Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008310.1 Hibiscus syriacus cultivar Beakdansim tig00111000_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: 3887810
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 15
Found at i:3577516 original size:18 final size:20
Alignment explanation
Indices: 3577478--3577516 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3577468 ATATTTTAAT
3577478 TTTTTAATAATAAAAATATA
1 TTTTTAATAATAAAAATATA
*
3577498 TTTTTAA-AA-AAATATATA
1 TTTTTAATAATAAAAATATA
3577516 T
1 T
3577517 ATACTCCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTTAATAATAAAAATATA
Found at i:3579088 original size:37 final size:36
Alignment explanation
Indices: 3579005--3579107 Score: 120
Period size: 37 Copynumber: 2.9 Consensus size: 36
3578995 TAATAGTTTC
* * *
3579005 ATAATATTATTATTTTAATAATTATATACT-TAATA
1 ATAATATTTTTATTTTAATAAATATATAATATAATA
* *
3579040 ATATATTATTTTTATTTTAATAAATATTTAATATAATT
1 ATA-A-TATTTTTATTTTAATAAATATATAATATAATA
*
3579078 ATAATAATTTTATTTTAATAAA-ATATAATA
1 ATAATATTTTTATTTTAATAAATATATAATA
3579108 ATACAAACAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 10 0.17
36 18 0.31
37 23 0.40
38 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
ATAATATTTTTATTTTAATAAATATATAATATAATA
Found at i:3580842 original size:41 final size:41
Alignment explanation
Indices: 3580785--3580866 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3580775 ACCAACGGTG
3580785 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
3580826 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
1 CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
3580867 ATACTCACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (41 bp):
CTGAACATTGATACACGAATGTACCAAAGCTGAACTGATAA
Found at i:3581020 original size:18 final size:18
Alignment explanation
Indices: 3580997--3581049 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
3580987 ATTTGTAATT
3580997 ATCTGATAACTATAAATC
1 ATCTGATAACTATAAATC
3581015 ATCTGATAACTATAAATC
1 ATCTGATAACTATAAATC
* *
3581033 ATATGATAACTGTAAAT
1 ATCTGATAACTATAAAT
3581050 ATTTAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (18 bp):
ATCTGATAACTATAAATC
Found at i:3583924 original size:75 final size:75
Alignment explanation
Indices: 3583824--3584000 Score: 239
Period size: 75 Copynumber: 2.4 Consensus size: 75
3583814 CATTGTACAA
* * *
3583824 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAACA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACA
** *
3583888 AAACTGTTTAG
65 AAACCATTCAG
* * * *
3583899 GGGGGAATCGGTTCCTCCTATGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAGCCA
1 GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAA
3583964 AACCATTCAG
66 AACCATTCAG
*
3583974 GGGGGAATCAGTTCCTCCTATGGGGGG
1 GGGGGAATCGGTTCCTCCTATGGGGGG
3584001 GGGAATCGGT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
75 88 0.99
76 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (75 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAACAA
AACCATTCAG
Found at i:3592615 original size:74 final size:75
Alignment explanation
Indices: 3592446--3592647 Score: 255
Period size: 75 Copynumber: 2.7 Consensus size: 75
3592436 CCGTTGTACA
* * * * *
3592446 AGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAAC
1 AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
** *
3592510 AAAACTGTTT
66 AAAACCATTC
*
3592520 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
* *
3592584 CCAAGCCATTC
65 CAAAACCATTC
* *
3592595 AGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTG
1 AGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTG
3592648 TAATTTTTGG
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
74 22 0.20
75 61 0.55
76 28 0.25
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (75 bp):
AGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAAC
AAAACCATTC
Found at i:3593638 original size:30 final size:29
Alignment explanation
Indices: 3593577--3593665 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 29
3593567 TAAAATCTAT
* * * *
3593577 AACTTTTCAAAATTACATTTTTGGTCCCTA
1 AACTTTTCAAAATT-TATATTTAGTCACTA
3593607 AACTTTTCAAAATTTATACTTTAGTCACTA
1 AACTTTTCAAAATTTATA-TTTAGTCACTA
3593637 AAC-TTTCAAAAAATTTAT-TTTAGTCACTA
1 AACTTTTC--AAAATTTATATTTAGTCACTA
3593666 GTCAAAATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
29 17 0.33
30 26 0.50
31 9 0.17
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.43
Consensus pattern (29 bp):
AACTTTTCAAAATTTATATTTAGTCACTA
Found at i:3594234 original size:22 final size:22
Alignment explanation
Indices: 3594204--3594254 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3594194 TTCGTCCATA
*
3594204 TATATATATGTATGCATGTATG
1 TATATATATATATGCATGTATG
* *
3594226 TGTATATATATATGTATGTATG
1 TATATATATATATGCATGTATG
3594248 TATATAT
1 TATATAT
3594255 TTAAAGCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TATATATATATATGCATGTATG
Found at i:3599816 original size:19 final size:20
Alignment explanation
Indices: 3599789--3599829 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3599779 TTGTTAAAAT
*
3599789 AAAATATTT-ATTTTATCAC
1 AAAAAATTTAATTTTATCAC
*
3599808 AAAAAATTTAATTTTGTCAC
1 AAAAAATTTAATTTTATCAC
3599828 AA
1 AA
3599830 TTAACTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAAATTTAATTTTATCAC
Found at i:3600506 original size:196 final size:197
Alignment explanation
Indices: 3599943--3600558 Score: 723
Period size: 197 Copynumber: 3.1 Consensus size: 197
3599933 TTATAATTTT
* * *
3599943 TTGTGACTAAATAAATTTATTACAATTCTTTATTGTGAAAGAATATTATTTATCATAATTTTTTA
1 TTGTGACTAAATAAATTTGTTACAATT-TTTATTGTGAAAGAATAATATTTGTCATAATTTTTTA
* * *
3600008 TATTGAGAAATTAACATTTGTTATAAATT-TTGATTATGCCTAAAGAAATTTGTCAAAAGTTTTT
65 TATT-AGAAATTAATATTTGTTATAAATTGTT-ATTATGACTAAATAAATTTGTCAAAAGTTTTT
* * * * *
3600072 ATTTCGA-GAAAATATTGTGACGAAATAATTTTGACATAATTTTTTACTTTGACTAATTTTAATA
128 ATTTTGATAAAAATATTGTGACGAAATAAATTTGACATAATTTTTTATTTTGACTAAATTTAATA
3600136 -TGTTA
193 TTG-TA
* * * * *** *
3600141 CTGTGAATAAATAAATTTGTTATAATTTGTTATTATGAAAGAA-AATGCATGTCCTAATTTTTTA
1 TTGTGACTAAATAAATTTGTTACAATTT-TTATTGTGAAAGAATAATATTTGTCATAATTTTTTA
* *
3600205 TATTTAGAAATTATTATTTGTTATAAATGGTTATTATGACTAAATAAATTTGTCAAAAGTTTTTA
65 TA-TTAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTTTTA
* *
3600270 TTTT--TAGAAAATATTATGACGAAATAAATTTGACATAATTTTTTATTTTAACTAAATTTAATA
129 TTTTGATA-AAAATATTGTGACGAAATAAATTTGACATAATTTTTTATTTTGACTAAATTTAATA
3600333 TTGTA
193 TTGTA
*
3600338 TTGTGACT-AATAAATTTGTTACAATTTATTATTGTGAAA-AATAATATTTGTTATAAATTTTTT
1 TTGTGACTAAATAAATTTGTTACAATTT-TTATTGTGAAAGAATAATATTTGTCAT-AATTTTTT
* * * * * **
3600401 ATA-TAGAAATTAATATTTGTTATTAATTGTTATTTTGGCTAAATAATTTTTTCATCA-TTTATT
64 ATATTAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTT-TT
* * *
3600464 ATTTTGATAAAAATATTGTGACTAAATAAATTTGATATAATTTCTTATTTTGACTAAATTTAATA
128 ATTTTGATAAAAATATTGTGACGAAATAAATTTGACATAATTTTTTATTTTGACTAAATTTAATA
3600529 TAT-TA
193 T-TGTA
* **
3600534 TTATGTTTAAATAAATTTGTTACAA
1 TTGTGACTAAATAAATTTGTTACAA
3600559 ATAATTGTTA
Statistics
Matches: 355, Mismatches: 50, Indels: 27
0.82 0.12 0.06
Matches are distributed among these distances:
194 3 0.01
195 54 0.15
196 94 0.26
197 162 0.46
198 42 0.12
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (197 bp):
TTGTGACTAAATAAATTTGTTACAATTTTTATTGTGAAAGAATAATATTTGTCATAATTTTTTAT
ATTAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTTTTATT
TTGATAAAAATATTGTGACGAAATAAATTTGACATAATTTTTTATTTTGACTAAATTTAATATTG
TA
Found at i:3600717 original size:133 final size:132
Alignment explanation
Indices: 3600473--3600740 Score: 360
Period size: 133 Copynumber: 2.0 Consensus size: 132
3600463 TATTTTGATA
* *
3600473 AAAATATTGTGACTAAATAAATTTGATATAATTTCTTATTTTGACTAAATTTAATATATTATTAT
1 AAAATAGTGTGACTAAATAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTAT
** ** *
3600538 GTTTAAATAAATTTGTTACAAATAATTGTTATTATGACTATATATTTGTCATAATTAGTTATTTT
66 GAATAAATAAATTTGTTACAAATAATTGTTATTATGAAAATATATTTGTCAT-ATTAGTTATATT
3600603 AAG
130 AAG
* * *
3600606 AAAATAGTGTGACTAAATAAATTTGACATAATTTCTTATTTTGATTAAATTTAATATGTTGTTAT
1 AAAATAGTGTGACTAAATAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTAT
* * * **
3600671 GAATAAATAAATTTGTTAC-AAT-TTTTTTATTATGAAAAATATTATTTTTCATATTTTTTATAT
66 GAATAAATAAATTTGTTACAAATAATTGTTATTATG-AAAATA-TATTTGTCATATTAGTTATAT
3600734 TAAG
129 TAAG
3600738 AAA
1 AAA
3600741 TTAATATTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
131 10 0.08
132 22 0.19
133 86 0.73
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (132 bp):
AAAATAGTGTGACTAAATAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATATTATTAT
GAATAAATAAATTTGTTACAAATAATTGTTATTATGAAAATATATTTGTCATATTAGTTATATTA
AG
Found at i:3600729 original size:33 final size:32
Alignment explanation
Indices: 3600675--3600755 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
3600665 TGTTATGAAT
*
3600675 AAATAA-ATTTGTTACA-ATTTTTT-TATTATGAA
1 AAATAATATTT-TT-CATATTTTTTATATTAAG-A
*
3600707 AAATATTATTTTTCATATTTTTTATATTAAGA
1 AAATAATATTTTTCATATTTTTTATATTAAGA
*
3600739 AATTAATATTTTTCATA
1 AAATAATATTTTTCATA
