Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 3 of 22
Found at i:958912 original size:2 final size:2
Alignment explanation
Indices: 958905--958931 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
958895 ATCATAAATA
958905 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
958932 AACATTACAA
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:967284 original size:48 final size:48
Alignment explanation
Indices: 967228--967327 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
967218 CTACTTCCGG
*
967228 ACATTCTTGATGATTGATCTCGAAAAAAAGTAAAGAGGCCTTGCCATA
1 ACATTCTTGATGATTGATCTCGAAAAAAAGTAAAGAGGCCTTACCATA
* *
967276 ACATTCTTGATGATTTATCTCGAAAAAAAGTAAAGAGGCCTTACTATA
1 ACATTCTTGATGATTGATCTCGAAAAAAAGTAAAGAGGCCTTACCATA
967324 ACAT
1 ACAT
967328 GTAAGTTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (48 bp):
ACATTCTTGATGATTGATCTCGAAAAAAAGTAAAGAGGCCTTACCATA
Found at i:967863 original size:163 final size:165
Alignment explanation
Indices: 967611--967924 Score: 377
Period size: 163 Copynumber: 1.9 Consensus size: 165
967601 TATTTTTCAA
* *
967611 AAATAAATAAAACCGCTTTGATATTAAAATACATCTTGAAAACTTCAACACTTATGACAAAATTC
1 AAATAAAAAAAACCGCTTTGATATTAAAATACATCTTGAAAACTCCAACACTTATGACAAAATTC
* ** * *
967676 AAAAAAAATCTCCTACTTAGAAATTTTTAAGGAGCTATCACTTATTATCTTCTTG-AAATTCCAT
66 AAAAAAAATCTCCTACTTAGAAATTTTCAAAAAGCTATCACTTAATAGCTTCTTGAAAATTCCAT
* *
967740 CATTGGAAAATCTTTATTTATTTATAGTGAAATTG
131 CAGTAGAAAATCTTTATTTATTTATAGTGAAATTG
* * *
967775 AAATAAACAAAAACC-CTTTGATATTGAAATAC-TCTTGAAAACTCCAACAGTTAT-AGCAAATT
1 AAATAAA-AAAAACCGCTTTGATATTAAAATACATCTTGAAAACTCCAACACTTATGA-CAAAAT
* * ** * * *
967837 TCAAGAAAAAT-TTCTTTTCTAGAAATTTTCAAAAAGCTATTACTTAATAGCTTTTTGAAAATTT
64 TCAAAAAAAATCTCCTACT-TAGAAATTTTCAAAAAGCTATCACTTAATAGCTTCTTGAAAATTC
* *
967901 CATCAGTAGAGAATTTTTATTTAT
128 CATCAGTAGAAAATCTTTATTTAT
967925 CTACTTTTTA
Statistics
Matches: 125, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
162 5 0.04
163 66 0.53
164 48 0.38
165 6 0.05
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (165 bp):
AAATAAAAAAAACCGCTTTGATATTAAAATACATCTTGAAAACTCCAACACTTATGACAAAATTC
AAAAAAAATCTCCTACTTAGAAATTTTCAAAAAGCTATCACTTAATAGCTTCTTGAAAATTCCAT
CAGTAGAAAATCTTTATTTATTTATAGTGAAATTG
Found at i:969100 original size:44 final size:44
Alignment explanation
Indices: 969037--969443 Score: 293
Period size: 44 Copynumber: 9.3 Consensus size: 44
969027 TTTGTAAAAA
* ** *
969037 AAGCTCCTCATATGGAGTTCGGTTATGTAACTTTAAAAAGGAAT
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
* ** *
969081 AAGCTCCTCATATGGAGTTCGGTTATGTAACTTTAAAAAGGAAT
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
*
969125 AAGCTCCTCATCT-G-GTACGAGGCTATGTAACTTT-AAAAGGGAT
1 AAGCTCCTCATCTGGAGTA--AGGCTATGTAACTTTAAAAAGGAAT
* * * *
969168 AAGCTCCTCATCTAAGAATGAGGCTATGTAACTTTAAAAAAG-AT
1 AAGCTCCTCATCT-GGAGTAAGGCTATGTAACTTTAAAAAGGAAT
* * * * *
969212 AAGCTCATCATTTGGAATAAGGCCACGTAACTTTAAAAAGGAAT
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
** * ** * *
969256 AAAATCTTCATCTAAAGTAAGGTTATGTAACTTTAAAAAGGAAA
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
* * * * * * * **
969300 AAGCTCTTCATTTGGAATGAGGCTACGCAACTTTATAACTGAAT
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
* * * * * * **
969344 AAGTTCTTCATCTAGATTAAGGCTATGCAAATTT-AAACTGAAT
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
* * * * * * * *
969387 AAGCTCCTTATTTGGAATGAGACTACGTAACTTTAAAAATGAAC
1 AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
*
969431 AAGCTCCTTATCT
1 AAGCTCCTCATCT
969444 TAAAAGCTGT
Statistics
Matches: 293, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
42 2 0.01
43 76 0.26
44 208 0.71
45 6 0.02
46 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (44 bp):
AAGCTCCTCATCTGGAGTAAGGCTATGTAACTTTAAAAAGGAAT
Found at i:969196 original size:88 final size:87
Alignment explanation
Indices: 969063--969443 Score: 361
Period size: 87 Copynumber: 4.3 Consensus size: 87
969053 GTTCGGTTAT
* * ** *
969063 GTAACTTTAAAAAGGAATAAGCTCCTCATATGGAGTTCGGTTATGTAACTTTAAAAAGGAATAAG
1 GTAACTTT-AAAAGGAATAAGCTCCTCATCTAGAGTAAGGCTATGTAACTTTAAAAAGGAATAAG
* * * *
969128 CTCCTCATCTGGTACGAGGCTAT
65 CTCCTCATTTGGAATGAGGCTAC
* * * *
969151 GTAACTTTAAAAGGGATAAGCTCCTCATCTAAGAATGAGGCTATGTAACTTTAAAAAAG-ATAAG
1 GTAACTTTAAAAGGAATAAGCTCCTCATCT-AGAGTAAGGCTATGTAACTTTAAAAAGGAATAAG
* * *
969215 CTCATCATTTGGAATAAGGCCAC
65 CTCCTCATTTGGAATGAGGCTAC
** * * * *
969238 GTAACTTTAAAAAGGAATAAAATCTTCATCTAAAGTAAGGTTATGTAACTTTAAAAAGGAAAAAG
1 GTAACTTT-AAAAGGAATAAGCTCCTCATCTAGAGTAAGGCTATGTAACTTTAAAAAGGAATAAG
*
969303 CTCTTCATTTGGAATGAGGCTAC
65 CTCCTCATTTGGAATGAGGCTAC
* ** * * * * * **
969326 GCAACTTTATAACTGAATAAGTTCTTCATCTAGATTAAGGCTATGCAAATTT-AAACTGAATAAG
1 GTAACTTTA-AAAGGAATAAGCTCCTCATCTAGAGTAAGGCTATGTAACTTTAAAAAGGAATAAG
* *
969390 CTCCTTATTTGGAATGAGACTAC
65 CTCCTCATTTGGAATGAGGCTAC
* * *
969413 GTAACTTTAAAAATGAACAAGCTCCTTATCT
1 GTAACTTT-AAAAGGAATAAGCTCCTCATCT
969444 TAAAAGCTGT
Statistics
Matches: 238, Mismatches: 50, Indels: 11
0.80 0.17 0.04
Matches are distributed among these distances:
87 125 0.53
88 113 0.47
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (87 bp):
GTAACTTTAAAAGGAATAAGCTCCTCATCTAGAGTAAGGCTATGTAACTTTAAAAAGGAATAAGC
TCCTCATTTGGAATGAGGCTAC
Found at i:969283 original size:131 final size:131
Alignment explanation
Indices: 969060--969334 Score: 304
Period size: 131 Copynumber: 2.1 Consensus size: 131
969050 GGAGTTCGGT
* * * ** ** *
969060 TATGTAACTTTAAAAAGGAATAAGCTCCTCATATGGAGTTCGGTTATGTAACTTTAAAAAGGAAT
1 TATGTAACTTTAAAAAAGAATAAGCTCATCATATGGAATAAGGCCACGTAACTTTAAAAAGGAAT
** * * *
969125 AAGCTCCTCATCTGGTACGAGGCTATGTAACTTT-AAAAGGGATAAGCTCCTCATCTAAGAATGA
66 AAAATCCTCATCTAGTAC-AGGCTATGTAACTTTAAAAAGGAAAAAGCTCCTCAT-TAAGAATGA
969189 GGC
129 GGC
*
969192 TATGTAACTTTAAAAAAG-ATAAGCTCATCATTTGGAATAAGGCCACGTAACTTTAAAAAGGAAT
1 TATGTAACTTTAAAAAAGAATAAGCTCATCATATGGAATAAGGCCACGTAACTTTAAAAAGGAAT
* * * **
969256 AAAATCTTCATCTAAAGTA-AGGTTATGTAACTTTAAAAAGGAAAAAGCTCTTCATTTGGAATGA
66 AAAATCCTCATCT--AGTACAGGCTATGTAACTTTAAAAAGGAAAAAGCTCCTCATTAAGAATGA
969320 GGC
129 GGC
* *
969323 TACGCAACTTTA
1 TATGTAACTTTA
969335 TAACTGAATA
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
131 82 0.69
132 34 0.29
133 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (131 bp):
TATGTAACTTTAAAAAAGAATAAGCTCATCATATGGAATAAGGCCACGTAACTTTAAAAAGGAAT
AAAATCCTCATCTAGTACAGGCTATGTAACTTTAAAAAGGAAAAAGCTCCTCATTAAGAATGAGG
C
Found at i:969369 original size:175 final size:175
Alignment explanation
Indices: 969063--969425 Score: 415
Period size: 175 Copynumber: 2.1 Consensus size: 175
969053 GTTCGGTTAT
** ** ** *
969063 GTAACTTTAAAAAGGAATAAGCTCCTCATATGGAGTTCGGTTATGTAACTTTAAAAAGGAATAAG
1 GTAACTTTAAAAAGGAATAAAATCCTCATATAAAGTAAGGTTATGTAACTTTAAAAAGGAAAAAG
* * * * *
969128 CTCCTCATCTGGTACGAGGCTATGTAACTTTAAAAGGGATAAGCTCCTCATCTAAGAATGAGGCT
66 CTCCTCATCTGGAACGAGGCTACGCAACTTTAAAAGGAATAAGCTCCTCATCTAAGAATAAGGCT
* * *
969193 ATGTAACTTTAAAAA-AGATAAGCTCATCATTTGGAATAAGGCCAC
131 ATGCAAATTTAAAAAGA-ATAAGCTCATCATTTGGAATAAGACCAC
* *
969238 GTAACTTTAAAAAGGAATAAAATCTTCATCTAAAGTAAGGTTATGTAACTTTAAAAAGGAAAAAG
1 GTAACTTTAAAAAGGAATAAAATCCTCATATAAAGTAAGGTTATGTAACTTTAAAAAGGAAAAAG
* * * ** * * *
969303 CTCTTCATTTGGAATGAGGCTACGCAACTTTATAACTGAATAAGTTCTTCATCT-AGATTAAGGC
66 CTCCTCATCTGGAACGAGGCTACGCAACTTTA-AAAGGAATAAGCTCCTCATCTAAGAATAAGGC
** * * * *
969367 TATGCAAATTTAAACTGAATAAGCTCCTTATTTGGAATGAGACTAC
130 TATGCAAATTTAAAAAGAATAAGCTCATCATTTGGAATAAGACCAC
969413 GTAACTTTAAAAA
1 GTAACTTTAAAAA
969426 TGAACAAGCT
Statistics
Matches: 155, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
175 138 0.89
176 17 0.11
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (175 bp):
GTAACTTTAAAAAGGAATAAAATCCTCATATAAAGTAAGGTTATGTAACTTTAAAAAGGAAAAAG
CTCCTCATCTGGAACGAGGCTACGCAACTTTAAAAGGAATAAGCTCCTCATCTAAGAATAAGGCT
ATGCAAATTTAAAAAGAATAAGCTCATCATTTGGAATAAGACCAC
Found at i:971051 original size:21 final size:21
Alignment explanation
Indices: 971007--971051 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
970997 TATTTACATG
*
971007 AATATAAGAAAATGAATTTGA
1 AATATAAGAAAATGAATTTAA
971028 AATATAAGAAAATG-ATTTCAA
1 AATATAAGAAAATGAATTT-AA
971049 AAT
1 AAT
971052 TTAATGTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (21 bp):
AATATAAGAAAATGAATTTAA
Found at i:979375 original size:163 final size:164
Alignment explanation
Indices: 979144--979438 Score: 434
Period size: 163 Copynumber: 1.8 Consensus size: 164
979134 AACTCTTTTA
* * *
979144 TATTAAAATATTTCTTGAAAACTCCAACACTTATGGCAACATTCAAGAAAAATCTCTCACTTAGA
1 TATTAAAATATTCCTTGAAAACTCCAACACTAATAGCAACATTCAAGAAAAATCTCTCACTTAGA
*
979209 AATTTTTAAGAAA-CTATCACTTATAACCTTCTTAAAATTCCATTATTGGAAAACCTTTATTTAT
66 AATTTTTAA-AAAGCTATCACTTATAACCTTCTTAAAATTCCATCATTGGAAAACCTTTATTTAT
979273 TTATATTGAGATTGAAATAAACAAAAAACCTTTGG
130 TTATATTGAGATTGAAATAAACAAAAAACCTTTGG
* * *
979308 TATTAAAATA-TCCTTGAAAACTCTAGCACTAATAGCAGA-ATTCAAGAAAAATCTGTCACTTAG
1 TATTAAAATATTCCTTGAAAACTCCAACACTAATAGCA-ACATTCAAGAAAAATCTCTCACTTAG
* * * ***
979371 AAATTTTTAAAAAGCTATCACTTATAACCTTTTTGAAATTCCATCATTGTAAAGTTTTTATTTAT
65 AAATTTTTAAAAAGCTATCACTTATAACCTTCTTAAAATTCCATCATTGGAAAACCTTTATTTAT
979436 TTA
130 TTA
979439 CTTTTTATCA
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
162 3 0.03
163 102 0.88
164 11 0.09
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (164 bp):
TATTAAAATATTCCTTGAAAACTCCAACACTAATAGCAACATTCAAGAAAAATCTCTCACTTAGA
AATTTTTAAAAAGCTATCACTTATAACCTTCTTAAAATTCCATCATTGGAAAACCTTTATTTATT
TATATTGAGATTGAAATAAACAAAAAACCTTTGG
Found at i:988291 original size:2 final size:2
Alignment explanation
Indices: 988284--988308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
988274 TGAATGCATT
988284 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 A
988309 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:990736 original size:11 final size:10
Alignment explanation
Indices: 990699--990750 Score: 63
Period size: 10 Copynumber: 5.3 Consensus size: 10
990689 TCTCTTTTCA
990699 TTTTTTCTCT
1 TTTTTTCTCT
