATTTCTTGTAGTGGATATATTAATTTATATATTTTAAAACTTAAAAGC
5411470 GCGCGTA
66 GCGCGTA
* * * * *
5411477 CACACACAAGGTATGCTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAAACTTAAATGC
1 CACACACAAAGCATGCTATTTCTTGTAGTGGATATATTAATTTATATATTTTAAAACTTAAAAGC
5411542 GC
66 GC
5411544 ACGCACGCAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (72 bp):
CACACACAAAGCATGCTATTTCTTGTAGTGGATATATTAATTTATATATTTTAAAACTTAAAAGC
GCGCGTA
Found at i:5411667 original size:78 final size:78
Alignment explanation
Indices: 5411567--5411713 Score: 240
Period size: 78 Copynumber: 1.9 Consensus size: 78
5411557 AATGCGTGCA
* * *
5411567 CACACATACACAAGGCATGTTATTTCTTGTGGTGGATATAATAATTTATATATTTTAAAACTTAA
1 CACACACACACAAAGCATGTTATTTCTTGTGGTGGATATAATAATTTATATATTTTAAAACATAA
5411632 ATGCTCGCACGAG
66 ATGCTCGCACGAG
* * *
5411645 CACACACACATAAAGCATGTTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAAACATAA
1 CACACACACACAAAGCATGTTATTTCTTGTGGTGGATATAATAATTTATATATTTTAAAACATAA
5411710 ATGC
66 ATGC
5411714 ACATGCACGC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 63 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (78 bp):
CACACACACACAAAGCATGTTATTTCTTGTGGTGGATATAATAATTTATATATTTTAAAACATAA
ATGCTCGCACGAG
Found at i:5411701 original size:172 final size:166
Alignment explanation
Indices: 5411408--5411723 Score: 452
Period size: 172 Copynumber: 1.9 Consensus size: 166
5411398 GGACGCGCAC
* *
5411408 ACACAAAGCATGCTATTTCTTGTAGTGGATATATTAATTTATATGTTTTAAAACTTAAAAGCGCG
1 ACACAAAGCATGCTATTTCTTGTAGTGGATATAATAATTTATATATTTTAAAACTTAAAAGCGCG
* * * * *
5411473 CGTACACACACAAGGTATGCTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAAACTTAA
66 AGCACACACACAAAGCATGCTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAAACATAA
*
5411538 ATGCGCACGCACGCACGCAAATGCGTGCACACACAT
131 ATGCACACGCACGCACGCAAATGCGTGCACACACAT
* * * *
5411574 ACACAAGGCATGTTATTTCTTGTGGTGGATATAATAATTTATATATTTTAAAACTTAAATGCTCG
1 ACACAAAGCATGCTATTTCTTGTAGTGGATATAATAATTTATATATTTTAAAACTTAAAAG--CG
*
5411639 CACGAGCACACACACATAAAGCATGTTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAA
64 --CGAGCACACACAC--AAAGCATGCTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAA
*
5411704 ACATAAATGCACATGCACGC
125 ACATAAATGCACACGCACGC
5411724 TCGTACATAC
Statistics
Matches: 130, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
166 55 0.42
168 2 0.02
170 11 0.08
172 62 0.48
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (166 bp):
ACACAAAGCATGCTATTTCTTGTAGTGGATATAATAATTTATATATTTTAAAACTTAAAAGCGCG
AGCACACACACAAAGCATGCTATTTTTTGTGGTGGATATATTAATTTATATATTTTAAAACATAA
ATGCACACGCACGCACGCAAATGCGTGCACACACAT
Found at i:5412079 original size:15 final size:15
Alignment explanation
Indices: 5412059--5412108 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
5412049 TTTTATTATC
5412059 GGAGTCGTTGTTAAT
1 GGAGTCGTTGTTAAT
** *
5412074 GGAGTCACTGTTAAC
1 GGAGTCGTTGTTAAT
*
5412089 GGAGTCGTTGTTATT
1 GGAGTCGTTGTTAAT
5412104 GGAGT
1 GGAGT
5412109 ATTGAGGGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.20, C:0.10, G:0.34, T:0.36
Consensus pattern (15 bp):
GGAGTCGTTGTTAAT
Found at i:5412173 original size:80 final size:81
Alignment explanation
Indices: 5412007--5412183 Score: 232
Period size: 80 Copynumber: 2.2 Consensus size: 81
5411997 TTTTAATTAT
* * *
5412007 TGGAGTCGCTGTTAATGGAGTATCGAGGGTTAAGGTTTATATTTTTATTATCGGAGTCGTTGTTA
1 TGGAGTCGTTGTTAATGGAGTATCGAGGGTTAAGGATTATATTTTTATTATCGGAGTCGCTGTTA
5412072 ATGGAGTCACTGTTAA
66 ATGGAGTCACTGTTAA