3600756 AATCCTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
31 2 0.05
32 30 0.71
33 10 0.24
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (32 bp):
AAATAATATTTTTCATATTTTTTATATTAAGA
Found at i:3608624 original size:13 final size:13
Alignment explanation
Indices: 3608606--3608635 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3608596 CTGCAGTAAG
3608606 GCGCGCCCCTGCA
1 GCGCGCCCCTGCA
3608619 GCGCGCCCCTGCA
1 GCGCGCCCCTGCA
3608632 GCGC
1 GCGC
3608636 TCTTTACGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.07, C:0.53, G:0.33, T:0.07
Consensus pattern (13 bp):
GCGCGCCCCTGCA
Found at i:3608951 original size:18 final size:19
Alignment explanation
Indices: 3608911--3608951 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
3608901 TAATAATTTG
*
3608911 TTTTCAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
*
3608930 -TTTAAATTTTTTTAA-TA
1 TTTTAAATTTATTTAAGTA
3608947 TTTTA
1 TTTTA
3608952 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:3608951 original size:26 final size:26
Alignment explanation
Indices: 3608922--3608973 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
3608912 TTTCAATTTA
*
3608922 TTTAAGTATTTAAATTTTTTTA-ATAT
1 TTTAAGTAATT-AATTTTTTTACATAT
**
3608948 TTTATTTAATTAATTTTTTTACATAT
1 TTTAAGTAATTAATTTTTTTACATAT
3608974 ATAAAATGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTAAGTAATTAATTTTTTTACATAT
Found at i:3612276 original size:23 final size:24
Alignment explanation
Indices: 3612239--3612288 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
3612229 ATTGAATGAA
*
3612239 AAAAATGAATAAAAATTGAAAATT
1 AAAAAGGAATAAAAATTGAAAATT
*
3612263 AAAAAGGAAT-AAAATTTAAAATT
1 AAAAAGGAATAAAAATTGAAAATT
3612286 AAA
1 AAA
3612289 CATAGGATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (24 bp):
AAAAAGGAATAAAAATTGAAAATT
Found at i:3614053 original size:29 final size:30
Alignment explanation
Indices: 3614013--3614086 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
3614003 CAAATTTTAG
*
3614013 TTAGTGATCAAAATGTAAAGTTT-GAAAGT
1 TTAGTGACCAAAATGTAAAGTTTAGAAAGT
* *
3614042 TTAGTGACCAAAGTATAAAGTTTAGAAAGT
1 TTAGTGACCAAAATGTAAAGTTTAGAAAGT
* *
3614072 TTAGGGACTAAAATG
1 TTAGTGACCAAAATG
3614087 GTAATTTCCT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.31
Consensus pattern (30 bp):
TTAGTGACCAAAATGTAAAGTTTAGAAAGT
Found at i:3615924 original size:12 final size:12
Alignment explanation
Indices: 3615907--3615931 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3615897 AGTTATGGAT
3615907 AGTAAGTTTAGA
1 AGTAAGTTTAGA
3615919 AGTAAGTTTAGA
1 AGTAAGTTTAGA
3615931 A
1 A
3615932 AATCACCATA
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:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
AGTAAGTTTAGA
Found at i:3616775 original size:30 final size:30
Alignment explanation
Indices: 3616696--3616779 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
3616686 ATTAGTACTA
* * * *
3616696 TAGTGTGCAAGGACACTTAATACAACACTG
1 TAGTGTGTAAGGACACTCAGTGCAACACTG
3616726 TAGTGTGTAAGGACACTCAGTGCAACACTG
1 TAGTGTGTAAGGACACTCAGTGCAACACTG
*
3616756 TGGTGTGTAAGGACACTCAGTGCA
1 TAGTGTGTAAGGACACTCAGTGCA
3616780 TATGGTAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (30 bp):
TAGTGTGTAAGGACACTCAGTGCAACACTG
Found at i:3618337 original size:30 final size:30
Alignment explanation
Indices: 3618278--3618339 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
3618268 TACTAGGTTG
**
3618278 TCAAACATTCTTAGTAAAGGTGGTGGATAT
1 TCAAACATTCTTAGTAAAGGTGGAAGATAT
* *
3618308 TCAAACATTCTTAGTTAAGTTGGAAGATAT
1 TCAAACATTCTTAGTAAAGGTGGAAGATAT
3618338 TC
1 TC
3618340 CAACTGTTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.35
Consensus pattern (30 bp):
TCAAACATTCTTAGTAAAGGTGGAAGATAT
Found at i:3619456 original size:21 final size:21
Alignment explanation
Indices: 3619432--3619475 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3619422 ATGTTTAATG
3619432 AAAAAGATACCAATTGTTACC
1 AAAAAGATACCAATTGTTACC
*
3619453 AAAAAGATATCAATTGTTACC
1 AAAAAGATACCAATTGTTACC
3619474 AA
1 AA
3619476 TTGTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTACC
Found at i:3619534 original size:20 final size:21
Alignment explanation
Indices: 3619509--3619556 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
3619499 TTAAGCTCCC
*
3619509 CTTTTTCATTAAGAAATT-AA
1 CTTTTTCATTAAAAAATTGAA
3619529 CTTTTTCATTAAAAAATTGAA
1 CTTTTTCATTAAAAAATTGAA
3619550 -TTTTTCA
1 CTTTTTCA
3619557 AACCAAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (21 bp):
CTTTTTCATTAAAAAATTGAA
Found at i:3620669 original size:19 final size:20
Alignment explanation
Indices: 3620626--3620673 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3620616 CTAAATCCTT
*
3620626 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
3620646 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
3620665 TTTTCAAAA
1 TTTTCAAAA
3620674 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:3621841 original size:20 final size:22
Alignment explanation
Indices: 3621816--3621855 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3621806 TGTTGTATAT
3621816 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
3621836 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
3621856 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:3621973 original size:17 final size:19
Alignment explanation
Indices: 3621947--3621996 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
3621937 GCAACCTTCG
*
3621947 TGCATGGATGCACA-A-CA
1 TGCATCGATGCACACAGCA
*
3621964 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACA-CAGCA
3621984 TGCATCGATGCAC
1 TGCATCGATGCAC
3621997 TAAGTGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 13 0.46
19 1 0.04
20 14 0.50
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (19 bp):
TGCATCGATGCACACAGCA
Found at i:3627172 original size:45 final size:45
Alignment explanation
Indices: 3627121--3627324 Score: 320
Period size: 45 Copynumber: 4.5 Consensus size: 45
3627111 ATAACAACCA
* *
3627121 TTCATGCTTATAATGCAACCATATGCATTTCAATTATGGCATCCT
1 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
**
3627166 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATTAT
1 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
* * *
3627211 TTCATGCCGATAATACACCCATATGCATTTAAATTATGGCATCCT
1 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
*
3627256 TTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCT
1 TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
3627301 TTCATG-TCGATAATGCACCCATAT
1 TTCATGCT-GATAATGCACCCATAT
3627325 AAATTTATTA
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 146 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (45 bp):
TTCATGCTGATAATGCACCCATATGCATTTCAATTATGGCATCCT
Found at i:3627955 original size:17 final size:17
Alignment explanation
Indices: 3627933--3627976 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
3627923 TCCCCTTGTT
3627933 AGTATCGATACCCCATC
1 AGTATCGATACCCCATC
3627950 AGTATCGATACCCCATC
1 AGTATCGATACCCCATC
3627967 AGTATCGATA
1 AGTATCGATA
3627977 TTGTTCGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.25
Consensus pattern (17 bp):
AGTATCGATACCCCATC
Found at i:3637630 original size:24 final size:23
Alignment explanation
Indices: 3637580--3637657 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
3637570 GCTTCAACTT
* *
3637580 TTTGGATTGTTTGATTTTGTGAC
1 TTTGGATTGTTTGATGTTGTGAA
3637603 TTTGGATTTGTTTGGATGTT-TGAA
1 TTTGGA-TTGTTT-GATGTTGTGAA
*
3637627 TTTGTGGATTGATTGAT-TT-TGAA
1 -TT-TGGATTGTTTGATGTTGTGAA
3637650 TTT-GATTG
1 TTTGGATTG
3637658 GATTTATGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
20 5 0.10
21 1 0.02
22 2 0.04
23 12 0.25
24 12 0.25
25 12 0.25
26 4 0.08
ACGTcount: A:0.17, C:0.01, G:0.27, T:0.55
Consensus pattern (23 bp):
TTTGGATTGTTTGATGTTGTGAA
Found at i:3643619 original size:45 final size:45
Alignment explanation
Indices: 3643550--3643810 Score: 405
Period size: 45 Copynumber: 5.8 Consensus size: 45
3643540 TCATTAATAA
* ** *
3643550 CATCCATTCATGCATATAATGCACCCATATGTATTTCAATTATGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
* *
3643595 CATCCTTTAATGCCGATAACGCACCCATATGCATTTCAATTATGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
* *
3643640 CATCCTTTCATGCCGATAATGCATCCATATGAATTTCAATTATGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
* * *
3643685 TATCCTTTCATGCCAATAATGCACCCATATCCATTTCAATTATGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
3643730 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
* *
3643775 CATCTTTTCATACCGATAATGCACCCATATGCATTT
1 CATCCTTTCATGCCGATAATGCACCCATATGCATTT
3643811 ATTATTTTTA
Statistics
Matches: 196, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 196 1.00
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.34
Consensus pattern (45 bp):
CATCCTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGG
Found at i:3649910 original size:34 final size:37
Alignment explanation
Indices: 3649866--3649967 Score: 158
Period size: 34 Copynumber: 2.8 Consensus size: 37
3649856 TTTCGTCCTA
3649866 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
*
3649901 -TAGGATTCAAACTCCTTAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
3649936 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
3649968 GTTCTACTAA
Statistics
Matches: 60, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
35 3 0.05
37 27 0.45
38 1 0.02
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:3649951 original size:37 final size:35
Alignment explanation
Indices: 3649866--3650001 Score: 159
Period size: 37 Copynumber: 3.8 Consensus size: 35
3649856 TTTCGTCCTA
3649866 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
3649901 -TAGGATTCAAACTCCTTAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
3649936 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
3649973 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
3650002 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 3 0.03
36 2 0.02
37 52 0.60
38 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3650586 original size:16 final size:15
Alignment explanation
Indices: 3650565--3650598 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
3650555 TATTATTATC
3650565 ATTATATGTATATTTT
1 ATTATAT-TATATTTT
*
3650581 ATTATATTTTATTTT
1 ATTATATTATATTTT
3650596 ATT
1 ATT
3650599 TTTACTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
ATTATATTATATTTT
Found at i:3650588 original size:10 final size:10
Alignment explanation
Indices: 3650557--3650600 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
3650547 TTTGCTACTA
3650557 TTATTATCATT
1 TTATTAT-ATT
*
3650568 ATATGTATATT
1 TTAT-TATATT
3650579 TTATTATATT
1 TTATTATATT
*
3650589 TTATTTTATT
1 TTATTATATT
3650599 TT
1 TT
3650601 TACTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 17 0.59
11 9 0.31
12 3 0.10
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (10 bp):
TTATTATATT
Found at i:3650722 original size:21 final size:21
Alignment explanation
Indices: 3650698--3650738 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3650688 ATATTACATT
*
3650698 ATTATTATTTTCCTTTATTAA
1 ATTATTATTTTCCGTTATTAA
* *
3650719 ATTATTTTTTTTCGTTATTA
1 ATTATTATTTTCCGTTATTA
3650739 TATTTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTATTATTTTCCGTTATTAA
Found at i:3655548 original size:16 final size:16
Alignment explanation
Indices: 3655522--3655573 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3655512 AGATCCAATC
3655522 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
3655537 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
* *
3655554 AA-AAAAAACAAAGAAA
1 AAGAACAAA-AAAGCAA
3655570 AAGA
1 AAGA
3655574 GAAACAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 8 0.26
16 18 0.58
17 5 0.16
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:3656670 original size:18 final size:18
Alignment explanation
Indices: 3656647--3656682 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3656637 TCAACATCAA
* *
3656647 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
3656665 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
3656683 GGATTCATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATCTTTGG
Found at i:3657150 original size:36 final size:35
Alignment explanation
Indices: 3657110--3657405 Score: 169
Period size: 36 Copynumber: 8.4 Consensus size: 35
3657100 ACTCATGATT
* * *
3657110 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAA-ATTTGTCTCTCTTGAGACA
* * * *
3657146 GTTT-TCACTAGAAGAATTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAATTTGTCTCTCTTGAGACA
* * *
3657181 GTTTCCCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAACAAA-TTTGTCTCTCTTGAGACA
* * *
3657217 GTTTCTCTTGAAACAAATTTCGTCTATCTTGAGATA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* * * * *
3657253 GTTTCCCTTGAAACAAA-----ATAT-TTGA-ATA
1 GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
* *
3657281 TGTTT-TCTTTGAAACAAATTTCGTCTCCCTTGAGACA
1 -GTTTCTC-TTAAAACAAATTT-GTCTCTCTTGAGACA
* ** *
3657318 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTAAAAC-AA-ATTTGTCTCTCTTGAGACA
* * * *
3657355 GTTTCTCTTGAATCAATTTTCGTCTATCTTGAGACA
1 GTTTCTCTTAAAACAAATTT-GTCTCTCTTGAGACA
* *
3657391 GTTACTCTTGAAACA
1 GTTTCTCTTAAAACA
3657406 CAAAATCTTC
Statistics
Matches: 209, Mismatches: 33, Indels: 36
0.75 0.12 0.13
Matches are distributed among these distances:
28 4 0.02
29 18 0.09
30 3 0.01
35 35 0.17
36 116 0.56
37 30 0.14
38 3 0.01
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (35 bp):
GTTTCTCTTAAAACAAATTTGTCTCTCTTGAGACA
Found at i:3658418 original size:105 final size:104
Alignment explanation
Indices: 3658075--3658733 Score: 870
Period size: 105 Copynumber: 6.3 Consensus size: 104
3658065 GCCATCCGCG
* * * * *
3658075 ATTTCAACTCCACGACGGAGGATATCGTGGCAC-TCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTTC-AGACAACGCAAGTTCAACTTCACGACGA
* * *
3658139 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACCGCTGCTTGTCAA-AAACAACTTCCCAA-TTCAGAGCCA
* *
3658184 ATTTCATCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
3658249 ACTGCTGCTTGTC---AACAACTTCTCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAAAAACAACTTCCCAA-TTCAGAGCCA
3658286 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3658351 ACCGCTGCTTGTCAATAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAAAAACAACTTCCCAAT-TCAGAGCCA
* *
3658391 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
3658456 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAAAAACAACTTCCCAAT-TCAGAGCCA
* *
3658496 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
3658561 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTCA
66 ACCGCTGCTTGTCAAAAACAACTTCCCAATTCAGAGCCA
* *
3658596 ATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
3658660 GACGGCTGGTTGTCAACAAACAA-TATCCCAGTTCCAGAGCCA
65 GACCGCTGCTTGTCAA-AAACAACT-TCCCAATT-CAGAGCCA
* *
3658702 ATTTCAACTTCACGACGTAGGATATTGGACTT
1 ATTTCAACTTCACAACGAAGGATATTGGACTT
3658734 GGAACAATGC
Statistics
Matches: 505, Mismatches: 32, Indels: 28
0.89 0.06 0.05
Matches are distributed among these distances:
99 1 0.00
100 79 0.16
101 4 0.01
102 103 0.20
103 3 0.01
104 4 0.01
105 208 0.41
106 77 0.15
107 5 0.01
109 21 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAAAAACAACTTCCCAATTCAGAGCCA
Found at i:3659324 original size:34 final size:37
Alignment explanation
Indices: 3659280--3659381 Score: 167
Period size: 34 Copynumber: 2.8 Consensus size: 37
3659270 TTTCGTCCTA
3659280 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
3659315 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
3659350 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
3659382 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGACATTTT
Found at i:3659365 original size:37 final size:35
Alignment explanation
Indices: 3659280--3659415 Score: 168
Period size: 37 Copynumber: 3.8 Consensus size: 35
3659270 TTTCGTCCTA
3659280 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
3659315 -TAGGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGA-A-TTT
*
3659350 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-T
* * * *
3659387 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
3659416 CCACAAGCAC
Statistics
Matches: 89, Mismatches: 6, Indels: 10
0.85 0.06 0.10
Matches are distributed among these distances:
33 1 0.01
34 29 0.33
35 3 0.03
36 2 0.02
37 53 0.60
38 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:3660009 original size:17 final size:18
Alignment explanation
Indices: 3659989--3660022 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3659979 TATTATTATC
3659989 ATTATA-TGTATATTTTT
1 ATTATATTGTATATTTTT
*
3660006 ATTATATTTTATATTTT
1 ATTATATTGTATATTTT
3660023 ATTTTTACTT
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTATATTGTATATTTTT
Found at i:3660137 original size:16 final size:16
Alignment explanation
Indices: 3660116--3660149 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3660106 CATGTATTTA
3660116 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
3660132 TATTATTTTACTTTAT
1 TATTATATTACATTAT
3660148 TA
1 TA
3660150 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:3660154 original size:21 final size:22
Alignment explanation
Indices: 3660130--3660180 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3660120 ATATTACATT
*
3660130 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
3660151 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
3660173 TTTATTAT
1 ATTATTAT
3660181 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:3664658 original size:23 final size:23
Alignment explanation
Indices: 3664628--3664674 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
3664618 TAGTTGTTGT
3664628 TGTTTTTTTTTTTCC-TTTCTCTG
1 TGTTTTTTTTTTTCCGTTT-TCTG
3664651 TGTTTTTTTTTTTCCGTTTTCTG
1 TGTTTTTTTTTTTCCGTTTTCTG
3664674 T
1 T
3664675 TTCAGTCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.00, C:0.15, G:0.11, T:0.74
Consensus pattern (23 bp):
TGTTTTTTTTTTTCCGTTTTCTG
Found at i:3665170 original size:3 final size:3
Alignment explanation
Indices: 3665162--3665250 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
3665152 TTAATATATT
*