*
990709 TTTTATC-CT
1 TTTTTTCTCT
*
990718 TATTTTCTCT
1 TTTTTTCTCT
990728 TTTTCTTCT-T
1 TTTT-TTCTCT
990738 TTTTTTCTCT
1 TTTTTTCTCT
990748 TTT
1 TTT
990751 ATAAGCATAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 11 0.31
10 20 0.57
11 4 0.11
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCTCT
Found at i:991098 original size:51 final size:51
Alignment explanation
Indices: 991038--991136 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
991028 TTTAAATTAT
* **
991038 TAATGAAATTTTATGTTATAATTTAATTTTAT-TTCAAAAGTAATTAATTTG
1 TAATAAAATTTTATACTATAATTTAATTTTATGTT-AAAAGTAATTAATTTG
*
991089 TAATAAAATTTTATACTATAATTTTATTTTATGTTAAAAGTAATTAAT
1 TAATAAAATTTTATACTATAATTTAATTTTATGTTAAAAGTAATTAAT
991137 GTTTTACTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.95
52 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (51 bp):
TAATAAAATTTTATACTATAATTTAATTTTATGTTAAAAGTAATTAATTTG
Found at i:998194 original size:79 final size:79
Alignment explanation
Indices: 998099--998253 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
998089 CAGATTTCCC
* * *
998099 TTACAAATTTTAGAGAAGAGAAAAGCATCGA-ATTT-CCTTAACAAATTCTAAGGAAGAGAAAAG
1 TTACAAATTATAGAGAAGAGAAAAACATC-ATATTTCCCTT-ACAAATTCTAAGAAAGAGAAAAG
998162 AAGGATTTGACTTCTT
64 AAGGATTTGACTTCTT
* * * *
998178 TTACAAATTATGGAGAAGAGAAAAATATCATGTTTCCCTTACAAATTCTAAGAAAGAGAAGAGAA
1 TTACAAATTATAGAGAAGAGAAAAACATCATATTTCCCTTACAAATTCTAAGAAAGAGAAAAGAA
*
998243 GGATTTTACTT
66 GGATTTGACTT
998254 TCATTTATTG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
78 1 0.02
79 61 0.92
80 4 0.06
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (79 bp):
TTACAAATTATAGAGAAGAGAAAAACATCATATTTCCCTTACAAATTCTAAGAAAGAGAAAAGAA
GGATTTGACTTCTT
Found at i:998578 original size:13 final size:13
Alignment explanation
Indices: 998516--998578 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
998506 ATTAAAATAA
* *
998516 AAAATATTAACAT
1 AAAATATAAAAAT
998529 AAAATATAAAATAT
1 AAAATATAAAA-AT
998543 AAGAATA-AAAAAT
1 AA-AATATAAAAAT
*
998556 TAAA-AT-AAAAT
1 AAAATATAAAAAT
998567 AAAATATAAAAA
1 AAAATATAAAAA
998579 AATGAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 9 0.22
12 4 0.10
13 16 0.39
14 8 0.20
15 4 0.10
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAATATAAAAAT
Found at i:998618 original size:24 final size:21
Alignment explanation
Indices: 998557--998618 Score: 54
Period size: 24 Copynumber: 2.8 Consensus size: 21
998547 ATAAAAAATT
*
998557 AAAATAAAATAAAAT-ATAAA
1 AAAATAAATTAAAATAATAAA
* *
998577 AAAATGAAATTTATATAATATAA
1 AAAAT-AAATTAAAATAATA-AA
998600 GCAAAATAAATTAAAATAA
1 --AAAATAAATTAAAATAA
998619 AATATATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 5 0.16
21 7 0.22
22 3 0.09
23 2 0.06
24 10 0.31
25 5 0.16
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAATAAATTAAAATAATAAA
Found at i:998665 original size:34 final size:33
Alignment explanation
Indices: 998613--998698 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
998603 AAATAAATTA
*
998613 AAAT-AAAATATATAATATAAAAAATTATATTAAAG
1 AAATGAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
998648 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAATGAAAATAAAATATAAAAAATTATAATAAG
998681 AAATGAAAATAAAATATA
1 AAATGAAAATAAAATATA
998699 TGACATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
33 20 0.43
34 15 0.33
35 5 0.11
36 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (33 bp):
AAATGAAAATAAAATATAAAAAATTATAATAAG
Found at i:998696 original size:15 final size:14
Alignment explanation
Indices: 998503--998696 Score: 58
Period size: 15 Copynumber: 13.2 Consensus size: 14
998493 TTATAATGTT
*
998503 ATAATTAAAATAAA
1 ATAAATAAAATAAA
*
998517 A-AATATTAACATAAA
1 ATAA-A-TAAAATAAA
*
998532 ATATAA-AATATAAGA
1 ATA-AATAAAATAA-A
*
998547 ATAAA-AAATTAAA
1 ATAAATAAAATAAA
998560 ATAAAATAAAATATAA
1 AT-AAATAAAATA-AA
* * **
998576 AAAAATGAAAT-TT
1 ATAAATAAAATAAA
**
998589 ATATAATATAAGCAAA
1 ATA-AATA-AAATAAA
998605 ATAAATTAAAATAAA
1 ATAAA-TAAAATAAA
* *
998620 ATATATAATAT-AA
1 ATAAATAAAATAAA
* * *
998633 A-AAATTATATTAA
1 ATAAATAAAATAAA
*
998646 AGAAATGAAAATAAA
1 ATAAAT-AAAATAAA
*
998661 ATATATAAGATTATAATA
1 ATAAATAA-A--ATAA-A
998679 ATAAATGAAAATAAA
1 ATAAAT-AAAATAAA
998694 ATA
1 ATA
998697 TATGACATTA
Statistics
Matches: 132, Mismatches: 28, Indels: 39
0.66 0.14 0.20
Matches are distributed among these distances:
12 7 0.05
13 13 0.10
14 31 0.23
15 53 0.40
16 14 0.11
17 5 0.04
18 7 0.05
19 2 0.02
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.28
Consensus pattern (14 bp):
ATAAATAAAATAAA
Found at i:998701 original size:15 final size:15
Alignment explanation
Indices: 998650--998715 Score: 53
Period size: 15 Copynumber: 4.1 Consensus size: 15
998640 TATTAAAGAA
998650 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
*
998665 AT-AAGATTATAATAATAA
1 ATGAA-A--ATAA-AATAT
998683 ATGAAAATAAAATAT
1 ATGAAAATAAAATAT
* *
998698 ATGACATTAAAAATAT
1 ATGAAAAT-AAAATAT
998714 AT
1 AT
998716 TTAAGAGATG
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
14 2 0.05
15 13 0.32
16 13 0.32
17 4 0.10
18 7 0.17
19 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (15 bp):
ATGAAAATAAAATAT
Found at i:998940 original size:15 final size:15
Alignment explanation
Indices: 998917--998971 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
998907 ATTTTCCCCA
*
998917 CAATGACATTACTTG
1 CAATCACATTACTTG
*
998932 CAATCACATTACCTG
1 CAATCACATTACTTG
998947 CAATCACATTA-TCTG
1 CAATCACATTACT-TG
*
998962 TAATCACATT
1 CAATCACATT
998972 GCATTGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (15 bp):
CAATCACATTACTTG
Found at i:1000135 original size:14 final size:12
Alignment explanation
Indices: 1000113--1000179 Score: 59
Period size: 13 Copynumber: 5.5 Consensus size: 12
1000103 GAGGAACTGA
1000113 TTTTTTCTTCTCT
1 TTTTTTCTT-TCT
1000126 TTTTTATCTTTCT
1 TTTTT-TCTTTCT
1000139 TTTTTT-TTT-T
1 TTTTTTCTTTCT
*
1000149 TTCTTTTCGTATCT
1 TT-TTTTC-TTTCT
*
1000163 TTCTTTC-TTCT
1 TTTTTTCTTTCT
1000174 TTTTTT
1 TTTTTT
1000180 TTTTTCCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
10 3 0.07
11 15 0.33
12 1 0.02
13 19 0.42
14 7 0.16
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTTCT
Found at i:1000139 original size:18 final size:18
Alignment explanation
Indices: 1000116--1000154 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1000106 GAACTGATTT
1000116 TTTCTTCTCTTTTTTATC
1 TTTCTTCTCTTTTTTATC
* * *
1000134 TTTCTTTTTTTTTTTTTC
1 TTTCTTCTCTTTTTTATC
1000152 TTT
1 TTT
1000155 TCGTATCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTTCTCTTTTTTATC
Found at i:1000150 original size:32 final size:33
Alignment explanation
Indices: 1000113--1000183 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
1000103 GAGGAACTGA
* *
1000113 TTTTTTCTTCTC-TTTTTTATCTTTCTT-TTTTT
1 TTTTTTCTTCTCGTATCTT-TCTTTCTTCTTTTT
*
1000145 TTTTTTCTTTTCGTATCTTTCTTTCTTCTTTTT
1 TTTTTTCTTCTCGTATCTTTCTTTCTTCTTTTT
1000178 TTTTTT
1 TTTTTT
1000184 TCCATTCCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 19 0.56
33 15 0.44
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.80
Consensus pattern (33 bp):
TTTTTTCTTCTCGTATCTTTCTTTCTTCTTTTT
Found at i:1001106 original size:2 final size:2
Alignment explanation
Indices: 1001099--1001123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1001089 GTTTCTCGTT
1001099 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 T
1001124 TCTTAATTGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1006570 original size:2 final size:2
Alignment explanation
Indices: 1006563--1006609 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1006553 TTTATATGTG
* * * *
1006563 TA TA TA TA TA CA TA AA TA TT TA TA TT 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
1006605 TA TA T
1 TA TA T
1006610 GTTTGAGATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1006727 original size:26 final size:26
Alignment explanation
Indices: 1006698--1006754 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1006688 TGTATTTATA
1006698 ATTTTTTGTATATTTCTAAAAATATT
1 ATTTTTTGTATATTTCTAAAAATATT
1006724 ATTTTTTGTATATTTCTAAAAATATT
1 ATTTTTTGTATATTTCTAAAAATATT
1006750 ATTTT
1 ATTTT
1006755 AGAAATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
ATTTTTTGTATATTTCTAAAAATATT
Found at i:1014577 original size:27 final size:27
Alignment explanation
Indices: 1014519--1014974 Score: 184
Period size: 28 Copynumber: 16.8 Consensus size: 27
1014509 TGATGATGTG
* *** *
1014519 TAACAATTAAATTTTTCAACATAATATG
1 TAACAACTAAA-TTTTCAACATTGCATA
*
1014547 TAACAACTAAATCTTCAACATTGCATA
1 TAACAACTAAATTTTCAACATTGCATA
* * *
1014574 TAACAATTACATTTTTCATCA-TG-ATGTA
1 TAACAACTA-AATTTTCAACATTGCA--TA
*
1014602 TAACAACTAAATTTTTCAACATAGCATA
1 TAACAACTAAA-TTTTCAACATTGCATA
* ** *
1014630 TAATAACTAAAACTTCAACA-TGACATT
1 TAACAACTAAATTTTCAACATTG-CATA
* * * * *
1014657 TAATAATTACATTTTTCATCA-TG-ATGTT
1 TAACAACTA-AATTTTCAACATTGCA--TA
* * ** *
1014685 TAACAATTAAATTTTTCAATATCACATG
1 TAACAACTAAA-TTTTCAACATTGCATA
* **
1014713 TAACAACTAAATTTTCAACATGGTGTA
1 TAACAACTAAATTTTCAACATTGCATA
* * * * *
1014740 TAACAATTACATTTTTTAACATGGCATG
1 TAACAACTA-AATTTTCAACATTGCATA
* *
1014768 TAACAATTAAATTTT-TA-A-T--ATA
1 TAACAACTAAATTTTCAACATTGCATA
* *
1014790 TAATAACTAAATTTTAAACA-TGACATA
1 TAACAACTAAATTTTCAACATTG-CATA
* * *
1014817 TAACAA-TCATATTTTTCAATA-TGTCGTA
1 TAACAACT-A-AATTTTCAACATTG-CATA
* **
1014845 TAACAACCAAATTTTCAACATAACATA
1 TAACAACTAAATTTTCAACATTGCATA
* * * *
1014872 TAACAACCAAATCTTCAACATGGCATG
1 TAACAACTAAATTTTCAACATTGCATA
* * *
1014899 TAAGAACTAAATTTTCAACA-CGACATG
1 TAACAACTAAATTTTCAACATTG-CATA
** * *
1014926 TAACAAAAAAAAATTTCAACATGGCATA
1 TAAC-AACTAAATTTTCAACATTGCATA
1014954 TAACAACTAAATTTTCAACAT
1 TAACAACTAAATTTTCAACAT
1014975 GACAAGCAAT
Statistics
Matches: 322, Mismatches: 80, Indels: 53
0.71 0.18 0.12
Matches are distributed among these distances:
22 15 0.05
23 1 0.00
24 2 0.01
25 1 0.00
26 6 0.02
27 146 0.45
28 147 0.46
29 2 0.01
30 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (27 bp):