* * * *
5412088 CGGAGTCGTTGTTATTGGAGTATTGAGGGTT-AGAGATTGTA-TTTTATTATCGGAGTCGCTGTT
1 TGGAGTCGTTGTTAATGGAGTATCGAGGGTTAAG-GATTATATTTTTATTATCGGAGTCGCTGTT
* * *
5412151 ATTGGAGTCATTGTTTA
65 AATGGAGTCACTGTTAA
*
5412168 TGGAGTCGTTGCTAAT
1 TGGAGTCGTTGTTAAT
5412184 CAAAATGTTA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 50 0.61
81 32 0.39
ACGTcount: A:0.21, C:0.08, G:0.29, T:0.41
Consensus pattern (81 bp):
TGGAGTCGTTGTTAATGGAGTATCGAGGGTTAAGGATTATATTTTTATTATCGGAGTCGCTGTTA
ATGGAGTCACTGTTAA
Found at i:5414207 original size:29 final size:31
Alignment explanation
Indices: 5414136--5414208 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 31
5414126 AATTTAACGG
*
5414136 TTTAATGATACAATTCAGATGAAAATCAAAA
1 TTTAATGATATAATTCAGATGAAAATCAAAA
** *
5414167 TTTAATCCTATAATT-A-AT-AAAATTAATAA
1 TTTAATGATATAATTCAGATGAAAATCAA-AA
5414196 TTTAATGATATAA
1 TTTAATGATATAA
5414209 ACAAAACACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 7 0.20
29 15 0.43
30 1 0.03
31 12 0.34
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (31 bp):
TTTAATGATATAATTCAGATGAAAATCAAAA
Found at i:5414620 original size:137 final size:139
Alignment explanation
Indices: 5414374--5414650 Score: 540
Period size: 137 Copynumber: 2.0 Consensus size: 139
5414364 ATTTCCTCAA
5414374 TATTATTGTGTTATACATATACAACTTTTGTTCTCTTATATTTTTCTTTAAAAAACTGATTAAGC
1 TATTATTGTGTTATACATATACAACTTTTGTTCTCTTATATTTTTCTTTAAAAAACTGATTAAGC
5414439 TGGCAGCAAATGTAAACCCACCGATAGAGTGCTTAAAGATGTTAATGCAATTTTA-TTT-TGTAG
66 TGGCAGCAAATGTAAACCCACCGATAGAGTGCTTAAAGATGTTAATGCAATTTTATTTTATGTAG
5414502 GTTCTAATT
131 GTTCTAATT
5414511 TATTATTGTGTTATACATATACAACTTTTGTTCTCTTATATTTTTCTTTAAAAAACTGATTAAGC
1 TATTATTGTGTTATACATATACAACTTTTGTTCTCTTATATTTTTCTTTAAAAAACTGATTAAGC
5414576 TGGCAGCAAATGTAAACCCACCGATAGAGTGCTTAAAGATGTTAATGCAATTTTATTTTATGTAG
66 TGGCAGCAAATGTAAACCCACCGATAGAGTGCTTAAAGATGTTAATGCAATTTTATTTTATGTAG
5414641 GTTCTAATT
131 GTTCTAATT
5414650 T
1 T
5414651 CAACATTTAT
Statistics
Matches: 138, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
137 120 0.87
138 3 0.02
139 15 0.11
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (139 bp):
TATTATTGTGTTATACATATACAACTTTTGTTCTCTTATATTTTTCTTTAAAAAACTGATTAAGC
TGGCAGCAAATGTAAACCCACCGATAGAGTGCTTAAAGATGTTAATGCAATTTTATTTTATGTAG
GTTCTAATT
Found at i:5415750 original size:29 final size:28
Alignment explanation
Indices: 5415718--5415775 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
5415708 TTTAATAATT
* *
5415718 TATTATTAATTTAATAATATTTTTTTGAA
1 TATTAATAATTTAATAA-ATTATTTTGAA
* *
5415747 TATTAATGATTTATTAAATTATTTTGAA
1 TATTAATAATTTAATAAATTATTTTGAA
5415775 T
1 T
5415776 GAAGACCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (28 bp):
TATTAATAATTTAATAAATTATTTTGAA
Found at i:5428183 original size:13 final size:13
Alignment explanation
Indices: 5428167--5428223 Score: 87
Period size: 13 Copynumber: 4.4 Consensus size: 13
5428157 TCAATGTGCA
*
5428167 TCATAAATGAGCG
1 TCATAAATGAGTG
*
5428180 TCATAAATGTGTG
1 TCATAAATGAGTG
*
5428193 TCATAAATGTGTG
1 TCATAAATGAGTG
5428206 TCATAAATGAGTG
1 TCATAAATGAGTG
5428219 TCATA
1 TCATA
5428224 GATTTATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (13 bp):
TCATAAATGAGTG
Found at i:5428189 original size:26 final size:26
Alignment explanation
Indices: 5428159--5428214 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
5428149 AATGACGTTC
5428159 AATGTGCATCATAAATGAGCGTCATA
1 AATGTGCATCATAAATGAGCGTCATA
** * *
5428185 AATGTGTGTCATAAATGTGTGTCATA