3665162 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3665210 TAG TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3665251 TGGATAAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3665977 original size:113 final size:113
Alignment explanation
Indices: 3665567--3666348 Score: 1354
Period size: 113 Copynumber: 6.9 Consensus size: 113
3665557 AGAGTCATTC
* * *
3665567 AAAAGGTTGAATAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
3665632 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3665679 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAATTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCT
* * * *
3665744 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAGGT
63 CATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3665795 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3665859 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3665907 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
3665972 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3666020 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
3666085 TATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3666133 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
3666198 TATGAACTTTTTCTGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
3666246 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
3666311 TATGAACTTTTTCTGGAAAAAATGATCCATCAAATGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT
3666349 AGATTTGAAT
Statistics
Matches: 641, Mismatches: 22, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
111 2 0.00
112 114 0.18
113 421 0.66
114 1 0.00
115 58 0.09
116 43 0.07
117 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:3667515 original size:84 final size:84
Alignment explanation
Indices: 3666981--3667799 Score: 1589
Period size: 83 Copynumber: 9.8 Consensus size: 84
3666971 ACTGAATCAA
3666981 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667045 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667064 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-CAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667128 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667147 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667211 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667230 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667294 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667313 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTC-ATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667377 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667396 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667461 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667480 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667545 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667564 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667629 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667648 ATCAGATAACTC-AAGAACACTTCCA-AAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667711 ATTGGTTCTGCCAAACCAG
66 ATTGGTTCTGCCAAACCAG
3667730 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
1 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
3667795 ATTGG
66 ATTGG
3667800 ACTAAGATAT
Statistics
Matches: 730, Mismatches: 0, Indels: 11
0.99 0.00 0.01
Matches are distributed among these distances:
82 70 0.10
83 392 0.54
84 268 0.37
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (84 bp):
ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCAATG
ATTGGTTCTGCCAAACCAG
Found at i:3668931 original size:9 final size:9
Alignment explanation
Indices: 3668919--3668993 Score: 52
Period size: 9 Copynumber: 8.6 Consensus size: 9
3668909 TTGACCCCCT
3668919 TTCTTTTTC
1 TTCTTTTTC
*
3668928 TTCTTTTTT
1 TTCTTTTTC
*
3668937 TTCATTTTC
1 TTCTTTTTC
*
3668946 TATTTTTTTC
1 T-TCTTTTTC
*
3668956 TT-TTCTTTT
1 TTCTT-TTTC
3668965 TTC-TTTTC
1 TTCTTTTTC
3668973 TT-TCTTTTC
1 TTCT-TTTTC
3668982 TT-TTTTT-
1 TTCTTTTTC
3668989 TTCTT
1 TTCTT
3668994 CAAGCATAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
7 2 0.04
8 13 0.25
9 31 0.58
10 7 0.13
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:3668951 original size:15 final size:13
Alignment explanation
Indices: 3668922--3668990 Score: 72
Period size: 12 Copynumber: 5.2 Consensus size: 13
3668912 ACCCCCTTTC
*
3668922 TTTTTCTTCT-TT
1 TTTTTCTTTTCTT
3668934 TTTTTCATTTTCTATT
1 TTTTTC-TTTTC--TT
3668950 TTTTTCTTTTC-T
1 TTTTTCTTTTCTT
3668962 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
3668975 TCTTTTCTTTT-TT
1 T-TTTTCTTTTCTT
3668988 TTT
1 TTT
3668991 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
12 20 0.40
13 8 0.16
14 9 0.18
15 5 0.10
16 8 0.16
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:3668965 original size:21 final size:20
Alignment explanation
Indices: 3668918--3668990 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
3668908 CTTGACCCCC
*
3668918 TTTCTTTTTC-TTCTTTT-T
1 TTTCTTTTTCTTTTTTTTCT
*
3668936 TTTCATTTTCTATTTTTTTCT
1 TTTCTTTTTCT-TTTTTTTCT
*
3668957 TTTCTTTTTTCTTTTCTTTCT
1 TTTC-TTTTTCTTTTTTTTCT
3668978 TTTCTTTTT-TTTT
1 TTTCTTTTTCTTTT
3668991 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 9 0.19
19 4 0.09
20 11 0.23
21 17 0.36
22 6 0.13
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTCTTTTTCTTTTTTTTCT
Found at i:3679156 original size:13 final size:13
Alignment explanation
Indices: 3679140--3679164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3679130 TTCGTTTTCT
3679140 GTTTCTGTCTCTG
1 GTTTCTGTCTCTG
3679153 GTTTCTGTCTCT
1 GTTTCTGTCTCT
3679165 CTTTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.20, T:0.56
Consensus pattern (13 bp):
GTTTCTGTCTCTG
Found at i:3679639 original size:3 final size:3
Alignment explanation
Indices: 3679631--3679746 Score: 205
Period size: 3 Copynumber: 38.7 Consensus size: 3
3679621 TTAATATATT
*
3679631 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3679679 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3679727 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
3679747 TGGATAAAAA
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 107 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3681538 original size:22 final size:21
Alignment explanation
Indices: 3681499--3681541 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
3681489 CCTCTACTCA
3681499 AATCATAAAAACAAGTTGTTG
1 AATCATAAAAACAAGTTGTTG
3681520 AATCACTAAAAA-AATGTTGTTG
1 AATCA-TAAAAACAA-GTTGTTG
3681542 GAAGGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (21 bp):
AATCATAAAAACAAGTTGTTG
Found at i:3687458 original size:2 final size:2
Alignment explanation
Indices: 3687451--3687485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3687441 ATTTCGTAAT
3687451 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
3687486 TGTAGATTGA
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:3691930 original size:6 final size:6
Alignment explanation
Indices: 3691921--3691945 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3691911 CAAAGACAAT
3691921 TGGAAA TGGAAA TGGAAA TGGAAA T
1 TGGAAA TGGAAA TGGAAA TGGAAA T
3691946 AGCCAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (6 bp):
TGGAAA
Found at i:3692146 original size:14 final size:14
Alignment explanation
Indices: 3692129--3692159 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3692119 TCCTACCTTC
3692129 AATTTCTTTTTGTA
1 AATTTCTTTTTGTA
3692143 AATTTCTTTTTGTA
1 AATTTCTTTTTGTA
3692157 AAT
1 AAT
3692160 AATATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (14 bp):
AATTTCTTTTTGTA
Found at i:3693348 original size:3 final size:3
Alignment explanation
Indices: 3693331--3694170 Score: 505
Period size: 3 Copynumber: 284.0 Consensus size: 3
3693321 AGTGTTTGGG
*
3693331 TTC TTC TT- TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
* *
3693376 TTC TTC TTC TTC TCC TTC -TC TTC TTC TCC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
3693423 TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TCC TTC TTC TTC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
3693471 TTCC TTC TTC TCC TTC -TC TTC CTC CTC -TC CTC TCC TCC TCC TCC
1 TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * * * * * * *
3693515 TCC TCC TCTC CTC CTC CTC CTC CTC TCC TCC TCC TCC TCC TCC TCC
1 TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
3693561 TCC TCC TCC TTC TCC TTC TCC TTC TCC TTC TTC -TC CTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * *
3693608 -TC CTC TTC TTTC TTCC TTC TTC TCC TTC TTC TCC TTC TTC TCC TTC
1 TTC TTC TTC -TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * * * *
3693654 TTC TCC TCC TTC -TC CTC CTC TCC TCC TCC TCC TTC TCC TCC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * *
3693701 TCC TCC TTC TCC TCC TTC -TC CTC TTC TCC TCC TTC -TC CTC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
3693747 TTC TCC TTC TTC TTC TTC -TC TTC TCC TTC TTC TCC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
3693793 TTC TTC TTC -TC TTC TTC TTC TTC TTTC TCC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
* * * * *