TAACAACTAAATTTTCAACATTGCATA
Found at i:1014588 original size:55 final size:55
Alignment explanation
Indices: 1014519--1015056 Score: 282
Period size: 55 Copynumber: 9.9 Consensus size: 55
1014509 TGATGATGTG
* * *
1014519 TAACAATTAAATTTTTCAACATAATATGTAACAACTAAATCTTCAACATTGCATA
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTGCATA
* * ** * *
1014574 TAACAATTACATTTTTCATCATGATGTATAACAACTAAATTTTTCAACATAGCATA
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAA-TTTTCAACATTGCATA
* * ** * * * * * *
1014630 TAATAACTAAA-ACTTCAACATGACATTTAATAATTACATTTTTCATCA-TG-ATGTT
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTA-AATTTTCAACATTGCA--TA
* * * **
1014685 TAACAATTAAATTTTTCAATATCACATGTAACAACTAAATTTTCAACATGGTGTA
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTGCATA
* * * * *
1014740 TAACAATTACATTTTTTAACATGGCATGTAACAATTAAATTTT-TA-A-T--ATA
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTGCATA
* * * * * * *
1014790 TAATAACTAAA-TTTTAAACATGACATATAACAA-TCATATTTTTCAATA-TGTCGTA
1 TAACAATTAAATTTTTCAACATGACATGTAACAACT-A-AATTTTCAACATTG-CATA
** * * * * * *
1014845 TAACAACCAAA-TTTTCAACATAACATATAACAACCAAATCTTCAACATGGCATG
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTGCATA
* * * ** * *
1014899 TAAGAACTAAA-TTTTCAACACGACATGTAACAAAAAAAAATTTCAACATGGCATA
1 TAACAATTAAATTTTTCAACATGACATGTAAC-AACTAAATTTTCAACATTGCATA
* * * * * * * * *
1014954 TAACAACTAAA-TTTTCAACATGACAAGCAATAATTATATTTTTAACA-TGACGTG
1 TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTG-CATA
* * * *
1015008 TAATAACTAAATTTTAT-AATATGACATGTAAC-ACTACATTTTTCAACAT
1 TAACAATTAAATTTT-TCAACATGACATGTAACAACTA-AATTTTCAACAT
1015057 GGCGCTAACA
Statistics
Matches: 364, Mismatches: 97, Indels: 43
0.72 0.19 0.09
Matches are distributed among these distances:
48 1 0.00
49 20 0.05
50 15 0.04
51 1 0.00
52 2 0.01
53 3 0.01
54 64 0.18
55 215 0.59
56 43 0.12
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (55 bp):
TAACAATTAAATTTTTCAACATGACATGTAACAACTAAATTTTCAACATTGCATA
Found at i:1014606 original size:83 final size:83
Alignment explanation
Indices: 1014502--1014974 Score: 380
Period size: 83 Copynumber: 5.8 Consensus size: 83
1014492 CATGTACAAT
* * * * *
1014502 TTTTTTATGATGATGTGTAACAATTAAATTTTTCAACATAATATGTAACAACTAAATCTTCAACA
1 TTTTTCATCATGATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAACA
1014567 TTGCATATAACAATTACA
66 TTGCATATAACAATTACA
* * * *
1014585 TTTTTCATCATGATGTATAACAACTAAATTTTTCAACATAGCATATAATAACTAAAACTTCAACA
1 TTTTTCATCATGATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAACA
* *
1014650 -TGACATTTAATAATTACA
66 TTG-CATATAACAATTACA
* * * * *
1014668 TTTTTCATCATGATGTTTAACAATTAAATTTTTCAATATCACATGTAACAACTAAATTTTCAACA
1 TTTTTCATCATGATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAACA
* **
1014733 TGGTGTATAACAATTACA
66 TTGCATATAACAATTACA
* * * * *
1014751 TTTTTTAACATGGCATG--TAACAATTAAATTTTT--A-AT---ATATAATAACTAAATTTTAAA
1 TTTTTCATCAT-G-ATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAA
* *
1014808 CA-TGACATATAACAATCATA
64 CATTG-CATATAACAATTACA
** *
1014828 TTTTTCAAT-ATG-TCGTATAACAACCAAA-TTTTCAACATAACATATAACAACCAAATCTTCAA
1 TTTTTC-ATCATGAT-GTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAA
* * * *
1014890 CATGGCATGTAAGAACTA-A
64 CATTGCATATAACAATTACA
* * * ** * ** ** ** *
1014909 ATTTTCAACACGACATGTAACAAAAAAAAATTTCAACATGGCATATAACAACTAAATTTTCAACA
1 TTTTTCATCATGATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAACA
1014974 T
66 T
1014975 GACAAGCAAT
Statistics
Matches: 310, Mismatches: 61, Indels: 39
0.76 0.15 0.10
Matches are distributed among these distances:
74 1 0.00
75 1 0.00
76 6 0.02
77 47 0.15
78 2 0.01
79 2 0.01
80 3 0.01
81 19 0.06
82 62 0.20
83 162 0.52
84 2 0.01
85 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.35
Consensus pattern (83 bp):
TTTTTCATCATGATGTATAACAATTAAATTTTTCAACATAACATATAACAACTAAATCTTCAACA
TTGCATATAACAATTACA
Found at i:1014975 original size:27 final size:27
Alignment explanation
Indices: 1014519--1015057 Score: 288
Period size: 27 Copynumber: 19.8 Consensus size: 27
1014509 TGATGATGTG
* * * *
1014519 TAACAATTAAATTTTTCAACATAATATG
1 TAACAACTAAA-TTTTCAACATGACATA
*
1014547 TAACAACTAAATCTTCAACATTG-CATA
1 TAACAACTAAATTTTCAACA-TGACATA
* * * **
1014574 TAACAATTACATTTTTCATCATGATGTA
1 TAACAACTA-AATTTTCAACATGACATA
1014602 TAACAACTAAATTTTTCAACAT-AGCATA
1 TAACAACTAAA-TTTTCAACATGA-CATA
* ** *
1014630 TAATAACTAAAACTTCAACATGACATT
1 TAACAACTAAATTTTCAACATGACATA
* * * * ** *
1014657 TAATAATTACATTTTTCATCATGATGTT
1 TAACAACTA-AATTTTCAACATGACATA
* * * *
1014685 TAACAATTAAATTTTTCAATATCACATG
1 TAACAACTAAA-TTTTCAACATGACATA
***
1014713 TAACAACTAAATTTTCAACATGGTGTA
1 TAACAACTAAATTTTCAACATGACATA
* * * * *
1014740 TAACAATTACATTTTTTAACATGGCATG
1 TAACAACTA-AATTTTCAACATGACATA
* *
1014768 TAACAATTAAATTTT-TA-AT---ATA
1 TAACAACTAAATTTTCAACATGACATA
* *
1014790 TAATAACTAAATTTTAAACATGACATA
1 TAACAACTAAATTTTCAACATGACATA
* * * *
1014817 TAACAA-TCATATTTTTCAATATGTCGTA
1 TAACAACT-A-AATTTTCAACATGACATA
* *
1014845 TAACAACCAAATTTTCAACATAACATA
1 TAACAACTAAATTTTCAACATGACATA
* * * *
1014872 TAACAACCAAATCTTCAACATGGCATG
1 TAACAACTAAATTTTCAACATGACATA
* * *
1014899 TAAGAACTAAATTTTCAACACGACATG
1 TAACAACTAAATTTTCAACATGACATA
** * *
1014926 TAACAAAAAAAAATTTCAACATGGCATA
1 TAAC-AACTAAATTTTCAACATGACATA
1014954 TAACAACTAAATTTTCAACATGACA-A
1 TAACAACTAAATTTTCAACATGACATA
* * * * * * *
1014980 GCAATAATTATATTTTTAACATGACGTG
1 -TAACAACTAAATTTTCAACATGACATA
* * * *
1015008 TAATAACTAAATTTTATAATATGACATG
1 TAACAACTAAATTTT-CAACATGACATA
*
1015036 TAAC-ACTACATTTTTCAACATG
1 TAACAACTA-AATTTTCAACATG
1015058 GCGCTAACAA
Statistics
Matches: 387, Mismatches: 102, Indels: 45
0.72 0.19 0.08
Matches are distributed among these distances:
22 15 0.04
23 1 0.00
24 2 0.01
25 2 0.01
26 3 0.01
27 192 0.50
28 172 0.44
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (27 bp):
TAACAACTAAATTTTCAACATGACATA
Found at i:1014995 original size:82 final size:82
Alignment explanation
Indices: 1014857--1015010 Score: 191
Period size: 82 Copynumber: 1.9 Consensus size: 82
1014847 ACAACCAAAT
* * *
1014857 TTTCAACATAACATATAACAACCAAATCTTCAACATGGCATGTAAGAACTAAATTTTCAACACGA
1 TTTCAACATAACATATAACAACCAAATCTTCAACATGACAAGCAAGAACTAAATTTTCAACACGA
1014922 CATGTAACAAAAAAAAA
66 CATGTAACAAAAAAAAA
** * * * * * * *
1014939 TTTCAACATGGCATATAACAACTAAATTTTCAACATGACAAGCAATAATTATATTTTTAACATGA
1 TTTCAACATAACATATAACAACCAAATCTTCAACATGACAAGCAAGAACTAAATTTTCAACACGA
*
1015004 CGTGTAA
66 CATGTAA
1015011 TAACTAAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
82 59 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (82 bp):
TTTCAACATAACATATAACAACCAAATCTTCAACATGACAAGCAAGAACTAAATTTTCAACACGA
CATGTAACAAAAAAAAA
Found at i:1015296 original size:19 final size:20
Alignment explanation
Indices: 1015254--1015301 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1015244 AAAAGTGTCC
*
1015254 AAATGTTTAGCCTTAATTTG
1 AAATATTTAGCCTTAATTTG
*
1015274 -AATATTTAGCC-TGATTTG
1 AAATATTTAGCCTTAATTTG
1015292 AAATAATTTA
1 AAAT-ATTTA
1015302 TAAGTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 13 0.54
20 5 0.21
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.44
Consensus pattern (20 bp):
AAATATTTAGCCTTAATTTG
Found at i:1016856 original size:9 final size:9
Alignment explanation
Indices: 1016801--1016860 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
1016791 GCCATCTAGA
*
1016801 TCTCTCCAC
1 TCTCTCAAC
*
1016810 TCTTTCAAC
1 TCTCTCAAC
*
1016819 TCTTTCAAC
1 TCTCTCAAC
*
1016828 TCTCTC-TC
1 TCTCTCAAC
* *
1016836 GCTATCCAAC
1 TCTCT-CAAC
1016846 TCTCTCAAC
1 TCTCTCAAC
1016855 TCTCTC
1 TCTCTC
1016861 TTACCATCCA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
8 4 0.10
9 32 0.80
10 4 0.10
ACGTcount: A:0.17, C:0.43, G:0.02, T:0.38
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:1016869 original size:27 final size:27
Alignment explanation
Indices: 1016815--1016905 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
1016805 TCCACTCTTT
* * *
1016815 CAACTCTTTCAACTCTCTCTCGCTATC
1 CAACTCTCTCAACTCTCTCTTGCCATC
*
1016842 CAACTCTCTCAACTCTCTCTTACCATC
1 CAACTCTCTCAACTCTCTCTTGCCATC
* * * *
1016869 CATCTTTCTCAGCTTTCTCTTGCCATC
1 CAACTCTCTCAACTCTCTCTTGCCATC
*
1016896 CAGCTCTCTC
1 CAACTCTCTC
1016906 TAATTTTACT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.16, C:0.42, G:0.04, T:0.37
Consensus pattern (27 bp):
CAACTCTCTCAACTCTCTCTTGCCATC
Found at i:1017234 original size:27 final size:27
Alignment explanation
Indices: 1017179--1017310 Score: 99
Period size: 27 Copynumber: 5.0 Consensus size: 27
1017169 CACTATAAAC
* *
1017179 ATGGCATGTAACAAAA---TTTTCAAA
1 ATGGCATGTAGCAAAATTTTTTTGAAA
* **
1017203 CATGGCGTGTAGCAATTTTTTTTTGAAA
1 -ATGGCATGTAGCAAAATTTTTTTGAAA
* * *
1017231 ATGGCATATAGCAAAATTATTTTGAAT
1 ATGGCATGTAGCAAAATTTTTTTGAAA
** ** * *
1017258 ATGGTGTGTAATAATATTTTTTTCAAA
1 ATGGCATGTAGCAAAATTTTTTTGAAA
*
1017285 ATGGCATGTAGTAAAATTTTTTTGAA
1 ATGGCATGTAGCAAAATTTTTTTGAA
1017311 CATGATGTGT
Statistics
Matches: 79, Mismatches: 25, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
25 12 0.15
27 60 0.76
28 7 0.09
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (27 bp):
ATGGCATGTAGCAAAATTTTTTTGAAA
Found at i:1017246 original size:52 final size:52
Alignment explanation
Indices: 1017179--1017304 Score: 135
Period size: 54 Copynumber: 2.4 Consensus size: 52
1017169 CACTATAAAC
* * * *
1017179 ATGGCATGTAACAAAATTTTCAAACATGGCGTGTAGCAATTTTTTTTTGAAA
1 ATGGCATGTAGCAAAATTTTCAAACATGGCGTGTAACAATATTTTTTTCAAA
* ** * * *
1017231 ATGGCATATAGCAAAATTATTTTGAATATGGTGTGTAATAATATTTTTTTCAAA
1 ATGGCATGTAGCAAAA-T-TTTCAAACATGGCGTGTAACAATATTTTTTTCAAA
*
1017285 ATGGCATGTAGTAAAATTTT
1 ATGGCATGTAGCAAAATTTT
1017305 TTTGAACATG
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
52 17 0.28
53 2 0.03
54 41 0.68
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.40
Consensus pattern (52 bp):
ATGGCATGTAGCAAAATTTTCAAACATGGCGTGTAACAATATTTTTTTCAAA
Found at i:1017288 original size:54 final size:54
Alignment explanation