1 AATGTGCATCATAAATGAGCGTCATA
5428211 AATG
1 AATG
5428215 AGTGTCATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (26 bp):
AATGTGCATCATAAATGAGCGTCATA
Found at i:5433712 original size:22 final size:22
Alignment explanation
Indices: 5433684--5433737 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
5433674 ATACTATGCT
5433684 AGTAGTATCGATACCTAGCAAG
1 AGTAGTATCGATACCTAGCAAG
5433706 AGTAGTATCGATACCTAGCAAG
1 AGTAGTATCGATACCTAGCAAG
5433728 AGTAGTATCG
1 AGTAGTATCG
5433738 GTACTGGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
AGTAGTATCGATACCTAGCAAG
Found at i:5435320 original size:32 final size:31
Alignment explanation
Indices: 5435279--5435384 Score: 106
Period size: 32 Copynumber: 3.3 Consensus size: 31
5435269 AAGCTGGTAA
5435279 TTCCTTGGGTAGGCTCTAAGGCCCTAAGGAAT
1 TTCCTTGGGTAGGCTCTAAGGCCC-AAGGAAT
* * *
5435311 TTCCTTGGGTAGGCTCTAAAGTCCCAAGGTAC
1 TTCCTTGGGTAGGCTCT-AAGGCCCAAGGAAT
* * *
5435343 TTCATTGGGTAAGCTCTCAGGCCCCAA-GATAT
1 TTCCTTGGGTAGGCTCTAAGG-CCCAAGGA-AT
*
5435375 TCCCTTGGGT
1 TTCCTTGGGT
5435385 TAGCACCTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 3 0.05
32 51 0.85
33 6 0.10
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (31 bp):
TTCCTTGGGTAGGCTCTAAGGCCCAAGGAAT
Found at i:5436407 original size:112 final size:112
Alignment explanation
Indices: 5436210--5436432 Score: 446
Period size: 112 Copynumber: 2.0 Consensus size: 112
5436200 GTATGGTTTG
5436210 TACATGCCCCTAGTTTATGATCGTACTCTTCTGAGCCGAAACTCTGATGTCAAGTAAGCATTATG
1 TACATGCCCCTAGTTTATGATCGTACTCTTCTGAGCCGAAACTCTGATGTCAAGTAAGCATTATG
5436275 TAATGACTATACCAAAGGATTTTATCAATTATGACTCAATATGTGCT
66 TAATGACTATACCAAAGGATTTTATCAATTATGACTCAATATGTGCT
5436322 TACATGCCCCTAGTTTATGATCGTACTCTTCTGAGCCGAAACTCTGATGTCAAGTAAGCATTATG
1 TACATGCCCCTAGTTTATGATCGTACTCTTCTGAGCCGAAACTCTGATGTCAAGTAAGCATTATG
5436387 TAATGACTATACCAAAGGATTTTATCAATTATGACTCAATATGTGC
66 TAATGACTATACCAAAGGATTTTATCAATTATGACTCAATATGTGC
5436433 AAAAAGTAAA
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (112 bp):
TACATGCCCCTAGTTTATGATCGTACTCTTCTGAGCCGAAACTCTGATGTCAAGTAAGCATTATG
TAATGACTATACCAAAGGATTTTATCAATTATGACTCAATATGTGCT
Found at i:5438410 original size:28 final size:28
Alignment explanation
Indices: 5438373--5438431 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
5438363 ATTAGATGAT
5438373 TTATAAGGAACAATCCCAAGTTCTGTGA
1 TTATAAGGAACAATCCCAAGTTCTGTGA
*
5438401 TTATATGGAACAATCCCAAGTTCTGTGA
1 TTATAAGGAACAATCCCAAGTTCTGTGA
5438429 TTA
1 TTA
5438432 ACCAATGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (28 bp):
TTATAAGGAACAATCCCAAGTTCTGTGA
Found at i:5438858 original size:27 final size:28
Alignment explanation
Indices: 5438820--5438882 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
5438810 GAAAGAACTG
* * *
5438820 AAATATCCTTGAACTGTAAAATGACC-A
1 AAATACCCTTGAACTATAAAATAACCTA
* *
5438847 AAATACCCTTGAAGTATGAAATAACCTA
1 AAATACCCTTGAACTATAAAATAACCTA
5438875 AAATACCC
1 AAATACCC
5438883 CCAAGCCCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.24
Consensus pattern (28 bp):
AAATACCCTTGAACTATAAAATAACCTA
Found at i:5442363 original size:13 final size:13
Alignment explanation
Indices: 5442345--5442370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5442335 CGACGTTTTT
5442345 GAAAAATTACTCC
1 GAAAAATTACTCC
5442358 GAAAAATTACTCC
1 GAAAAATTACTCC
5442371 CCCTTACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GAAAAATTACTCC
Found at i:5442411 original size:13 final size:13
Alignment explanation