3693837 TCC TTC TTC TCC TTC TGC -TC TTC -TC TTCC TTC TGC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC
* * * * *
3693881 TTC TCC TTC TTC TCC TTC TCC TTC -TC TTC TCC TTC TCC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
3693927 -TC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * *
3693974 TTC TCC TTC TCC TTC TCC TTC -TC ATTC TCC TTC TCC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
3694019 TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * *
3694067 TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
3694115 TTC TTC TCC TTC TCC TTC TCC TTC TTC TTC TTC TTC TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3694162 TTC TTC TTC
1 TTC TTC TTC
3694171 CGGAGATCAT
Statistics
Matches: 661, Mismatches: 148, Indels: 56
0.76 0.17 0.06
Matches are distributed among these distances:
2 39 0.06
3 601 0.91
4 21 0.03
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.53
Consensus pattern (3 bp):
TTC
Found at i:3694439 original size:13 final size:12
Alignment explanation
Indices: 3694415--3694452 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
3694405 CTTTATTATC
3694415 TAAATTAAGAAT
1 TAAATTAAGAAT
3694427 TAAATTAAAGAAT
1 TAAATT-AAGAAT
3694440 TAAA--AAGAAT
1 TAAATTAAGAAT
3694450 TAA
1 TAA
3694453 GAATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.36
12 6 0.24
13 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (12 bp):
TAAATTAAGAAT
Found at i:3696057 original size:39 final size:38
Alignment explanation
Indices: 3696029--3696102 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
3696019 AGTATCCGCT
*
3696029 ATTAAAAATTTTAGTTTTTGCTTCATTTTAGTACTCGAC
1 ATTAAAAAATTTAG-TTTTGCTTCATTTTAGTACTCGAC
* *
3696068 GTTAAAAAATTTAGTTTTGTTTCATTTTAGTACTC
1 ATTAAAAAATTTAGTTTTGCTTCATTTTAGTACTC
3696103 CAGTTCAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 20 0.62
39 12 0.38
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (38 bp):
ATTAAAAAATTTAGTTTTGCTTCATTTTAGTACTCGAC
Found at i:3696591 original size:18 final size:18
Alignment explanation
Indices: 3696568--3696602 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3696558 AATATTGTAG
3696568 ATAATA-ATATAAAGTATT
1 ATAATATATA-AAAGTATT
3696586 ATAATATATAAAAGTAT
1 ATAATATATAAAAGTAT
3696603 GAGTTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
ATAATATATAAAAGTATT
Found at i:3697482 original size:34 final size:33
Alignment explanation
Indices: 3697439--3697510 Score: 126
Period size: 34 Copynumber: 2.2 Consensus size: 33
3697429 TCGTTCAACC
*
3697439 ATATGCACTAGTTATACTTTACTGTAGTCCCGA
1 ATATGCACTAGTTATACTTTACTGTAGTCCAGA
3697472 ATATGACACTAGTTATACTTTACTGTAGTCCAGA
1 ATATG-CACTAGTTATACTTTACTGTAGTCCAGA
3697506 ATATG
1 ATATG
3697511 GCACATAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 5 0.14
34 32 0.86
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (33 bp):
ATATGCACTAGTTATACTTTACTGTAGTCCAGA
Found at i:3697575 original size:59 final size:59
Alignment explanation
Indices: 3697472--3697625 Score: 218
Period size: 59 Copynumber: 2.6 Consensus size: 59
3697462 GTAGTCCCGA
* * * * * *
3697472 ATATGACACTAGTTATACTTTACTGTAGTCCAGAATATGGCACATAAAGTTGTGCCCACC
1 ATATG-CACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAAGTTGTGCCCAAC
* *
3697532 ATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAGGTTGTGCCTAAC
1 ATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAAGTTGTGCCCAAC
*
3697591 ATATGCACTAGTTACACTTTAGTGCAATCCCGAAT
1 ATATGCACTAGTTATACTTTAGTGCAATCCCGAAT
3697626 GTGCAGCCTG
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
59 80 0.94
60 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (59 bp):
ATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAAGTTGTGCCCAAC
Found at i:3709460 original size:35 final size:35
Alignment explanation
Indices: 3709420--3709491 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
3709410 TTTTACGCTA
* **
3709420 TTATACCTTTCATTTATTTCATCCTTTCATGCCTT
1 TTATACATTTCATTTATGGCATCCTTTCATGCCTT
3709455 TTATACATTTCATTTATGGCATCCTTTCATGCCTT
1 TTATACATTTCATTTATGGCATCCTTTCATGCCTT
3709490 TT
1 TT
3709492 GTACTCTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.53
Consensus pattern (35 bp):
TTATACATTTCATTTATGGCATCCTTTCATGCCTT
Found at i:3709482 original size:80 final size:80
Alignment explanation
Indices: 3709376--3709541 Score: 233
Period size: 80 Copynumber: 2.1 Consensus size: 80
3709366 AATACACCCA
* * * * * *
3709376 TATAGATTTCAATTATGACATTCTTTCATGCCTTTTTTACGCTATTATACCTTTCATTTATTTCA
1 TATACATTTCAATTATGACATCCTTTCATGCCTTTTGTACGCTATTATACATTTCATTTATGTAA
* *
3709441 TCCTTTCATGCCTTT
66 TCATTTCATACCTTT
* * *
3709456 TATACATTTCATTTATGGCATCCTTTCATGCCTTTTGTACTCTATTATACATTTCATTTATGTAA
1 TATACATTTCAATTATGACATCCTTTCATGCCTTTTGTACGCTATTATACATTTCATTTATGTAA
3709521 TCATTTCATACCTTT
66 TCATTTCATACCTTT
3709536 TATACA
1 TATACA
3709542 CTATTATACA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.23, C:0.20, G:0.06, T:0.50
Consensus pattern (80 bp):
TATACATTTCAATTATGACATCCTTTCATGCCTTTTGTACGCTATTATACATTTCATTTATGTAA
TCATTTCATACCTTT
Found at i:3709505 original size:45 final size:45
Alignment explanation
Indices: 3709455--3709599 Score: 218
Period size: 45 Copynumber: 3.2 Consensus size: 45
3709445 TTCATGCCTT
* * *
3709455 TTATACATTTCATTTATGGCATCCTTTCATGCCTTTTGTACTCTA
1 TTATACATTTCATTTATGGAATCCTTTCATGCCTTTTATACACTA
* * *
3709500 TTATACATTTCATTTATGTAATCATTTCATACCTTTTATACACTA
1 TTATACATTTCATTTATGGAATCCTTTCATGCCTTTTATACACTA
* *
3709545 TTATACATTTCATTTATGGAATCCTTTCACGCCTTTCATACACTA
1 TTATACATTTCATTTATGGAATCCTTTCATGCCTTTTATACACTA
3709590 TTATACATTT
1 TTATACATTT
3709600 AATCTATGAT
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 89 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.48
Consensus pattern (45 bp):
TTATACATTTCATTTATGGAATCCTTTCATGCCTTTTATACACTA
Found at i:3709615 original size:45 final size:45
Alignment explanation
Indices: 3709455--3709619 Score: 199
Period size: 45 Copynumber: 3.7 Consensus size: 45
3709445 TTCATGCCTT
** * *
3709455 TTATACATTTCATTTATGGCATCCTTTCATGCCTTTTGTACTCTA
1 TTATACATTTCATTTATGATATCCTTTCATGCCTTTTATACACTA
* *
3709500 TTATACATTTCATTTATG-TAATCATTTCATACCTTTTATACACTA
1 TTATACATTTCATTTATGAT-ATCCTTTCATGCCTTTTATACACTA
* *
3709545 TTATACATTTCATTTATGGA-ATCCTTTCACGCCTTTCATACACTA
1 TTATACATTTCATTTAT-GATATCCTTTCATGCCTTTTATACACTA
* * *
3709590 TTATACATTTAATCTATGATGTCCTTTCAT
1 TTATACATTTCATTTATGATATCCTTTCAT
3709620 ACCACGTATG
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
44 2 0.02
45 100 0.97
46 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (45 bp):
TTATACATTTCATTTATGATATCCTTTCATGCCTTTTATACACTA
Found at i:3709789 original size:81 final size:81
Alignment explanation
Indices: 3709682--3710227 Score: 751
Period size: 81 Copynumber: 6.7 Consensus size: 81
3709672 ACCCAAAAGC
* * * * *
3709682 ATTTAGCCCTTCATCTAACTTGCATAATGGACA-CTTTCCTACCAAATGCAAAGCTAGGCCATTA
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTT-CTGCCAAATGCAAAGCTAGGCCATTA
3709746 ATCTTTTACTCAACGGT
65 ATCTTTTACTCAACGGT
* * * *
3709763 ATGTAACCATTCATCTAACTGCCATAATTGAAACCTTTATGCCAAATGCACAA-CTAGGCCATTA
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-AAGCTAGGCCATTA
*
3709827 ATCTTTTACTCAACAGT
65 ATCTTTTACTCAACGGT
* **
3709844 ATTTAACCATTCATCTAACTGGCATAATTAACACCTTTCTGCCAAATGCACAA-CTAGATCATTA
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-AAGCTAGGCCATTA
* *
3709908 ATCTTTTACTAAACGAT
65 ATCTTTTACTCAACGGT
* *
3709925 ATTTAA-AATTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGCACAA-CTAGGCCATT
1 ATTTAACCA-TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCA-AAGCTAGGCCATT
3709988 AATCTTTTACTCAACGGT
64 AATCTTTTACTCAACGGT
* * * *
3710006 ATTTAACTATTCATCTAACTGGCATAATTGACACCTTTTTGCCTAATGCACAGCTAGGCCATTAA
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAA
3710071 TCTTTTACTCAACGGT
66 TCTTTTACTCAACGGT
* *
3710087 ATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAA
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAA
*
3710152 TCGTTTACTCAACGGT
66 TCTTTTACTCAACGGT
* * * * *
3710168 ATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTTTCCCAAATACACAGCTAGGCC
1 ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCC
3710228 TCAAAGGCAC
Statistics
Matches: 420, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
80 2 0.00
81 411 0.98
82 7 0.02
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (81 bp):
ATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCAAAGCTAGGCCATTAA
TCTTTTACTCAACGGT
Found at i:3710268 original size:68 final size:68
Alignment explanation
Indices: 3710177--3710634 Score: 603
Period size: 68 Copynumber: 6.7 Consensus size: 68
3710167 TATTTAACCG
* ** * *
3710177 TTCATCTAACTGGCATAATTGACACCTTTTTCCCAAATACACAGCTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3710242 CCT
66 CCT
* * * * *
3710245 TTTATCTAACTCGCATAATTGACACCTTTTTGTGAAATGCACAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3710310 CCT
66 CCT
* * * * * * * * *
3710313 TTAATCTAATTGGTATAATTGACACCTTTCTATTAAATGCACAATTAGACCTTAAAGGCATTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3710378 CCT
66 CCT
* * * *