Indices: 1017220--1017322 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
1017210 TGTAGCAATT
* * *
1017220 TTTTTTTGAAAATGGCATATAGCAAAATTATTTTGAATATGGTGTGTAATAATA
1 TTTTTTTCAAAATGGCATATAGCAAAATTATTTTGAACATGATGTGTAATAATA
* * *
1017274 TTTTTTTCAAAATGGCATGTAGTAAAATTTTTTTGAACATGATGTGTAA
1 TTTTTTTCAAAATGGCATATAGCAAAATTATTTTGAACATGATGTGTAA
1017323 CAACAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (54 bp):
TTTTTTTCAAAATGGCATATAGCAAAATTATTTTGAACATGATGTGTAATAATA
Found at i:1017321 original size:27 final size:27
Alignment explanation
Indices: 1017220--1017322 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 27
1017210 TGTAGCAATT
** * **
1017220 TTTTTTTGAAAATGGCATATAGCAAAA
1 TTTTTTTGAAAATGGTGTGTAATAAAA
* * *
1017247 TTATTTTGAATATGGTGTGTAATAATA
1 TTTTTTTGAAAATGGTGTGTAATAAAA
* ** *
1017274 TTTTTTTCAAAATGGCATGTAGTAAAA
1 TTTTTTTGAAAATGGTGTGTAATAAAA
* *
1017301 TTTTTTTGAACATGATGTGTAA
1 TTTTTTTGAAAATGGTGTGTAA
1017323 CAACAATATT
Statistics
Matches: 55, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (27 bp):
TTTTTTTGAAAATGGTGTGTAATAAAA
Found at i:1022206 original size:27 final size:26
Alignment explanation
Indices: 1022074--1022232 Score: 101
Period size: 27 Copynumber: 6.1 Consensus size: 26
1022064 CAACAATATC
** *
1022074 TTTTT-AATATGACATATAATAACTT
1 TTTTTCAATATGATGTATAATAAATT
* *
1022099 TTTTTCAACATTGCATG--TAATAAAACT
1 TTTTTCAATA-TG-ATGTATAAT-AAATT
* * * * * *
1022126 ATTTTGAATATGACGTGTAA-CAATA
1 TTTTTCAATATGATGTATAATAAATT
* *
1022151 TTTTTCAATATGGTGTATAATAAAAT
1 TTTTTCAATATGATGTATAATAAATT
* *
1022177 TTTTTCAATGTGACGTATAATAATATT
1 TTTTTCAATATGATGTATAATAA-ATT
* *
1022204 TTTTTCAATATGATGTATAACAAAAT
1 TTTTTCAATATGATGTATAATAAATT
1022230 TTT
1 TTT
1022233 AGAACATGTG
Statistics
Matches: 98, Mismatches: 28, Indels: 15
0.70 0.20 0.11
Matches are distributed among these distances:
25 24 0.24
26 36 0.37
27 37 0.38
28 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (26 bp):
TTTTTCAATATGATGTATAATAAATT
Found at i:1022221 original size:53 final size:52
Alignment explanation
Indices: 1022074--1022232 Score: 157
Period size: 53 Copynumber: 3.1 Consensus size: 52
1022064 CAACAATATC
* * *
1022074 TTTTTAATATGACATATAATAA-CTTTTTTTCAACATTGCATG--TAATAAAACT
1 TTTTTAATATGACGTATAATAATATTTTTTTCAATA-TG-ATGTATAATAAAA-T
* * * *
1022126 ATTTTGAATATGACGTGTAACAATA--TTTTTCAATATGGTGTATAATAAAAT
1 -TTTTTAATATGACGTATAATAATATTTTTTTCAATATGATGTATAATAAAAT
* *
1022177 TTTTTCAATGTGACGTATAATAATATTTTTTTCAATATGATGTATAACAAAAT
1 TTTTT-AATATGACGTATAATAATATTTTTTTCAATATGATGTATAATAAAAT
1022230 TTT
1 TTT
1022233 AGAACATGTG
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
50 6 0.07
51 19 0.22
52 17 0.20
53 45 0.52
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (52 bp):
TTTTTAATATGACGTATAATAATATTTTTTTCAATATGATGTATAATAAAAT
Found at i:1023266 original size:14 final size:14
Alignment explanation
Indices: 1023231--1023272 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1023221 AGTAAGTTTC
*
1023231 TTCTTTTTTGTTTT
1 TTCTTTTTTGTGTT
**
1023245 TTAATTTTTGTGTT
1 TTCTTTTTTGTGTT
1023259 TTCTTTTTTG-GTT
1 TTCTTTTTTGTGTT
1023272 T
1 T
1023273 GTTTTGTAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.79
Consensus pattern (14 bp):
TTCTTTTTTGTGTT
Found at i:1050568 original size:30 final size:31
Alignment explanation
Indices: 1050527--1050585 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1050517 CATGGCGTGT
1050527 ATAACA-TTTTTTTCAACAGAACGTGTAATA
1 ATAACATTTTTTTTCAACAGAACGTGTAATA
* * *
1050557 ATAATATTTTTTTTCAACATAGCGTGTAA
1 ATAACATTTTTTTTCAACAGAACGTGTAA
1050586 CAACTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (31 bp):
ATAACATTTTTTTTCAACAGAACGTGTAATA
Found at i:1056768 original size:25 final size:25
Alignment explanation
Indices: 1056731--1056819 Score: 65
Period size: 25 Copynumber: 3.6 Consensus size: 25
1056721 AAAAGAAAGA
* *
1056731 TATTGAGAGAATGCTTTTTATGTAT
1 TATTGAAACAATGCTTTTTATGTAT
****** *
1056756 TATTGAAACAATGAAAAGAAAG-A-
1 TATTGAAACAATGCTTTTTATGTAT
* *
1056779 TATTGAGAGAATGCTTTTTATGTAT
1 TATTGAAACAATGCTTTTTATGTAT
1056804 TATTGAAACAATGCTT
1 TATTGAAACAATGCTT
1056820 GGATGAAAAA
Statistics
Matches: 42, Mismatches: 20, Indels: 4
0.64 0.30 0.06
Matches are distributed among these distances:
23 13 0.31
24 2 0.05
25 27 0.64
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (25 bp):
TATTGAAACAATGCTTTTTATGTAT
Found at i:1056791 original size:48 final size:48
Alignment explanation
Indices: 1056720--1056816 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
1056710 GAAATAGGAA
1056720 GAAAAGAAAGATATTGAGAGAATGCTTTTTATGTATTATTGAAACAAT
1 GAAAAGAAAGATATTGAGAGAATGCTTTTTATGTATTATTGAAACAAT
1056768 GAAAAGAAAGATATTGAGAGAATGCTTTTTATGTATTATTGAAACAAT
1 GAAAAGAAAGATATTGAGAGAATGCTTTTTATGTATTATTGAAACAAT
1056816 G
1 G
1056817 CTTGGATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (48 bp):
GAAAAGAAAGATATTGAGAGAATGCTTTTTATGTATTATTGAAACAAT
Found at i:1057405 original size:2 final size:2
Alignment explanation
Indices: 1057398--1057422 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1057388 CCATAATTGA
1057398 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
1057423 CACACACACG
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:1071598 original size:31 final size:31
Alignment explanation
Indices: 1071552--1071624 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
1071542 ATATGATTTC
1071552 TCTTTTCAGCTTTCTACACTCAAGAGTCCCCAT
1 TCTTTT-AG-TTTCTACACTCAAGAGTCCCCAT
*
1071585 TCTTTTAGTTTCTACACTCTAGAGTCCCCAT
1 TCTTTTAGTTTCTACACTCAAGAGTCCCCAT
*
1071616 TCGTTTAGT
1 TCTTTTAGT
1071625 ACCTAACACA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 30 0.79
32 2 0.05
33 6 0.16
ACGTcount: A:0.19, C:0.29, G:0.11, T:0.41
Consensus pattern (31 bp):
TCTTTTAGTTTCTACACTCAAGAGTCCCCAT
Found at i:1076792 original size:28 final size:28
Alignment explanation
Indices: 1076761--1076854 Score: 86
Period size: 27 Copynumber: 3.4 Consensus size: 28
1076751 AAATAATTAT
* *
1076761 ATTTTTCAATA-AAGGGTATAACAACTAA
1 ATTTTTCAATATAA-CGTATAACAAATAA
* * *
1076789 ATTTTT-AACATTACGTATAACAAATAC
1 ATTTTTCAATATAACGTATAACAAATAA
* * *
1076816 ATTTTTCAATATAATGTTTAACAATTAA
1 ATTTTTCAATATAACGTATAACAAATAA
1076844 A-TTTTCAATAT
1 ATTTTTCAATAT
1076855 GATATATAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
27 30 0.57
28 23 0.43
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.40
Consensus pattern (28 bp):
ATTTTTCAATATAACGTATAACAAATAA
Found at i:1076806 original size:27 final size:28
Alignment explanation
Indices: 1076776--1076848 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
1076766 TCAATAAAGG
* *
1076776 GTATAACAACTAAATTTTT-AACATTAC
1 GTATAACAAATAAATTTTTCAACATAAC
* * *
1076803 GTATAACAAATACATTTTTCAATATAAT
1 GTATAACAAATAAATTTTTCAACATAAC
* *
1076831 GTTTAACAATTAAATTTT
1 GTATAACAAATAAATTTT
1076849 CAATATGATA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
27 17 0.46
28 20 0.54
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (28 bp):
GTATAACAAATAAATTTTTCAACATAAC
Found at i:1076820 original size:55 final size:55
Alignment explanation
Indices: 1076724--1076876 Score: 148
Period size: 55 Copynumber: 2.8 Consensus size: 55
1076714 ATATAGCGTG
* * * *
1076724 TAACAACTAAATTTTCAACATGCCATAAAATAATTATATTTTTCAATA-AAGGGTA
1 TAACAACTAAATTTTCAACATGACATAAAACAAATACATTTTTCAATATAA-GGTA
* * * * * *
1076779 TAACAACTAAATTTTTAACATTACGTATAACAAATACATTTTTCAATATAATGTT
1 TAACAACTAAATTTTCAACATGACATAAAACAAATACATTTTTCAATATAAGGTA
* * * *
1076834 TAACAATTAAATTTTCAATATGATATATAAA-AACTACATTTTT
1 TAACAACTAAATTTTCAACATGACATA-AAACAAATACATTTTT
1076877 AAAGCGATTT
Statistics
Matches: 78, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
55 74 0.95
56 4 0.05
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.39
Consensus pattern (55 bp):
TAACAACTAAATTTTCAACATGACATAAAACAAATACATTTTTCAATATAAGGTA
Found at i:1076874 original size:27 final size:26
Alignment explanation
Indices: 1076804--1076875 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 26
1076794 TAACATTACG
*
1076804 TATAACAAATACATTTTTCAATATAATG
1 TATAA-AAATACA-TTTTCAATATAATA
* * * *
1076832 TTTAACAATTAAATTTTCAATATGATA
1 TATAA-AAATACATTTTCAATATAATA
1076859 TATAAAAACTACATTTT
1 TATAAAAA-TACATTTT
1076876 TAAAGCGATT
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 2 0.06
27 23 0.66
28 10 0.29
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.42
Consensus pattern (26 bp):
TATAAAAATACATTTTCAATATAATA
Found at i:1080569 original size:15 final size:15
Alignment explanation
Indices: 1080551--1080580 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1080541 CCTTAAGCTC
*
1080551 TTTTTTTTTTTAAAA
1 TTTTGTTTTTTAAAA
1080566 TTTTGTTTTTTAAAA
1 TTTTGTTTTTTAAAA
1080581 GAGTTTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (15 bp):
TTTTGTTTTTTAAAA
Found at i:1084276 original size:16 final size:16
Alignment explanation
Indices: 1084255--1084290 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1084245 TCCAAATCAG
*
1084255 TATTTATAATTATAAA
1 TATTTATAAATATAAA
*
1084271 TATTTATAAATATAAT
1 TATTTATAAATATAAA
1084287 TATT
1 TATT
1084291 AATATCGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTATAAATATAAA
Found at i:1084974 original size:74 final size:75
Alignment explanation
Indices: 1084882--1085022 Score: 205
Period size: 74 Copynumber: 1.9 Consensus size: 75
1084872 ATCCAAACCC
* * *
1084882 TATATTTATAAATATGTATTCATTAAATGACGATTATT-TAAATATTTTTTATTATAATTATTAA
1 TATATTTATAAATATGTATTCATCAAATGACGATCATTGAAAAT-TTTTTTATTATAATTATTAA
1084946 TAATATTTAAA
65 TAATATTTAAA
* * *
1084957 TATA-TTATAAATGTGTATTCATCCAATGATGATCATTGAAAATTTTTTTATTATAATTATTAAT
1 TATATTTATAAATATGTATTCATCAAATGACGATCATTGAAAATTTTTTTATTATAATTATTAAT
1085021 AA
66 AA
1085023 GATTATTACA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
74 51 0.86
75 8 0.14
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (75 bp):
TATATTTATAAATATGTATTCATCAAATGACGATCATTGAAAATTTTTTTATTATAATTATTAAT
AATATTTAAA
Found at i:1085037 original size:21 final size:21
Alignment explanation