Indices: 5442393--5442418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5442383 CACTTCTCCC
5442393 TTTAAAACACTTA
1 TTTAAAACACTTA
5442406 TTTAAAACACTTA
1 TTTAAAACACTTA
5442419 ACACTTCTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAACACTTA
Found at i:5442655 original size:15 final size:15
Alignment explanation
Indices: 5442629--5442676 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 15
5442619 TTCAAACATC
*
5442629 CAAACAAATCCAAAGT
1 CAAAC-AATCCAAAAT
*
5442645 CTAACAATCCACAAAAT
1 CAAACAAT-C-CAAAAT
5442662 CAAACAATCCAAAAT
1 CAAACAATCCAAAAT
5442677 ATTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 9 0.33
16 6 0.22
17 12 0.44
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (15 bp):
CAAACAATCCAAAAT
Found at i:5444726 original size:20 final size:21
Alignment explanation
Indices: 5444643--5444724 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
5444633 CAGAACCCCA
*
5444643 GGGGGATATCGATTCCCCT-GT
1 GGGGGA-ATCGATTCCCCTCAT
* * *
5444664 GGGGGGAATCGGTTCCCCTTAAAA
1 -GGGGGAATCGATTCCCC-T-CAT
*
5444688 GGGGGAATCGGTTCCCCTCAT
1 GGGGGAATCGATTCCCCTCAT
*
5444709 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
5444725 TCTGGACCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 25 0.50
22 8 0.16
23 17 0.34
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAT
Found at i:5452263 original size:2 final size:2
Alignment explanation
Indices: 5452258--5452325 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
5452248 GTGTGTGACA
5452258 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5452300 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
5452326 GTTTGGTCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5458348 original size:20 final size:19
Alignment explanation
Indices: 5458316--5458363 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
5458306 TCCAGTGTGG
5458316 TCAAATTTCACATTC-TAACA
1 TCAAA-TTCACATTCAT-ACA
5458336 TCAAATTCAACATTCATACA
1 TCAAATTC-ACATTCATACA
*
5458356 TTAAATTC
1 TCAAATTC
5458364 CAGCTTAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 21 0.84
21 1 0.04
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (19 bp):
TCAAATTCACATTCATACA
Found at i:5459555 original size:31 final size:31
Alignment explanation
Indices: 5459518--5459581 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5459508 AATACATAAC
5459518 TTTTAAAAATTACACTTTGGTCC-CTAAACTT
1 TTTTAAAAATTACA-TTTGGTCCACTAAACTT
** * *
5459549 TTTTAAACTTTATATTTTGTCCACTAAACTT
1 TTTTAAAAATTACATTTGGTCCACTAAACTT
5459580 TT
1 TT
5459582 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTTAAAAATTACATTTGGTCCACTAAACTT
Found at i:5459597 original size:30 final size:31
Alignment explanation
Indices: 5459537--5459605 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
5459527 TTACACTTTG
*
5459537 GTCC-CTAAACTTTTTTAAACTTTATATTTT
1 GTCCACTAAACTTTTTAAAACTTTATATTTT
* *
5459567 GTCCACTAAAC-TTTTAAAATTTTATGTTTT
1 GTCCACTAAACTTTTTAAAACTTTATATTTT
*
5459597 GGCCACTAA
1 GTCCACTAA
5459606 TCAAAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (31 bp):
GTCCACTAAACTTTTTAAAACTTTATATTTT
Found at i:5462077 original size:2 final size:2
Alignment explanation
Indices: 5462070--5462123 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
5462060 TAAAGTTAAC
5462070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5462112 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5462124 CATTATTAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.