3710381 TTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTATGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3710446 CCT
66 CCT
* * * * * *
3710449 TTCATCTAATTGGAATAATTGACACCTTTTTTTCAAATGCACAATTAGGCCTCAAA-GAACCTTA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCA-CTTA
3710513 GCCT
65 GCCT
*
3710517 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGTACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
3710582 CCT
66 CCT
* * *
3710585 TTCATCTAACTGACATAATTGACACATTTCTGCCAAATGCACAGTTAGGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGC
3710635 TATTAATCTT
Statistics
Matches: 337, Mismatches: 51, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
67 2 0.01
68 333 0.99
69 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3710975 original size:55 final size:55
Alignment explanation
Indices: 3710847--3711061 Score: 288
Period size: 55 Copynumber: 3.9 Consensus size: 55
3710837 ACATATATTT
* * * *
3710847 CCCATACGGAAATTCATACACTTAGTATGGATTTATTAG-TTCGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
* * * *
3710901 CCCATACGAAAATTCATACACTTAGTACGAATTTCTTAGTTTTGTACACAAAGTA
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
* *
3710956 CCCATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACAAAAAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
* * *
3711011 CCAATATGGAAATTCATACACTTAGTTTGAATTTCTTAGCTTTTTGCACAC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAG--TTTTGCACAC
3711062 TCGCTGCCAT
Statistics
Matches: 139, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
54 35 0.25
55 95 0.68
57 9 0.06
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTG
Found at i:3712660 original size:45 final size:45
Alignment explanation
Indices: 3712605--3713060 Score: 509
Period size: 45 Copynumber: 10.0 Consensus size: 45
3712595 AATGAATAAA
*
3712605 CAAAATAATAATGCATATGGGTGCATTATAGGTATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* *
3712650 CAAAATAATAATGCATATGAGTGCATTATAGGCATGAAAGGAAGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
3712695 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * *
3712740 CAAAATAATAATGAATATGGGTGCATTATAGGCATGAAAGAATGA
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* *
3712785 CAAAATAATAAAGCATATGGGTGCATTATCA-GCATGAAAGGATGG
1 CAAAATAATAATGCATATGGGTGCATTAT-AGGCATGAAAGGATGC
* * *
3712830 TAAAATAATAATGCATATGGGTACATTATAGGCATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
*
3712875 CATAAATAA-AATGCATGAAAT-GATGCATTA-AGGCATGAAAGGATGC
1 CA-AAATAATAATGCAT---ATGGGTGCATTATAGGCATGAAAGGATGC
* * * *
3712921 CATAAATAA-AAAGCATGAAGGGATGCATTA-AGGAATGAAAGTATGC
1 CA-AAATAATAATGCAT-ATGGG-TGCATTATAGGCATGAAAGGATGC
* * *
3712967 CATAAAT-AGAATGCATGAAAGGATGCATTA-AGGCATGAAAGGATGC
1 CA-AAATAATAATGCAT--ATGGGTGCATTATAGGCATGAAAGGATGC
* ** *
3713013 CATAAATAA-AATGCATGAAAGAATGAATTA-AGGCATGAAAGGATGC
1 CA-AAATAATAATGCAT--ATGGGTGCATTATAGGCATGAAAGGATGC
3713059 CA
1 CA
3713061 TAAAAAATTA
Statistics
Matches: 366, Mismatches: 34, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
44 2 0.01
45 214 0.58
46 136 0.37
47 12 0.03
48 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
Found at i:3712890 original size:26 final size:25
Alignment explanation
Indices: 3712859--3713064 Score: 137
Period size: 20 Copynumber: 8.9 Consensus size: 25
3712849 GGTACATTAT
*
3712859 AGGCATGAAATGATGCCATAAATAAA
1 AGGCATGAAAGGATGCCATAAAT-AA
* *
3712885 ATGCATGAAATGATG-CAT---T-A
1 AGGCATGAAAGGATGCCATAAATAA
3712905 AGGCATGAAAGGATGCCATAAATAAA
1 AGGCATGAAAGGATGCCATAAAT-AA
* *
3712931 AAGCATGAAGGGATG-CAT---T-A
1 AGGCATGAAAGGATGCCATAAATAA
* *
3712951 AGGAATGAAAGTATGCCATAAATAGA
1 AGGCATGAAAGGATGCCATAAATA-A
*
3712977 ATGCATGAAAGGATG-CAT---T-A
1 AGGCATGAAAGGATGCCATAAATAA
3712997 AGGCATGAAAGGATGCCATAAATAAA
1 AGGCATGAAAGGATGCCATAAAT-AA
* * *
3713023 ATGCATGAAA-GA----ATGAATTA
1 AGGCATGAAAGGATGCCATAAATAA
3713043 AGGCATGAAAGGATGCCATAAA
1 AGGCATGAAAGGATGCCATAAA
3713065 AAATTAATGA
Statistics
Matches: 139, Mismatches: 18, Indels: 47
0.68 0.09 0.23
Matches are distributed among these distances:
20 51 0.37
21 16 0.12
22 3 0.02
24 3 0.02
25 15 0.11
26 51 0.37
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (25 bp):
AGGCATGAAAGGATGCCATAAATAA
Found at i:3729405 original size:20 final size:20
Alignment explanation
Indices: 3729380--3729420 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3729370 CCTAGTTAAA
3729380 GTCTTAATTTAAACCGATTG
1 GTCTTAATTTAAACCGATTG
3729400 GTCTTAATTTAAACCGATTG
1 GTCTTAATTTAAACCGATTG
3729420 G
1 G
3729421 ATCAGACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
GTCTTAATTTAAACCGATTG
Found at i:3739135 original size:20 final size:18
Alignment explanation
Indices: 3739093--3739140 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
3739083 TTTTGTCAAA
*
3739093 GTCAATGGTCAACGGTCG
1 GTCAACGGTCAACGGTCG
3739111 GTCAACGGTCAACAGGTCGG
1 GTCAACGGTCAAC-GGTC-G
3739131 GTCAACGGTC
1 GTCAACGGTC
3739141 GGGTCGGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.44
19 4 0.15
20 11 0.41
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (18 bp):
GTCAACGGTCAACGGTCG
Found at i:3739142 original size:12 final size:13
Alignment explanation
Indices: 3739117--3739145 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3739107 GTCGGTCAAC
3739117 GGTCAACAGGTCG
1 GGTCAACAGGTCG
3739130 GGTCAAC-GGTCG
1 GGTCAACAGGTCG
3739142 GGTC
1 GGTC
3739146 GGCTCAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
GGTCAACAGGTCG
Found at i:3748919 original size:18 final size:18
Alignment explanation
Indices: 3748878--3748912 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3748868 ACTCGACCCG
*
3748878 GCTGCCCGACCTGACTCA
1 GCTGCCCGACCCGACTCA
3748896 GCTGCCCGACCCGACTC
1 GCTGCCCGACCCGACTC
3748913 GACTGCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.49, G:0.23, T:0.14
Consensus pattern (18 bp):
GCTGCCCGACCCGACTCA
Found at i:3749003 original size:21 final size:21
Alignment explanation
Indices: 3748954--3749004 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3748944 CCGACCATTA
3748954 ACCGTTGACCACCGTTAATGG
1 ACCGTTGACCACCGTTAATGG
* *
3748975 ACCTTTGACCATCGTTAATCGG
1 ACCGTTGACCACCGTTAAT-GG
3748997 -CCGTTGAC
1 ACCGTTGAC
3749005 TTTTTCTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (21 bp):
ACCGTTGACCACCGTTAATGG
Found at i:3750425 original size:24 final size:24
Alignment explanation
Indices: 3750364--3750437 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
3750354 TGAAGATTTT
3750364 ATCTAATTTCTGTTCTGATTT-TCG
1 ATCTAATTTCTGTTCTGATTTCT-G
* *
3750388 CTCTGAATTT-TGTTATGATTTCTG
1 ATCT-AATTTCTGTTCTGATTTCTG
3750412 ATCTAATTTCTGTTCTGATTTCTG
1 ATCTAATTTCTGTTCTGATTTCTG
3750436 AT
1 AT
3750438 ATCTCTGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.12
24 32 0.74
25 6 0.14
ACGTcount: A:0.18, C:0.15, G:0.14, T:0.54
Consensus pattern (24 bp):
ATCTAATTTCTGTTCTGATTTCTG
Found at i:3750614 original size:30 final size:31
Alignment explanation
Indices: 3750578--3750652 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
3750568 TAAGACGACC
* * *
3750578 CTTGGGTAGGCTCTGTGG-CATGAGATTTTT
1 CTTGGGTAGGCTCCGTGGCCATGAGAATTAT
*
3750608 CTTGGGTAGGCCTCCGTGGCCCTGAGAATTAT
1 CTTGGGTAGG-CTCCGTGGCCATGAGAATTAT
3750640 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
3750653 ACAGGCCCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 10 0.26
31 10 0.26
32 19 0.49
ACGTcount: A:0.13, C:0.20, G:0.33, T:0.33
Consensus pattern (31 bp):
CTTGGGTAGGCTCCGTGGCCATGAGAATTAT
Found at i:3752626 original size:16 final size:17
Alignment explanation
Indices: 3752605--3752644 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
3752595 CGTACGACCA
3752605 GACCCGACTG-TAACCC
1 GACCCGACTGCTAACCC
*
3752621 GACCCGACTGCCTGACCC
1 GACCCGACTG-CTAACCC
3752639 GACCCG
1 GACCCG
3752645 TTGACCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
18 11 0.52
ACGTcount: A:0.20, C:0.47, G:0.23, T:0.10
Consensus pattern (17 bp):
GACCCGACTGCTAACCC
Found at i:3754097 original size:12 final size:12
Alignment explanation
Indices: 3754080--3754167 Score: 79
Period size: 12 Copynumber: 7.3 Consensus size: 12
3754070 ATTTTATCTT
3754080 ATTTTTGTTCTG
1 ATTTTTGTTCTG
3754092 ATTTTTGTTCT-
1 ATTTTTGTTCTG
* *
3754103 ATATTCTATTCTG
1 AT-TTTTGTTCTG
*
3754116 ATTTTTGCTCTG
1 ATTTTTGTTCTG
* * *
3754128 AATTATGTTATG
1 ATTTTTGTTCTG
* **
3754140 ATTTCTACTCTG
1 ATTTTTGTTCTG
3754152 ATTTTTGTTCTG
1 ATTTTTGTTCTG
3754164 ATTT
1 ATTT
3754168 CTGATATCTC
Statistics
Matches: 57, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
11 2 0.04
12 53 0.93
13 2 0.04
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.60
Consensus pattern (12 bp):
ATTTTTGTTCTG
Found at i:3754128 original size:36 final size:36
Alignment explanation
Indices: 3754080--3754167 Score: 115
Period size: 36 Copynumber: 2.4 Consensus size: 36
3754070 ATTTTATCTT
* * *
3754080 ATTTTTGTTCTGATTTTTGTTCT-ATATTCTATTCTG
1 ATTTTTGTTCTGATTTATGTTATGAT-TTCTACTCTG
* *
3754116 ATTTTTGCTCTGAATTATGTTATGATTTCTACTCTG
1 ATTTTTGTTCTGATTTATGTTATGATTTCTACTCTG
3754152 ATTTTTGTTCTGATTT
1 ATTTTTGTTCTGATTT
3754168 CTGATATCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 42 0.95