Indices: 1085004--1085043 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1084994 GAAAATTTTT
* *
1085004 TTATTATAATTATTAATAAGA
1 TTATTACAATTATAAATAAGA
*
1085025 TTATTACATTTATAAATAA
1 TTATTACAATTATAAATAA
1085044 AAAATTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (21 bp):
TTATTACAATTATAAATAAGA
Found at i:1085152 original size:22 final size:21
Alignment explanation
Indices: 1085127--1085192 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
1085117 AATATTTTAA
1085127 ATTAATTTTTTTAAAGTTATAT
1 ATTAATTTTTTTAAA-TTATAT
* *
1085149 ATTAA-TATTTTAAATTAAAT
1 ATTAATTTTTTTAAATTATAT
* *
1085169 ATTAATATTTATAAAATT-TAT
1 ATTAAT-TTTTTTAAATTATAT
1085190 ATT
1 ATT
1085193 TAAAAGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
20 10 0.28
21 13 0.36
22 13 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAATTTTTTTAAATTATAT
Found at i:1085161 original size:21 final size:20
Alignment explanation
Indices: 1085112--1085192 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
1085102 TATAATTTAA
1085112 ATATTAATATTTTAAA-T-T
1 ATATTAATATTTTAAATTAT
1085130 A-ATT--T-TTTTAAAGTTAT
1 ATATTAATATTTTAAA-TTAT
*
1085147 ATATTAATATTTTAAATTAA
1 ATATTAATATTTTAAATTAT
1085167 ATATTAATATTTATAAAATT-T
1 ATATTAATATTT-T-AAATTAT
1085188 ATATT
1 ATATT
1085193 TAAAAGTGTT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
16 1 0.02
17 5 0.10
18 4 0.08
20 16 0.31
21 13 0.25
22 5 0.10
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATATTAATATTTTAAATTAT
Found at i:1085172 original size:20 final size:20
Alignment explanation
Indices: 1085108--1085183 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
1085098 ATTGTATAAT
1085108 TTAAATATTAATATTTTAAA
1 TTAAATATTAATATTTTAAA
1085128 TT--A-ATT--T-TTTTAAA
1 TTAAATATTAATATTTTAAA
*
1085142 GTTATATATTAATATTTTAAA
1 -TTAAATATTAATATTTTAAA
1085163 TTAAATATTAATATTTATAAA
1 TTAAATATTAATATTT-TAAA
1085184 ATTTATATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
14 7 0.15
15 3 0.06
17 4 0.09
18 4 0.09
20 18 0.38
21 11 0.23
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
TTAAATATTAATATTTTAAA
Found at i:1087563 original size:56 final size:56
Alignment explanation
Indices: 1087483--1087594 Score: 179
Period size: 56 Copynumber: 2.0 Consensus size: 56
1087473 AGCAAACTGG
* *
1087483 CTTGAGAGTTGGAAGCGTTGTAGATAAGGAAACAAATAGAGAGAAGCAAAACACAA
1 CTTGAGAGTTGGAAGCGTTCTAGATAAGGAAACAAATAGAGAGAAGCAAAAAACAA
* * *
1087539 CTTGAGAGTTGGAAGCTTTCTAGATGAGGAAACAAATAGTGAGAAGCAAAAAACAA
1 CTTGAGAGTTGGAAGCGTTCTAGATAAGGAAACAAATAGAGAGAAGCAAAAAACAA
1087595 GCAACCTGGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.18
Consensus pattern (56 bp):
CTTGAGAGTTGGAAGCGTTCTAGATAAGGAAACAAATAGAGAGAAGCAAAAAACAA
Found at i:1100171 original size:59 final size:59
Alignment explanation
Indices: 1100108--1100224 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
1100098 AATTTATTAA
* * * * *
1100108 AAATATTAATAAATTT-TTATTATAATTTTAATATAATTATT-TATTTTATTTTATTTTTT
1 AAATATTAA-AAATTTATAATTAAAACTTTAAAATAATTATTGTA-TTTACTTTATTTTTT
*
1100167 AAATATTAAAAATTTATAATTAAAACTTTAAAATGATTATTGTATTTACTTTATTTTT
1 AAATATTAAAAATTTATAATTAAAACTTTAAAATAATTATTGTATTTACTTTATTTTT
1100225 ATTGTTAGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 6 0.12
59 42 0.84
60 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (59 bp):
AAATATTAAAAATTTATAATTAAAACTTTAAAATAATTATTGTATTTACTTTATTTTTT
Found at i:1102542 original size:14 final size:14
Alignment explanation
Indices: 1102520--1102588 Score: 52
Period size: 14 Copynumber: 4.7 Consensus size: 14
1102510 TTAAAATAAT
*
1102520 AATAAAAATTAAAA
1 AATATAAATTAAAA
1102534 AATATAAATATATTAAA
1 AATATAAAT-TA--AAA
*
1102551 ATTTATAAATT-AAA
1 A-ATATAAATTAAAA
*
1102565 AGT-TAAATTAAAAA
1 AATATAAATT-AAAA
1102579 AATATAAATT
1 AATATAAATT
1102589 CAACCTATCA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
12 6 0.14
13 1 0.02
14 17 0.39
15 8 0.18
17 5 0.11
18 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (14 bp):
AATATAAATTAAAA
Found at i:1104268 original size:3 final size:3
Alignment explanation
Indices: 1104260--1104284 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1104250 CTCATCAAAC
1104260 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
1104285 AAAGCTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1113788 original size:41 final size:41
Alignment explanation
Indices: 1113739--1113818 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
1113729 ATTTTTCTTC
*
1113739 AATTAATTTTTGCTCTACTTTATGCTATTTAATTGGTTTGT
1 AATTAATTTTAGCTCTACTTTATGCTATTTAATTGGTTTGT
* * *
1113780 AATTAATTTTAGCTCTGCTTTCTGTTATTTAATTGGTTT
1 AATTAATTTTAGCTCTACTTTATGCTATTTAATTGGTTT
1113819 TGTTTTATGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.56
Consensus pattern (41 bp):
AATTAATTTTAGCTCTACTTTATGCTATTTAATTGGTTTGT
Found at i:1114582 original size:15 final size:15
Alignment explanation
Indices: 1114562--1114597 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1114552 GTGATTACAC
*
1114562 GTGATTGCAAGTAAT
1 GTGATTGCAAGCAAT
1114577 GTGATTGCAAGCAAT
1 GTGATTGCAAGCAAT
1114592 GTGATT
1 GTGATT
1114598 ACAGGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (15 bp):
GTGATTGCAAGCAAT
Found at i:1114811 original size:60 final size:59
Alignment explanation
Indices: 1114738--1114925 Score: 205
Period size: 56 Copynumber: 3.3 Consensus size: 59
1114728 CTAATTATTA
**
1114738 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTT-TT
* *
1114798 AAATATATTTTTAATATCA--TATA--TTTTATT-TTTATTTATTATTATAATA--ATTTAT
1 AAATATATTTTTAATAT-ATTTATATTTTTTATTATTAATTT-TTA-TATAATATCATTTTT
* * *
1114853 -ATTTTATTTTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATTTT
1 AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCAT-TTTT
1114911 AAATATATTTTTAAT
1 AAATATATTTTTAAT
1114926 GTCATATATT
Statistics
Matches: 106, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
53 1 0.01
54 14 0.13
55 12 0.11
56 19 0.18
57 18 0.17
58 10 0.09
59 16 0.15
60 15 0.14
61 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (59 bp):
AAATATATTTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTTT
Found at i:1114858 original size:23 final size:24
Alignment explanation
Indices: 1114824--1114887 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
1114814 TCATATATTT
*
1114824 TATTTTTA-TTTATTATTATAATA
1 TATTTATATTTTATTATTATAATA
1114847 -ATTTATATTTTATT-TT-TAATA
1 TATTTATATTTTATTATTATAATA
1114868 TATTTATATTTATATTATTA
1 TATTTATATTT-TATTATTA
1114888 ATTTTTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
21 5 0.14
22 18 0.51
23 10 0.29
24 2 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TATTTATATTTTATTATTATAATA
Found at i:1114879 original size:21 final size:21
Alignment explanation
Indices: 1114824--1114897 Score: 73
Period size: 22 Copynumber: 3.4 Consensus size: 21
1114814 TCATATATTT
*
1114824 TATTTTTATTTATTATTATAATA
1 TATTTATATTTATT-TT-TAATA
1114847 -ATTTATATTTTATTTTTAATA
1 TATTTATA-TTTATTTTTAATA
1114868 TATTTATATTTATATTATTAAT-
1 TATTTATATTTAT-TT-TTAATA
1114890 T-TTTATAT
1 TATTTATAT
1114898 AATATCATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
21 17 0.37
22 18 0.39
23 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TATTTATATTTATTTTTAATA
Found at i:1114896 original size:15 final size:14
Alignment explanation
Indices: 1114760--1114975 Score: 61
Period size: 15 Copynumber: 15.4 Consensus size: 14
1114750 AATATATTTA
1114760 TATTTTT-TATTAT
1 TATTTTTATATTAT
1114773 TAATTTTTATATAATAT
1 T-ATTTTTATAT--TAT
* *
1114790 CATTTCTTA-AATA-
1 TATTT-TTATATTAT
*
1114803 TATTTTTAATATCA-
1 TATTTTT-ATATTAT
1114817 TATATTTTAT-TT-T
1 TAT-TTTTATATTAT
*
1114830 TATTTAT-TATTAT
1 TATTTTTATATTAT
* *
1114843 AATAATTTATATT-T
1 TAT-TTTTATATTAT
1114857 TATTTTTA-ATATATT
1 TATTTTTATAT-TA-T
*
1114872 TATATTTATATTAT
1 TATTTTTATATTAT
1114886 TAATTTTTATATAATAT
1 T-ATTTTTATAT--TAT
* *
1114903 CATATTTTA-AATA-
1 TAT-TTTTATATTAT
1114916 TATTTTTA-ATGTCA-
1 TATTTTTATAT-T-AT
1114930 TATATTTTAT-TT-T
1 TAT-TTTTATATTAT
*
1114943 TATTTAT-TATTAT
1 TATTTTTATATTAT
*
1114956 AATTTTATATATT-T
1 TATTTT-TATATTAT
1114970 TATTTT
1 TATTTT
1114976 CATTTCTTTA
Statistics
Matches: 151, Mismatches: 22, Indels: 59
0.65 0.09 0.25
Matches are distributed among these distances:
11 2 0.01
12 20 0.13
13 29 0.19
14 36 0.24
15 40 0.26
16 10 0.07
17 14 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTTATATTAT
Found at i:1114898 original size:23 final size:24
Alignment explanation
Indices: 1114830--1114898 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 24
1114820 ATTTTATTTT
*
1114830 TATTTATTATTA-TAATAATTTATA
1 TATTTA-TATTATTAATATTTTATA
*
1114854 T-TTTAT-TT-TTAATATATT-TA
1 TATTTATATTATTAATATTTTATA
1114874 TATTTATATTATTAAT-TTTTATA
1 TATTTATATTATTAATATTTTATA
1114897 TA
1 TA
1114899 ATATCATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
20 3 0.08
21 14 0.38
22 6 0.16
23 13 0.35
24 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTATATTATTAATATTTTATA
Found at i:1114946 original size:27 final size:26
Alignment explanation
Indices: 1114803--1114975 Score: 127
Period size: 27 Copynumber: 6.2 Consensus size: 26
1114793 TTCTTAAATA
1114803 TATTTTTAATATCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
* *
1114830 TATTTATTATTATA-ATAATTTATATTT
1 TATTT-TTAATATATATATTTTAT-TTT
1114857 TATTTTTAATATATTTATATTTATATTATT
1 TATTTTTAATATA--TATATTT-TATT-TT
* ** *
1114887 AATTTTTATATAATATCATATTTTAAATA
1 TATTTTTA-AT-ATAT-ATATTTTATTTT
*
1114916 TATTTTTAATGTCATATATTTTATTTT
1 TATTTTTAATAT-ATATATTTTATTTT
*
1114943 TATTTATTATTATA-AT-TTTATATATTT
1 TATTT-TTAATATATATATTT-TAT-TTT
1114970 TATTTT
1 TATTTT
1114976 CATTTCTTTA
Statistics
Matches: 117, Mismatches: 15, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
25 3 0.03
26 21 0.18
27 38 0.32
28 15 0.13
29 14 0.12
30 15 0.13
31 8 0.07
32 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (26 bp):
TATTTTTAATATATATATTTTATTTT
Found at i:1114946 original size:113 final size:114
Alignment explanation
Indices: 1114747--1114975 Score: 392