37 2 0.05
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.60
Consensus pattern (36 bp):
ATTTTTGTTCTGATTTATGTTATGATTTCTACTCTG
Found at i:3757794 original size:24 final size:24
Alignment explanation
Indices: 3757766--3757848 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
3757756 ATCTGATTTG
**
3757766 TGTTCTGATTTTTGTTCTATATTC
1 TGTTCTGATTTTTACTCTATATTC
* * * *
3757790 TGTTCTAATTTCTACTCTGTATTA
1 TGTTCTGATTTTTACTCTATATTC
3757814 TGTTCTGATTTTTACTCTGAT-TTC
1 TGTTCTGATTTTTACTCT-ATATTC
*
3757838 TGTTTTGATTT
1 TGTTCTGATTT
3757849 CTGATATCTC
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 46 0.98
25 1 0.02
ACGTcount: A:0.14, C:0.13, G:0.12, T:0.60
Consensus pattern (24 bp):
TGTTCTGATTTTTACTCTATATTC
Found at i:3761548 original size:24 final size:24
Alignment explanation
Indices: 3761518--3761579 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
3761508 ATGAACTCTA
3761518 TTATGATTTCTGATCTGAATTATG
1 TTATGATTTCTGATCTGAATTATG
* * * *
3761542 TTCTGATTTTTGCTCTGATTTATG
1 TTATGATTTCTGATCTGAATTATG
*
3761566 TTATGGTTTCTGAT
1 TTATGATTTCTGAT
3761580 ATCTCTGTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.55
Consensus pattern (24 bp):
TTATGATTTCTGATCTGAATTATG
Found at i:3768719 original size:20 final size:19
Alignment explanation
Indices: 3768690--3768744 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3768680 GGTAACGAAT
*
3768690 TTGACTAAACCGATTGGAAA
1 TTGACAAAACCGATT-GAAA
* *
3768710 TTGACAAAACTGGTTGAAA
1 TTGACAAAACCGATTGAAA
3768729 TTGGACAAAACCGATT
1 TT-GACAAAACCGATT
3768745 TCAATTTCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (19 bp):
TTGACAAAACCGATTGAAA
Found at i:3775800 original size:21 final size:20
Alignment explanation
Indices: 3775774--3775812 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3775764 TAAATTTACA
*
3775774 AAGTATCGATACTTATTATAT
1 AAGTATAGATACTT-TTATAT
3775795 AAGTATAGATACTTTTAT
1 AAGTATAGATACTTTTAT
3775813 TCCAGTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (20 bp):
AAGTATAGATACTTTTATAT
Found at i:3775812 original size:152 final size:153
Alignment explanation
Indices: 3775622--3775927 Score: 373
Period size: 152 Copynumber: 2.0 Consensus size: 153
3775612 GAAAATGTCC
* * ** * * *** *
3775622 AAGTTTCGATACTTTTTATACCCGTATCGATACTTTTATTCTAGTATGGTTCTCAAACAATTTGC
1 AAGTATCGATACTTATTATACAAGTATAGATACTTTTATTCCAGTATACATCTCAAACAACTTGC
* * * * * * *
3775687 TCGCAACAAAGTATCGATACCCATAT-ATAAAGTATCAATACTTGGAATTTCG-AAACCTATTAC
66 ACACAAAAAAGTATCGACACACATATAAAAAAGTATCAATACTTAGAATTTCGAAAACCT-TTAC
3775750 TTTAAAGTAATAGGTAAATTTACA
130 TTTAAAGTAATAGGTAAATTTACA
*
3775774 AAGTATCGATACTTATTATATAAGTATAGATACTTTTATTCCAGTATACATCTCAAACAACTTGC
1 AAGTATCGATACTTATTATACAAGTATAGATACTTTTATTCCAGTATACATCTCAAACAACTTGC
* * * *
3775839 ACACAAAAAATTATCGACACAGATATAAAAAAGTATCGATACTTAGAATTTTGAAAACCTTTACT
66 ACACAAAAAAGTATCGACACACATATAAAAAAGTATCAATACTTAGAATTTCGAAAACCTTTACT
* *
3775904 TTATAGTAATAGTTAAATTTACA
131 TTAAAGTAATAGGTAAATTTACA
3775927 A
1 A
3775928 TGTAAACGGT
Statistics
Matches: 128, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
152 73 0.57
153 49 0.38
154 6 0.05
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (153 bp):
AAGTATCGATACTTATTATACAAGTATAGATACTTTTATTCCAGTATACATCTCAAACAACTTGC
ACACAAAAAAGTATCGACACACATATAAAAAAGTATCAATACTTAGAATTTCGAAAACCTTTACT
TTAAAGTAATAGGTAAATTTACA
Found at i:3776824 original size:30 final size:30
Alignment explanation
Indices: 3776788--3776857 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
3776778 GGTCAACTCG
*
3776788 TTGACTTTGAACGAGTCAACCTGTTGACCA
1 TTGACTTTGAACGAGTCAACCCGTTGACCA
** *
3776818 TTGACTTTGTCCGAGTCAACCCGTTGACCG
1 TTGACTTTGAACGAGTCAACCCGTTGACCA
3776848 TTGACTTTGA
1 TTGACTTTGA
3776858 CCAAAAGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (30 bp):
TTGACTTTGAACGAGTCAACCCGTTGACCA
Found at i:3780605 original size:200 final size:194
Alignment explanation
Indices: 3780146--3781260 Score: 825
Period size: 200 Copynumber: 5.6 Consensus size: 194
3780136 GAAAACATTT
* * * * * *
3780146 AGTATCAATGCTTGGGATTTCGAAACCTATTAGTTTAAAGTAATAGGTAAATTTATAATGGAAAC
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * * *
3780211 GATAAAAATCTATCGTTTAATGATAATTGGCGTAAACATAAAGTATCGATACTTTTTATTTAGGC
66 GGTAAAAATCTAT-GTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-TTTTATATAGGT
* * * * *
3780276 ATCGATACTTTTATTATAGTATGCATCTCAAA-ATATTTGTACGCAAAATGTATCGATACACATA
129 ATCGATACTTTTATGATA--A-GCATCCCAAACA-ATTTGCACGCAAAAAGTCTCGATACACATA
3780340 TATA-A
190 TA-ACA
* * * * * *
3780345 AATATCGATACTTGGAATTCCAAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGTAAAC
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
*
3780410 GGTAAAAATCTATGATTTTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATAGG
66 GGTAAAAATCTATG--TTTAATGATAATAGGCGTAAACATAAAGTATCGATACTT-TTATATAGG
* * * *
3780475 TATTGATAATGTTGTAATCGATAAGTATCCCAAACAATTTGCAAGCAAAAAGTCTCGATACACAT
128 TATCGATACT-TT-T-AT-GATAAGCATCCCAAACAATTTGCACGCAAAAAGTCTCGATACACAT
3780540 ATAACA
189 ATAACA
* * *
3780546 AGTATCAATACTTGGTATTTTGAAACCTATTACTTTAAA-CAATAGGTAAATTAACAATGTAAAC
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* *
3780610 GGTAAAAATCTACTGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACATTTAATATAGA
66 GGTAAAAATCTA-T-GTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-TTTTATATAGG
*
3780675 TATCGATACTTTTATTA-AAGCATGCTTCTCAAACAATTTGCACGTC-AAAAG-CATCGATACAC
128 TATCGATACTTTTATGATAAGCAT-C--C-CAAACAATTTGCACG-CAAAAAGTC-TCGATACAC
*
3780737 ATGT-ACAA
187 ATATAAC-A
* * * * * * *
3780745 AGTATCGATGCTTGGAATTTTGAAACCTATTACTATAAAGTAAAAGGTAAATTAACAATGCAAAG
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * * * *
3780810 GGTAAAAGTTTTACCGGTGTAATGATAATAGGCGTATATAC-T-AAGTATCTATACTTTATATAT
66 GGTAAAA-ATCTA--TGTTTAATGATAATAGGCGTA-A-ACATAAAGTATCGATACTTT-TATAT
* * * * * * * ** * *
3780873 AGGTATCGATACTGTTAGTCCAATATGCTTCTC-AATAATTTGCATGTTAAATGTATCGATACAC
125 AGGTATCGATACTTTTA-T--GATAAGCATCCCAAACAATTTGCACGCAAAAAGTCTCGATACAC
*
3780937 ATGT-ACAA
187 ATATAAC-A
** ** * * * * * *
3780945 AGTATTGATACCCGTAATTTCAAAACCGATTACTTTAAAGTAATAGGTAATTTTACAATGTAAAT
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * ** * * ** * **
3781010 TGTAAAAGTCTATCAGTACATTGATAATAGGCGTAAATACCAAGTATCGATACTGTCTATGCAGG
66 GGTAAAAATCTAT--GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACT-TTTATATAGG
* * * * * * * * *
3781075 TATCGATACTTTCGT-TCCAGTATGCTTCTCAAATAATTTGTACGTAAAAGGTATCGATACACAT
128 TATCGATACTTT--TAT-GA-TAAGCATCCCAAACAATTTGCACGCAAAAAGTCTCGATACACAT
3781139 ATATA-A
189 ATA-ACA
* ** * * * * * * *
3781145 AGTATCGATACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGTTTAATTTATAACGAAAAT
1 AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
* * * * *
3781210 GGTAAAAGTATAACTATATAATGATAATAGGCGTAAACATCAAGTATCGAT
66 GGTAAAAATCT-A-TGTTTAATGATAATAGGCGTAAACATAAAGTATCGAT
3781261 TCGTGGAATT
Statistics
Matches: 752, Mismatches: 120, Indels: 87
0.78 0.13 0.09
Matches are distributed among these distances:
195 5 0.01
196 2 0.00
197 3 0.00
198 9 0.01
199 198 0.26
200 382 0.51
201 130 0.17
202 10 0.01
203 4 0.01
204 5 0.01
205 4 0.01
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (194 bp):
AGTATCAATACTTGGAATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTAACAATGTAAAC
GGTAAAAATCTATGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTATATAGGTAT
CGATACTTTTATGATAAGCATCCCAAACAATTTGCACGCAAAAAGTCTCGATACACATATAACA
Found at i:3780884 original size:21 final size:22
Alignment explanation
Indices: 3780844--3780885 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3780834 ATAATAGGCG
*
3780844 TATATACTAAGTATCTATACTT
1 TATATACTAAGTATCGATACTT
*
3780866 TATATA-TAGGTATCGATACT
1 TATATACTAAGTATCGATACT
3780886 GTTAGTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (22 bp):
TATATACTAAGTATCGATACTT
Found at i:3780992 original size:400 final size:397
Alignment explanation
Indices: 3780162--3781257 Score: 1104
Period size: 400 Copynumber: 2.7 Consensus size: 397
3780152 AATGCTTGGG
* * * * *
3780162 ATTTCGAAACCTATTAGTTTAAAGTAATAGGTAAATTTATAATGGAAACGATAAAAATCTATCGT
1 ATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATAGT
* * *
3780227 TTAATGATAATTGGCGTAAACATAAAGTATCGATACTTTTTATTTAGGCATCGATACTTTTATTA
66 TTAATGATAATAGGCGTAAACATAAAGTATCGATAC--TTTATATAGGTATCGATACTTTTATTA
* * * *
3780292 TAGTATGCATCTCAAAATATTTGTACG-CAAAATGTATCGATACACATATATAAAATATCGATAC
129 AAGTATGCTTCTCAAAA-ATTTGTACGTCAAAAGGTATCGATACACATATATAAAGTATCGATAC
* * * * * *
3780356 TTGGAATTCCAAAACCTATTACTTTAAAGTAATAGGTTAATTTACAATGTAAACGGTAAAAATCT
193 TTGGAATTTCGAAACCTATTACTTTAAAGTAAAAGGTAAATTAACAATGCAAACGGTAAAAATCT
* * * *
3780421 ATGATTTTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATAGGTATTGATAATG
258 ACGAGTGTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATAGGTATCGATAATG
* * *
3780486 TTGTAATCGATAAGTATCCCAAACAATTTGCAAGCAAAAAGTCTCGATACACATATAACAAGTAT
323 TTGT-ACCAATAAGTATCCCAAACAATTTGCAAGCAAAAAGTATCGATACACATATAACAAGTAT
**
3780551 CAATACTTGGT
387 CAATACTCCGT
* * * *
3780562 ATTTTGAAACCTATTACTTTAAA-CAATAGGTAAATTAACAATGTAAACGGTAAAAATCTACTGG