Period size: 113 Copynumber: 2.0 Consensus size: 114
1114737 AAAATATAAG
*
1114747 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
1114812 TATCATATATTTTATTTTTATTTATTATTATAATAATT-TATATTTTATT
66 TATCATATATTTTATTTTTATTTATTATTATAAT-ATTATATATTTTATT
1114861 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTA
1 TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTA
* *
1114924 ATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATT
65 ATATCATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
1114974 TT
1 TT
1114976 CATTTCTTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
112 2 0.02
113 91 0.83
114 17 0.15
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (114 bp):
TTTAATATATTTATATTTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAA
TATCATATATTTTATTTTTATTTATTATTATAATATTATATATTTTATT
Found at i:1114966 original size:10 final size:9
Alignment explanation
Indices: 1114850--1114972 Score: 50
Period size: 9 Copynumber: 14.1 Consensus size: 9
1114840 TATAATAATT
1114850 TATATTTTA
1 TATATTTTA
*
1114859 T-T-TTTAA
1 TATATTTTA
1114866 TATATTTATA
1 TATATTT-TA
* *
1114876 TTTATATTA
1 TATATTTTA
1114885 T-TAATTTT-
1 TAT-ATTTTA
**
1114893 TATATAATA
1 TATATTTTA
1114902 TCATATTTTAAA
1 T-ATATTTT--A
1114914 TATATTTT-
1 TATATTTTA
* *
1114922 TA-ATGTCA
1 TATATTTTA
1114930 TATA-TTT-
1 TATATTTTA
1114937 TAT-TTTTA
1 TATATTTTA
*
1114945 TTTATTATTA
1 TATATT-TTA
1114955 TA-ATTTTA
1 TATATTTTA
1114963 TATATTTTA
1 TATATTTTA
1114972 T
1 T
1114973 TTTCATTTCT
Statistics
Matches: 83, Mismatches: 15, Indels: 32
0.64 0.12 0.25
Matches are distributed among these distances:
7 14 0.17
8 19 0.23
9 26 0.31
10 15 0.18
11 7 0.08
12 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (9 bp):
TATATTTTA
Found at i:1114966 original size:33 final size:33
Alignment explanation
Indices: 1114929--1115014 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 33
1114919 TTTTAATGTC
*
1114929 ATATATTTTATTTTTATTTA-TTATTATAATTTT
1 ATATATTTTATTTTTATTTATTTAATAT-ATTTT
* *
1114962 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTTTATTTATTTAATATATTTT
* *
1114995 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
1115015 TAATTTGTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTATTTAATATATTTT
Found at i:1115038 original size:31 final size:30
Alignment explanation
Indices: 1115003--1115136 Score: 138
Period size: 31 Copynumber: 4.6 Consensus size: 30
1114993 TTTTATATTA
*
1115003 TATATTTTATTTTAATTTGTT-TTATCTATAT
1 TATATTTTATTTTAATTT-TTATTCT-TATAT
** * *
1115034 TATA-TAAATATTAA-TTTT-TT-ATAT-T
1 TATATTTTATTTTAATTTTTATTCTTATAT
1115059 T-TATTTTATTTTAATTTTTATTCTTATAT
1 TATATTTTATTTTAATTTTTATTCTTATAT
1115088 TATATATTTATTTTAATTTTTATTCTTATAT
1 TATAT-TTTATTTTAATTTTTATTCTTATAT
1115119 TATATATTTATTTTAATT
1 TATAT-TTTATTTTAATT
1115137 ATAATATTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
24 2 0.02
25 9 0.10
26 7 0.08
27 2 0.02
28 7 0.08
29 4 0.05
30 10 0.11
31 47 0.53
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (30 bp):
TATATTTTATTTTAATTTTTATTCTTATAT
Found at i:1115085 original size:6 final size:5
Alignment explanation
Indices: 1115055--1115133 Score: 50
Period size: 5 Copynumber: 13.4 Consensus size: 5
1115045 TAATTTTTTA
1115055 TATTT TATTT TATTT TAATTTT TATTCT TATATT ATATATT TATTT TAATTTT
1 TATTT TATTT TATTT T-A-TTT TATT-T TAT-TT -TAT-TT TATTT T-A-TTT
1115108 TATTCT TATATT ATATATT TATTT TA
1 TATT-T TAT-TT -TAT-TT TATTT TA
1115134 ATTATAATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
5 22 0.34
6 20 0.31
7 22 0.34
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:1115109 original size:186 final size:182
Alignment explanation
Indices: 1114789--1115147 Score: 408
Period size: 186 Copynumber: 1.9 Consensus size: 182
1114779 TTATATAATA
*
1114789 TCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTTATTTATTATTATAATAATTTATA
1 TCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATAATTTATA
*
1114854 TTTTATTTTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATAT
66 TTTAATTTTT-ATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATAT
* * * *
1114919 TTTTAATGTCATATATTTTATTTTTATTTATTATTATAATTTTATATATTTTATTT
130 TTTT-AT-TCATATATTATATATTTATTT-TAATTATAATATTATATATTTTATTT
* * * * *
1114975 TCATTTCTTTAATATATTTTTTATATTATATATTTTATTTTAATTTGTT-TTAT-CTATATTATA
1 TCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATA-ATT-TA
* * *
1115038 TAAATATTAATTTTT-TATATTT-TATTT-TATT-TTAATTTTTATTCTTATATTATATATTT-A
64 T--AT-TTAATTTTTATATATTTATATTTATATTATTAATTTTTA-TATAATATCATAT-TTTAA
* * *
1115098 TTTTAATTTTTATTCTTATATTATATATTTATTTTAATTATAATATTATA
124 ATAT-ATTTTTATTCATATATTATATATTTATTTTAATTATAATATTATA
1115148 AAATATTTTT
Statistics
Matches: 148, Mismatches: 17, Indels: 19
0.80 0.09 0.10
Matches are distributed among these distances:
183 14 0.09
184 30 0.20
185 26 0.18
186 61 0.41
187 7 0.05
188 2 0.01
189 8 0.05
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (182 bp):
TCATTTCTTAAATATATTTTTAATATCATATATTTTATTTTAATTTATTATTATAATAATTTATA
TTTAATTTTTATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATT
TTTATTCATATATTATATATTTATTTTAATTATAATATTATATATTTTATTT
Found at i:1163126 original size:26 final size:26
Alignment explanation
Indices: 1163091--1163147 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1163081 TAGTTAATTA
* * *
1163091 AATTG-TTTAATTAAATTATTGAGCTT
1 AATTGATTAAATTAAATAATTAAG-TT
1163117 AATTGATTAAATTAAATAATTAAGTT
1 AATTGATTAAATTAAATAATTAAGTT
1163143 AATTG
1 AATTG
1163148 GGCTTCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (26 bp):
AATTGATTAAATTAAATAATTAAGTT
Found at i:1163137 original size:35 final size:35
Alignment explanation
Indices: 1162975--1163139 Score: 147
Period size: 35 Copynumber: 4.7 Consensus size: 35
1162965 AAGTTGTACC
* * *
1162975 TAATTAATTAAATTATTTAATTAAGTCATTGATC-
1 TAATTGATTAAATTATTTAATTAAATCATTGAGCT
* * * *
1163009 TAGTTGATTAAAATTATTTAATTAAGTCATTGGGCC
1 TAATTGATT-AAATTATTTAATTAAATCATTGAGCT
*
1163045 TAATTGATTAAAAATT-TTTAATTAAATTATT-AGGCT
1 TAATTGATT--AAATTATTTAATTAAATCATTGA-GCT
* * * *
1163081 TAGTTAATTAAATTGTTTAATTAAATTATTGAGCT
1 TAATTGATTAAATTATTTAATTAAATCATTGAGCT
**
1163116 TAATTGATTAAATTAAATAATTAA
1 TAATTGATTAAATTATTTAATTAA
1163140 GTTAATTGGG
Statistics
Matches: 109, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
34 12 0.11
35 60 0.55
36 31 0.28
37 6 0.06
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (35 bp):
TAATTGATTAAATTATTTAATTAAATCATTGAGCT
Found at i:1163152 original size:71 final size:71
Alignment explanation
Indices: 1162973--1163152 Score: 186
Period size: 71 Copynumber: 2.5 Consensus size: 71
1162963 TTAAGTTGTA
* * ** * *
1162973 CCTAATTAATTAAATTATTTAATTAAGTCATTGATC-TAGTTGATTAAAATTATTTAATTAAGTC
1 CCTAATTGATTAAATTATTTAATTAAGTTATTGGGCTTAGTTAATTAAAATTATTTAATTAAATC
*
1163037 ATTGGG
66 ATTGAG
* * *
1163043 CCTAATTGATTAAAAATT-TTTAATTAAATTATTAGGCTTAGTTAATT-AAATTGTTTAATTAAA
1 CCTAATTGATT--AAATTATTTAATTAAGTTATTGGGCTTAGTTAATTAAAATTATTTAATTAAA
*
1163106 TTATTGAG
64 TCATTGAG
* **
1163114 CTTAATTGATTAAATTAAATAATTAAGTTAATTGGGCTT
1 CCTAATTGATTAAATTATTTAATTAAGTT-ATTGGGCTT
1163153 CTTAAAGACT
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
69 5 0.06
70 19 0.21
71 52 0.58
72 13 0.15
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (71 bp):
CCTAATTGATTAAATTATTTAATTAAGTTATTGGGCTTAGTTAATTAAAATTATTTAATTAAATC
ATTGAG
Found at i:1167418 original size:30 final size:30
Alignment explanation
Indices: 1167384--1167444 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1167374 TTCAATCAAA
* *
1167384 CCCTTATAATTTTATTTTGAGCCAAATAAG
1 CCCTTAAAATTTTATTTTGAACCAAATAAG
*
1167414 CCCTTAAAATTTTATTTTTAACCAAATAAG
1 CCCTTAAAATTTTATTTTGAACCAAATAAG
1167444 C
1 C
1167445 GTTTATGACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
CCCTTAAAATTTTATTTTGAACCAAATAAG
Found at i:1175736 original size:126 final size:125
Alignment explanation
Indices: 1175507--1175753 Score: 386
Period size: 126 Copynumber: 2.0 Consensus size: 125
1175497 ATGAGGTGTG
* * * *
1175507 CAAAGCCACCGCTTATAAGCCACCCAGGACTTCCCTACCTGCCTAATGTGGGAATTTTGGAAGTA
1 CAAAGCCACCGCTAATAAGCCACCCAGGACTCCCCTACCTGCCCAATGTGGGAATTTTGGAAGCA
*
1175572 CCTTGCCTACTTCCTTCCTGAAATGCTAGACGTGACATCCTCACCCACCCAATCCGGCGA
66 CCTTGCCAACTTCCTTCCTGAAATGCTAGACGTGACATCCTCACCCACCCAATCCGGCGA
* * *
1175632 CAAAGGCCACCGCTAATAAGCCGCTCAGGGCTCCCCTACCTGCCCAATGTGGGAATTTTGGAAGC
1 CAAA-GCCACCGCTAATAAGCCACCCAGGACTCCCCTACCTGCCCAATGTGGGAATTTTGGAAGC
* * *
1175697 ACCTTGCCAACTTCCTTCCTGAAATGCTAGATGTGACATCCTCACCCGCTCAATCCG
65 ACCTTGCCAACTTCCTTCCTGAAATGCTAGACGTGACATCCTCACCCACCCAATCCG
1175754 ATGACACTTT
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 4 0.04
126 106 0.96
ACGTcount: A:0.24, C:0.34, G:0.19, T:0.23
Consensus pattern (125 bp):
CAAAGCCACCGCTAATAAGCCACCCAGGACTCCCCTACCTGCCCAATGTGGGAATTTTGGAAGCA
CCTTGCCAACTTCCTTCCTGAAATGCTAGACGTGACATCCTCACCCACCCAATCCGGCGA
Found at i:1179473 original size:47 final size:47
Alignment explanation
Indices: 1179416--1179526 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
1179406 ATTTTGTATG
*
1179416 ATTTTACTTATTTGTTACATAAAA-TTATAAAAATGCATGATGTCA-TT
1 ATTTTACTTATTTGTTACATAAAATTTAT-AAAATGCATAATGT-AGTT
* **
1179463 ATTTTTCTTATTTGTTAGGTAAAATTTATAAAATGCATAATGTAGTT
1 ATTTTACTTATTTGTTACATAAAATTTATAAAATGCATAATGTAGTT
1179510 ATTTTACTTATTTGTTA
1 ATTTTACTTATTTGTTA
1179527 AACAAATGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.91
48 4 0.07
ACGTcount: A:0.34, C:0.06, G:0.10, T:0.50
Consensus pattern (47 bp):
ATTTTACTTATTTGTTACATAAAATTTATAAAATGCATAATGTAGTT
Found at i:1182696 original size:12 final size:12
Alignment explanation
Indices: 1182679--1182715 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1182669 AACTATTGCG
1182679 ATTGCATTGGAT
1 ATTGCATTGGAT
*
1182691 ATTGCATTGGCT
1 ATTGCATTGGAT
1182703 ATTGCATTGGAT
1 ATTGCATTGGAT
1182715 A
1 A
1182716 GCGGATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (12 bp):
ATTGCATTGGAT
Found at i:1183073 original size:3 final size:3
Alignment explanation
Indices: 1183067--1183120 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
1183057 TTGATGATGG
1183067 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1183115 TGTA TT
1 T-TA TT
1183121 TAGTTTCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1192877 original size:2 final size:2
Alignment explanation
Indices: 1192870--1192903 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1192860 GGGAAATTTT
1192870 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
1192904 AAGAACATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1193290 original size:2 final size:2
Alignment explanation
Indices: 1193283--1193317 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1193273 AAAAATCTTT
1193283 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 T
1193318 TAGGGGCGAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1197369 original size:32 final size:31
Alignment explanation
Indices: 1197329--1197416 Score: 99
Period size: 26 Copynumber: 3.2 Consensus size: 31
1197319 TTTGTTATTA
1197329 TCTATTATTTTTATTTTTCACTTTTGTGCTT
1 TCTATTATTTTTATTTTTCACTTTTGTGCTT
1197360 TC---TA--TTTATTTTTCACTTTTGTGCTT
1 TCTATTATTTTTATTTTTCACTTTTGTGCTT
1197386 TC---TA--TTTATTTTT-ACTTTTGTGCTT
1 TCTATTATTTTTATTTTTCACTTTTGTGCTT
1197411 TCTATT
1 TCTATT
1197417 TAACTTTGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
25 14 0.26
26 35 0.65
28 3 0.06
31 2 0.04
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (31 bp):
TCTATTATTTTTATTTTTCACTTTTGTGCTT
Found at i:1197403 original size:25 final size:26
Alignment explanation
Indices: 1197338--1197418 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
1197328 ATCTATTATT
1197338 TTTATTTTTCACTTTTGTGCTTTCTA
1 TTTATTTTTCACTTTTGTGCTTTCTA
1197364 TTTATTTTTCACTTTTGTGCTTTCTA
1 TTTATTTTTCACTTTTGTGCTTTCTA
1197390 TTTATTTTT-ACTTTTGTGCTTTCTA
1 TTTATTTTTCACTTTTGTGCTTTCTA
1197415 TTTA
1 TTTA
1197419 ACTTTGTAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
25 20 0.36
26 35 0.64
ACGTcount: A:0.12, C:0.14, G:0.07, T:0.67
Consensus pattern (26 bp):
TTTATTTTTCACTTTTGTGCTTTCTA
Found at i:1225922 original size:16 final size:17
Alignment explanation
Indices: 1225903--1225936 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1225893 CTTTTTAACT
1225903 ATTTAATAT-TTTTTTA
1 ATTTAATATCTTTTTTA
*
1225919 ATTTAATCTCTTTTTTA
1 ATTTAATATCTTTTTTA
1225936 A
1 A
1225937 AAATGCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTAATATCTTTTTTA
Found at i:1226741 original size:4 final size:4
Alignment explanation
Indices: 1226732--1226804 Score: 82
Period size: 4 Copynumber: 18.8 Consensus size: 4
1226722 CAGTGTACAT
* *
1226732 ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC AT-- ATAT ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1226776 TATTAC ATAC ATAC ATAC ATAC ATAC ATA
1 -A-TAC ATAC ATAC ATAC ATAC ATAC ATA
1226805 TATATATATA
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
2 4 0.06
4 53 0.85
5 2 0.03
6 3 0.05
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAC
Found at i:1226746 original size:14 final size:14
Alignment explanation
Indices: 1226736--1226820 Score: 95
Period size: 14 Copynumber: 6.2 Consensus size: 14
1226726 GTACATATAC
1226736 ATACATACATACAT
1 ATACATACATACAT
1226750 ATACATACATACAT
1 ATACATACATACAT
* *
1226764 ATATATATATAC-T
1 ATACATACATACAT
1226777 ATTACATACATAC--
1 A-TACATACATACAT
1226790 ATACATACATACAT
1 ATACATACATACAT
* * *
1226804 ATATATATATATAT
1 ATACATACATACAT
1226818 ATA
1 ATA
1226821 TATAAAAGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
12 11 0.18
13 3 0.05
14 47 0.77
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
ATACATACATACAT
Found at i:1226812 original size:46 final size:45
Alignment explanation
Indices: 1226733--1226822 Score: 135
Period size: 48 Copynumber: 1.9 Consensus size: 45
1226723 AGTGTACATA
1226733 TACATACATACATACATATACATACATACATATATATATATACTAT
1 TACATACATACATACATATACATA-ATACATATATATATATACTAT
*
1226779 TACATACATACATACATACATACATATATATATATATATATATA
1 TACATACATACATACAT--ATACATA-ATACATATATATATATA
1226823 TAAAAGCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
46 17 0.43
48 23 0.57
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (45 bp):
TACATACATACATACATATACATAATACATATATATATATACTAT
Found at i:1226813 original size:8 final size:8
Alignment explanation
Indices: 1226730--1226824 Score: 77
Period size: 8 Copynumber: 11.6 Consensus size: 8
1226720 AACAGTGTAC
1226730 ATATACAT
1 ATATACAT
*
1226738 ACATACAT
1 ATATACAT
1226746 ACATATACAT
1 --ATATACAT
*
1226756 ACATACAT
1 ATATACAT
1226764 ATAT--AT
1 ATATACAT
1226770 ATATACTATT
1 ATATAC-A-T
*
1226780 ACATACAT
1 ATATACAT
*
1226788 ACATACAT
1 ATATACAT
*
1226796 ACATACAT
1 ATATACAT
*
1226804 ATATATAT
1 ATATACAT
*
1226812 ATATATAT
1 ATATACAT
1226820 ATATA
1 ATATA
1226825 AAAGCCGTGC
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
6 6 0.08
8 53 0.72
9 2 0.03
10 13 0.18
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATACAT
Found at i:1226824 original size:12 final size:12
Alignment explanation
Indices: 1226732--1226816 Score: 73
Period size: 12 Copynumber: 6.9 Consensus size: 12
1226722 CAGTGTACAT
*
1226732 ATACATACATAC
1 ATACATATATAC
1226744 ATACATATACATAC
1 ATACATAT--ATAC
*
1226758 ATACATATATAT
1 ATACATATATAC
*
1226770 ATATACTAT-TAC
1 ATACA-TATATAC
*
1226782 ATACATACATAC
1 ATACATATATAC
* *
1226794 ATACATACATAT
1 ATACATATATAC
*
1226806 ATATATATATA
1 ATACATATATA
1226817 TATATATAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
11 2 0.03
12 43 0.72
13 3 0.05
14 12 0.20
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (12 bp):
ATACATATATAC
Found at i:1233237 original size:2 final size:2
Alignment explanation
Indices: 1233232--1233260 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1233222 ATCCTACATT
1233232 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 T
1233261 TCTAAAAGCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1234211 original size:22 final size:22
Alignment explanation
Indices: 1234168--1234212 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1234158 TGCGACACTT
* * * *
1234168 CTTCTTCAGTGTTGCGGTGCTG
1 CTTCTTCAGCGCTGCAGCGCTG
1234190 CTTCTTCAGCGCTGCAGCGCTG
1 CTTCTTCAGCGCTGCAGCGCTG
1234212 C
1 C
1234213 AGCGCTGAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.31, G:0.29, T:0.33
Consensus pattern (22 bp):
CTTCTTCAGCGCTGCAGCGCTG
Found at i:1237599 original size:44 final size:44
Alignment explanation
Indices: 1237536--1237621 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
1237526 GTTCCTGGGA
*
1237536 CATGGTCGAATGATAAATGGGAGAAGAATAAAAGTTGTGAAACG
1 CATGGCCGAATGATAAATGGGAGAAGAATAAAAGTTGTGAAACG
*
1237580 CATGGCCGAATGATAAATGGGAGAAGAATAAGAGTTGTGAAA
1 CATGGCCGAATGATAAATGGGAGAAGAATAAAAGTTGTGAAA
1237622 GTAGACAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (44 bp):
CATGGCCGAATGATAAATGGGAGAAGAATAAAAGTTGTGAAACG
Found at i:1241708 original size:17 final size:18
Alignment explanation
Indices: 1241679--1241713 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1241669 GAGATTGGTA
1241679 ATAACAGCTTTTTGGTTT
1 ATAACAGCTTTTTGGTTT
1241697 ATAACAGCTTTTTGGTT
1 ATAACAGCTTTTTGGTT
1241714 CTCACATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.49
Consensus pattern (18 bp):
ATAACAGCTTTTTGGTTT
Found at i:1245283 original size:26 final size:26
Alignment explanation
Indices: 1245242--1245320 Score: 128
Period size: 25 Copynumber: 3.2 Consensus size: 26
1245232 ATCTATTATT
1245242 TTTATTTTTCAC-TTTGTGCTTTCTA
1 TTTATTTTTCACTTTTGTGCTTTCTA
*
1245267 TTTGTTTTTCACTTTTGTGCTTTCTA
1 TTTATTTTTCACTTTTGTGCTTTCTA
1245293 TTTATTTTT-ACTTTTGTGCTTT-TA
1 TTTATTTTTCACTTTTGTGCTTTCTA
1245317 TTTA
1 TTTA
1245321 ACTTTGTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
24 6 0.12
25 24 0.47
26 21 0.41
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (26 bp):
TTTATTTTTCACTTTTGTGCTTTCTA
Found at i:1249841 original size:16 final size:17
Alignment explanation
Indices: 1249804--1249846 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1249794 TGGAGTAGCG
1249804 TTGTGGTGCTAGTTGCTT
1 TTGT-GTGCTAGTTGCTT
* *
1249822 TTGTTTGCTTGTTG-TT
1 TTGTGTGCTAGTTGCTT
1249838 TTGTGTGCT
1 TTGTGTGCT
1249847 GAAGTGGCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 8 0.36
18 4 0.18
ACGTcount: A:0.02, C:0.09, G:0.30, T:0.58
Consensus pattern (17 bp):
TTGTGTGCTAGTTGCTT
Found at i:1252453 original size:2 final size:2
Alignment explanation
Indices: 1252436--1252473 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1252426 TCATTTGAGA
* *
1252436 AT AT GT AT AT AC 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
1252474 GGGTTATGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1254215 original size:2 final size:2
Alignment explanation
Indices: 1254210--1254240 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1254200 TGTGTGTGTG
*
1254210 TA TA TA TA TA TA CA 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 T
1254241 TCATTGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1262333 original size:213 final size:212
Alignment explanation
Indices: 1261883--1262412 Score: 579
Period size: 213 Copynumber: 2.5 Consensus size: 212
1261873 ATCTAACATG
* * * * * * *
1261883 AACTCTTACAGATTTACGTCAATATTGTAACAATA-TTATTTCAA--TTACGAATTTTTACATTT
1 AACTCTTACACATTTACATCAATATTTTAATAATATTTATTTTAACCTTATGAAGTTTTACATTT
* * * * ** * * *
1261945 ATTCTTATGAATTTACGTTAAGATTTTTAAAAAATTACTTTTCGTTTTAAGTATTTTTATACTTA
66 A-TCTTTTAAATTTACGTTAAAATTTTTAAAAAATTAATTTTCACTATAAATATTTTTATACTCA
*
1262010 TTATTATACATTTACATTAATATTTATAAATAATTAATTTTCACTAAAAACATATTTATTTGTCT
130 TTATTATACATTTACATTAACATTTATAAATAATTAATTTTCACTAAAAACATATTTATTTGTCT
1262075 AACATGAATTGTTACACT
195 AACATGAATTGTTACACT
* * * * *
1262093 AACTTTTATACATTTACGTCAATATTTTAATTATATTTATTTTAACCTTATTAAGTTTTACATTT
1 AACTCTTACACATTTACATCAATATTTTAATAATATTTATTTTAACCTTATGAAGTTTTACATTT
* * *
1262158 ATGCTTTTAAATTTACGTCAAAATTTTTAAAAATTTAATTTTCACTATAAATATTTTTATTCTCA
66 AT-CTTTTAAATTTACGTTAAAATTTTTAAAAAATTAATTTTCACTATAAATATTTTTATACTCA
* * * * *
1262223 TTATTGTACATTTACATTAACATTTGTAAATAGTTAATTTTCACTAAAAATATGTTTACTTTGTC
130 TTATTATACATTTACATTAACATTTATAAATAATTAATTTTCACTAAAAACATATTTA-TTTGTC
*
1262288 TAATAT-AACTTGTTACGA-T
194 TAACATGAA-TTGTTAC-ACT
** * * * *
1262307 AACTCTTACACATTTA-ATTGATATTTTAATAATCTTTATTTTAACTTTATGAATTTTTACTTTT
1 AACTCTTACACATTTACATCAATATTTTAATAATATTTATTTTAACCTTATGAAGTTTTACATTT
* * **
1262371 AT-TTTTATATATTTACATTAAAATTCTTAAAAAGCTAATTTT
66 ATCTTTTA-A-ATTTACGTTAAAATTTTTAAAAAATTAATTTT
1262413 TATTATAAGT
Statistics
Matches: 266, Mismatches: 45, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
210 29 0.11
211 13 0.05
212 2 0.01
213 188 0.71
214 33 0.12
215 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (212 bp):
AACTCTTACACATTTACATCAATATTTTAATAATATTTATTTTAACCTTATGAAGTTTTACATTT
ATCTTTTAAATTTACGTTAAAATTTTTAAAAAATTAATTTTCACTATAAATATTTTTATACTCAT
TATTATACATTTACATTAACATTTATAAATAATTAATTTTCACTAAAAACATATTTATTTGTCTA
ACATGAATTGTTACACT
Found at i:1272653 original size:18 final size:18
Alignment explanation
Indices: 1272627--1272665 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1272617 AAAAGAGTTC
*
1272627 AATAAATAATTTATAAAT
1 AATAAATAATTCATAAAT
*
1272645 AATACATAATTCATAAAT
1 AATAAATAATTCATAAAT
1272663 AAT
1 AAT
1272666 TTTTTATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAAATAATTCATAAAT
Found at i:1273080 original size:12 final size:12
Alignment explanation
Indices: 1273060--1273099 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1273050 GAGAGTTTTA
1273060 AAAAT-AAAAA-
1 AAAATAAAAAAT
*
1273070 AAGATAAAAAAT
1 AAAATAAAAAAT
1273082 AAAATAAAAAAT
1 AAAATAAAAAAT
1273094 AAAATA
1 AAAATA
1273100 GAAAGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 17 0.65
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1273097 original size:17 final size:15
Alignment explanation
Indices: 1273059--1273117 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 15
1273049 AGAGAGTTTT
1273059 AAAAATAAAAAAAGATA
1 AAAAATAAAAAAA-A-A
1273076 AAAAATAAAATAAAAA
1 AAAAATAAAA-AAAAA
1273092 ATAAAATAGAAAGAAAAA
1 A-AAAATA-AAA-AAAAA
1273110 AAGAAATA
1 AA-AAATA
1273118 GTACCTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
16 2 0.05
17 18 0.49
18 17 0.46
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
AAAAATAAAAAAAAA
Found at i:1273118 original size:18 final size:18
Alignment explanation
Indices: 1273077--1273110 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1273067 AAAAAGATAA
*
1273077 AAAATA-AAATAAAAAAT
1 AAAATAGAAAGAAAAAAT
1273094 AAAATAGAAAGAAAAAA
1 AAAATAGAAAGAAAAAA
1273111 AGAAATAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAATAGAAAGAAAAAAT
Found at i:1274505 original size:13 final size:13
Alignment explanation
Indices: 1274489--1274517 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1274479 TTCTTTTAGT
1274489 ATATATACTTTAA
1 ATATATACTTTAA
1274502 ATATATACTTTAA
1 ATATATACTTTAA
1274515 ATA
1 ATA
1274518 CATAAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATACTTTAA
Found at i:1274506 original size:15 final size:14
Alignment explanation
Indices: 1274472--1274514 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1274462 AATTACTATT
*
1274472 ATATATATTCTTTTA
1 ATATATATAC-TTTA
*
1274487 GTATATATACTTTA
1 ATATATATACTTTA
1274501 A-ATATATACTTTA
1 ATATATATACTTTA
1274514 A
1 A
1274515 ATACATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.52
14 4 0.16
15 8 0.32
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATATATACTTTA
Found at i:1276507 original size:5 final size:5
Alignment explanation
Indices: 1276499--1276523 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1276489 TCTTTTTTTG
1276499 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
1276524 CATATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1285053 original size:23 final size:24
Alignment explanation
Indices: 1285009--1285053 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1284999 ATTGAAAAAG
*
1285009 TAAATATGAAAAATAACAATAATA
1 TAAATATGAAAAATAAAAATAATA
1285033 TAAATA-GAAAAA-AAAAGATAA
1 TAAATATGAAAAATAAAA-ATAA
1285054 AAACAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 3 0.16
23 10 0.53
24 6 0.32
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (24 bp):
TAAATATGAAAAATAAAAATAATA
Found at i:1309320 original size:47 final size:47
Alignment explanation
Indices: 1309251--1309341 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
1309241 CACAAAGAGA
1309251 AACACAACATAACTAAATATATCCCAAAATAATTCTTCTAAATTTGC
1 AACACAACATAACTAAATATATCCCAAAATAATTCTTCTAAATTTGC
* * *
1309298 AACACAACATAACTCAATATATCCTAACATAATTCTTCTAAATT
1 AACACAACATAACTAAATATATCCCAAAATAATTCTTCTAAATT
1309342 GCCACTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (47 bp):
AACACAACATAACTAAATATATCCCAAAATAATTCTTCTAAATTTGC
Found at i:1309941 original size:21 final size:21
Alignment explanation
Indices: 1309912--1309989 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
1309902 TGTTTTGGGT
*
1309912 AGGAAGTATTGATACTCATGA
1 AGGAAGTATCGATACTCATGA
* *
1309933 AGAAAGTATCGACAAC-CATGA
1 AGGAAGTATCGA-TACTCATGA
*
1309954 AGGAGGTATCGATACTCATGA
1 AGGAAGTATCGATACTCATGA
*
1309975 AGGAAGTATTGATAC
1 AGGAAGTATCGATAC
1309990 ATGGAAGGCA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 2 0.04
21 43 0.91
22 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.23
Consensus pattern (21 bp):
AGGAAGTATCGATACTCATGA
Found at i:1317399 original size:39 final size:39
Alignment explanation
Indices: 1317350--1317426 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
1317340 ATAACTCCTT
* *
1317350 TCACTTATTGTTAGTTTAATAAATCCA-TTTCACTAACTC
1 TCACTAATTGTTAGTCTAATAAA-CCATTTTCACTAACTC
* *
1317389 TCACTAATTGTTGGTCTAATAAACCATTTTCATTAACT
1 TCACTAATTGTTAGTCTAATAAACCATTTTCACTAACT
1317427 ATTGACTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 3 0.09
39 30 0.91
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.43
Consensus pattern (39 bp):
TCACTAATTGTTAGTCTAATAAACCATTTTCACTAACTC
Found at i:1317472 original size:52 final size:52
Alignment explanation
Indices: 1317392--1317492 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
1317382 CTAACTCTCA
* * * *
1317392 CTAATTGTTGGTCTAATAAACCATTTTCATTAACTATTGACTAATTTTTAAG
1 CTAATTGTTGGTCAAATAAACCACTTTCATCAACTATTGACTAAATTTTAAG
* *
1317444 CTAATTGTTGGTCAAATAAGTCC-CTTTCATCAACTGTTGACTAAATTTT
1 CTAATTGTTGGTCAAATAA-ACCACTTTCATCAACTATTGACTAAATTTT
1317493 GTTAATCAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 40 0.95
53 2 0.05
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (52 bp):
CTAATTGTTGGTCAAATAAACCACTTTCATCAACTATTGACTAAATTTTAAG
Found at i:1317770 original size:5 final size:6
Alignment explanation
Indices: 1317757--1317794 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
1317747 CTATTCTATC
*
1317757 TTTATT TTTATT TTTATT TTTATCT TTAATT TTTATT T
1 TTTATT TTTATT TTTATT TTTAT-T TTTATT TTTATT T
1317795 ATCAATTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:1317965 original size:12 final size:12
Alignment explanation
Indices: 1317939--1317981 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
1317929 TCATAAATTC
1317939 AGATAAAAAATTAA
1 AGAT-AAAAA-TAA
1317953 AGATAAAAATAA
1 AGATAAAAATAA
* *
1317965 AAATAAAGATAA
1 AGATAAAAATAA
1317977 AGATA
1 AGATA
1317982 GAATAGATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 17 0.65
13 5 0.19
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (12 bp):
AGATAAAAATAA
Found at i:1319011 original size:26 final size:26
Alignment explanation
Indices: 1318982--1319041 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
1318972 CATTTATAAG
1318982 AAATATAATTACTATTATATATA-TTA
1 AAATATAATTACTA-TATATATACTTA
** * *
1319008 AAATATTTTTAGTATATATATACTTT
1 AAATATAATTACTATATATATACTTA
1319034 AAATATAA
1 AAATATAA
1319042 ACATATTTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (26 bp):
AAATATAATTACTATATATATACTTA
Found at i:1324447 original size:19 final size:20
Alignment explanation
Indices: 1324423--1324461 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1324413 TTCTTTAACC
*
1324423 CCATTTTCTTCA-TTTTTTT
1 CCATTTACTTCACTTTTTTT
1324442 CCATTTACTTCACTTTTTTT
1 CCATTTACTTCACTTTTTTT
1324462 TTCCTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (20 bp):
CCATTTACTTCACTTTTTTT
Found at i:1337809 original size:15 final size:15
Alignment explanation
Indices: 1337789--1337828 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1337779 CTTTATAATG
1337789 TAATATAATTACAAA
1 TAATATAATTACAAA
*
1337804 TAATATGATTACAAA
1 TAATATAATTACAAA
*
1337819 TAATGTAATT
1 TAATATAATT
1337829 GTAGGAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (15 bp):
TAATATAATTACAAA
Found at i:1338016 original size:28 final size:28
Alignment explanation
Indices: 1337984--1338106 Score: 74
Period size: 29 Copynumber: 4.3 Consensus size: 28
1337974 ACAAGTTTAA
1337984 TATATTTTTAATTTTTATTATTAATTTT
1 TATATTTTTAATTTTTATTATTAATTTT
* * * * *
1338012 TATATAATATCATTTTT-TAAATATATTTT
1 TATAT-TTTTAATTTTTATTATTA-ATTTT
* *
1338041 TAATTATTTTTATTTTTTATTA-TAA-TAT
1 T-A-TATTTTTAATTTTTATTATTAATTTT
* *
1338069 TATATATTTT-ATTTTTATTTCTTAATATTA
1 TATAT-TTTTAATTTTTA-TTATTAAT-TTT
1338099 TATATTTT
1 TATATTTT
1338107 ATTTTATTTT
Statistics
Matches: 70, Mismatches: 15, Indels: 19
0.67 0.14 0.18
Matches are distributed among these distances:
26 9 0.13
27 7 0.10
28 15 0.21
29 18 0.26
30 16 0.23
31 5 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (28 bp):
TATATTTTTAATTTTTATTATTAATTTT
Found at i:1338081 original size:33 final size:32
Alignment explanation
Indices: 1338044--1338119 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 32
1338034 ATATTTTTAA
*
1338044 TTATTTTTATTTTTTATTATAATATTATATATT
1 TTATTTTTATTTTTTACT-TAATATTATATATT
1338077 TTATTTTTA---TTT-CTTAATATTATATATT
1 TTATTTTTATTTTTTACTTAATATTATATATT
1338105 TTA-TTTTATTTTTTA
1 TTATTTTTATTTTTTA
1338120 AAAATTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
27 5 0.13
28 17 0.45
29 1 0.03
30 6 0.16
33 9 0.24
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (32 bp):
TTATTTTTATTTTTTACTTAATATTATATATT
Done.