1 ATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTA-TAG
*
3780626 TTTAATGATAATAGGCGTAAACATAAAGTATCGATACATTTAATATAGATATCGATACTTTTATT
65 TTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-TTT-ATATAGGTATCGATACTTTTATT
* * * * * *
3780691 AAAGCATGCTTCTCAAACAATTTGCACGTCAAAA-GCATCGATACACATGTACAAAGTATCGATG
128 AAAGTATGCTTCTCAAA-AATTTGTACGTCAAAAGGTATCGATACACATATATAAAGTATCGATA
* * * *
3780755 CTTGGAATTTTGAAACCTATTACTATAAAGTAAAAGGTAAATTAACAATGCAAAGGGTAAAAGTT
192 CTTGGAATTTCGAAACCTATTACTTTAAAGTAAAAGGTAAATTAACAATGCAAACGGTAAAA-AT
* *
3780820 TTACCG-GTGTAATGATAATAGGCGTATATAC-T-AAGTATCTATACTT-TATATATAGGTATCG
256 CTA-CGAGTGTAATGATAATAGGCGTA-A-ACATAAAGTATCAATACTTAT-TATATAGGTATCG
* * * * * ** * *
3780881 ATACTGTTAGT-CCAATATGCT-TCTC-AATAATTTGCATGTTAAATGTATCGATACACATGT-A
317 ATAATGTT-GTACCAATAAG-TATCCCAAACAATTTGCAAGCAAAAAGTATCGATACACATATAA
**
3780942 CAAAGTATTGATAC-CCGT
380 C-AAGTATCAATACTCCGT
* * * ** *
3780960 AATTTCAAAACCGATTACTTTAAAGTAATAGGTAATTTTACAATGTAAATTGTAAAAGTCTATCA
1 -ATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTAT-A
** * * ** ** **
3781025 GTACATTGATAATAGGCGTAAATACCAAGTATCGATACTGTCTATGCAGGTATCGATACTTTCGT
64 GTTTAATGATAATAGGCGTAAACATAAAGTATCGATACT-T-TATATAGGTATCGATACTTTTAT
**
3781090 TCCAGTATGCTTCTCAAATAATTTGTACGT-AAAAGGTATCGATACACATATATAAAGTATCGAT
127 TAAAGTATGCTTCTCAAA-AATTTGTACGTCAAAAGGTATCGATACACATATATAAAGTATCGAT
** * * * * * * * * *
3781154 ACTTATAATTTCGAAACCTATTACTTTAAAGTAATAGTTTAATTTATAACGAAAATGGTAAAAGT
191 ACTTGGAATTTCGAAACCTATTACTTTAAAGTAAAAGGTAAATTAACAATGCAAACGGTAAAAAT
* * * *
3781219 ATAACTA-TATAATGATAATAGGCGTAAACATCAAGTATC
256 CT-ACGAGTGTAATGATAATAGGCGTAAACATAAAGTATC
3781258 GATTCGTGGA
Statistics
Matches: 574, Mismatches: 100, Indels: 45
0.80 0.14 0.06
Matches are distributed among these distances:
397 2 0.00
398 6 0.01
399 127 0.22
400 371 0.65
401 61 0.11
402 5 0.01
403 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (397 bp):
ATTTCGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTATAGT
TTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTATATAGGTATCGATACTTTTATTAAA
GTATGCTTCTCAAAAATTTGTACGTCAAAAGGTATCGATACACATATATAAAGTATCGATACTTG
GAATTTCGAAACCTATTACTTTAAAGTAAAAGGTAAATTAACAATGCAAACGGTAAAAATCTACG
AGTGTAATGATAATAGGCGTAAACATAAAGTATCAATACTTATTATATAGGTATCGATAATGTTG
TACCAATAAGTATCCCAAACAATTTGCAAGCAAAAAGTATCGATACACATATAACAAGTATCAAT
ACTCCGT
Found at i:3781850 original size:226 final size:224
Alignment explanation
Indices: 3781449--3782059 Score: 965
Period size: 226 Copynumber: 2.7 Consensus size: 224
3781439 ATGTACGCGG
* * * *
3781449 TAATATATTGATAATATTGAAAACAAATCAAGTAATTAACCTATTTTGTTATCGTTAGATTTTTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTA
* *
3781514 AGGTACCATAAGCTTTAAAAAAGCGCTACCTATTACGTTAAATAAGCGCTACTTTTTATGTTATT
66 AGG--CCATCAGCTTTAAAAAAGCGCTACCTATTACGTTAAATAAGCGCTACTTGTTATGTTATT
* *
3781579 ATGGTTGATAATGTTTCTAGTAATAAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAA
129 ATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAA
3781644 CTTAAACTTTGGTAACATTTTAGGCT-CTACC
194 CTTAAACTTTGGTAACATTTTAGG-TGCTACC
* *
3781675 TAATATGTTGATAATATTGATAACAAATCAAGTAACTAACCTATTTTGTTAGCGTCAGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTA
* * *
3781740 AGGCCCCATCAGCTTTAAACATA-CGCTACCTATTACATTAAATAAGCTCTACTTGTTATGTTAT
66 AGG--CCATCAGCTTTAAA-AAAGCGCTACCTATTACGTTAAATAAGCGCTACTTGTTATGTTAT
*
3781804 TATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCA
128 TATGGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCA
*
3781869 GCTTAAACTTTGGTAACATTTTAGGTGCTACC
193 ACTTAAACTTTGGTAACATTTTAGGTGCTACC
*
3781901 TAATATGTTGATAATATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTA
1 TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTA
* *
3781966 AGGCCATACAAGCTTTAAAAAAGCGCTACCTATTATGTTACATAAGCGCTACTTGTTATGTTATT
66 AGGCCAT-C-AGCTTTAAAAAAGCGCTACCTATTACGTTAAATAAGCGCTACTTGTTATGTTATT
*
3782031 ATGGTTGATAATATTTCCAGTAATTAACC
129 ATGGTTGATAATGTTTCCAGTAATTAACC
3782060 GGTTTGACTT
Statistics
Matches: 353, Mismatches: 27, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
224 4 0.01
225 4 0.01
226 343 0.97
227 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (224 bp):
TAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTA
AGGCCATCAGCTTTAAAAAAGCGCTACCTATTACGTTAAATAAGCGCTACTTGTTATGTTATTAT
GGTTGATAATGTTTCCAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATCAACT
TAAACTTTGGTAACATTTTAGGTGCTACC
Found at i:3789855 original size:2 final size:2
Alignment explanation
Indices: 3789850--3789874 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3789840 ACACACACAC
3789850 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
3789875 ACTGATGATA
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:3790913 original size:12 final size:12
Alignment explanation
Indices: 3790896--3790920 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3790886 TTAGAAATTG
3790896 AAAAAAATGAAA
1 AAAAAAATGAAA
3790908 AAAAAAATGAAA
1 AAAAAAATGAAA
3790920 A
1 A
3790921 TGTCTCGAAA
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAATGAAA
Found at i:3791292 original size:19 final size:19
Alignment explanation
Indices: 3791253--3791292 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3791243 GGACTAATTA
* * *
3791253 TAGGTAGAAAATGATATTC
1 TAGGTAGAAAATAAAAATC
3791272 TAGGTAGAAAATAAAAATC
1 TAGGTAGAAAATAAAAATC
3791291 TA
1 TA
3791293 TACTTTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (19 bp):
TAGGTAGAAAATAAAAATC
Found at i:3794872 original size:18 final size:18
Alignment explanation
Indices: 3794849--3794898 Score: 84
Period size: 17 Copynumber: 2.8 Consensus size: 18
3794839 GATTTAAGCC
3794849 AAATTTTGTATGTGAATG
1 AAATTTTGTATGTGAATG
3794867 AAA-TTTGTATGTGAATG
1 AAATTTTGTATGTGAATG
*
3794884 AAATTATGTATGTGA
1 AAATTTTGTATGTGA
3794899 TGACCAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:3798275 original size:200 final size:199
Alignment explanation
Indices: 3797724--3799334 Score: 1471
Period size: 200 Copynumber: 8.1 Consensus size: 199
3797714 TGTCCAACTT
* ** * ** ** *
3797724 TCGATACTTTTTATATTTGTATCGATACTTTTATTCTAGTATGGTTCTCAAACAATTTGCTTGCA
1 TCGATAC-TTTAATATAAGTATCGATA-TTTTATTCCAGTATGCATCTCAAACAATTTGCACGAA
* * * * *
3797789 ACAAAGTATCGATACCA-ATATATA-AAGTATCAATACTT-GAATTTTAAAACCTATTACATTAA
64 AAAAAGTATCGATA-CATATATA-ACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTAA
** * * * * * *
3797851 AGTAATAGGTAAATTTACAATAAAAACAATAAAAATATACCAGTTTAATGATAATAGGCATATAC
127 AGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAAC
3797916 ATAAAGTA
192 ATAAAGTA
* * * * *
3797924 TTGATACTTATTATATAAGTACCAATACTTTTATTCCAGTATGCATCTCAAACAATTTTCACGCA
1 TCGATACTT-TAATATAAGTATCGATA-TTTTATTCCAGTATGCATCTCAAACAATTTGCACG--
*
3797989 AAAAAAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTAGTTTAA
62 AAAAAAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTAA
* *
3798054 AGTAATAGGTTAATATACAATGTAAACAGTAAAAATCTA-CAGGTTTAATGATAATAGGCGTAAA
127 AGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTATC-GGTTTAATGATAATAGGCGTAAA
3798118 CATAAAGTA
191 CATAAAGTA
* * ** *
3798127 TCGATACGTTTAATAT-AGATATCGATATTGTTATTCCCGTACGTTTCTCAAACAATTTGCATG-
1 TCGATAC-TTTAATATAAG-TATCGATATT-TTATTCCAGTATGCATCTCAAACAATTTGCACGA
** * * * * * * *
3798190 TTAAGAGCATCGATACACATGT-ACAAACTATCGATACTTGGAATTTTGAATCCTTTTACTTTAA
63 AAAAAAGTATCGATACATATATAAC-AAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTAA
* * *
3798254 AGTAATAGGTAAATTTACAATGGAAGCTGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAAC
127 AGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAAC
3798319 ATAAAGTA
192 ATAAAGTA
* *
3798327 TAGATACTTATATAAATACTTATTATATAAGTATCGATGATTTTATTCAAGTATGCATCTCAAAC
1 TCGATAC---------T--TTA--ATATAAGTATCGAT-ATTTTATTCCAGTATGCATCTCAAAC
* * **
3798392 AATTTGCACGCAAAAAATTGT-TCGATACATATATAAAAAAGTATCGATAAATAGAATTTTGAAA
52 AATTTGCACG-AAAAAA-AGTATCGATACATATAT-AACAAGTATCGATACTTAGAATTTTGAAA
* * * *
3798456 CCTTTTACTTTAAAGTAATAGGTAAATTTATAATGCAAA-AATAAAAAATCTACCGGTTTAATGA
114 CCTTTTACTTTAAAGTAATAGGTAAATTTACAATGTAAACAGT-AAAAATCTATCGGTTTAATGA
*
3798520 TAATAGGCATAAACATAAAGTA
178 TAATAGGCGTAAACATAAAGTA
* * *
3798542 TCGATACCTATT-ATATAAGTATCGATATTTTTATTCTAGTATGCATCTCAAACAATTTACA-GG
1 TCGATA-CT-TTAATATAAGTATCGATA-TTTTATTCCAGTATGCATCTCAAACAATTTGCACGA
* * *
3798605 AAAAAAGTATCGATGCATATATAACAAGTATCGATACATAGAATTTTAAAACCTTTTACTTTAAA
63 AAAAAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTAAA
* ** *
3798670 GTTATATATAAATTTACAATGTAAAC-GATAAAAATCTATCGGTTTAATGATAATAGGTGTAAAC
128 GTAATAGGTAAATTTACAATGTAAACAG-TAAAAATCTATCGGTTTAATGATAATAGGCGTAAAC
3798734 ATAAAGTA
192 ATAAAGTA
* * **
3798742 TCGATAC--T--T-T---TA-C----------TCCAATATGCTTCTCAAACAATTTGCACG-TCA
1 TCGATACTTTAATATAAGTATCGATATTTTATTCCAGTATGCATCTCAAACAATTTGCACGAAAA
* * * * * *
3798787 AAAGCATCGATACACATGT-ACAATGTATCGATACTTGGAATTTAGAAACCTATTACTTTAAAGT
66 AAAGTATCGATACATATATAACAA-GTATCGATACTTAGAATTTTGAAACCTTTTACTTTAAAGT
* * * *
3798851 AATAGGTAAATTTACAATGGAATCGGTAAAAATCTATAGGTTTAATGATAATAGGCGTAAACATA
130 AATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAACATA
3798916 AAGTA
195 AAGTA
** * * * * * *
3798921 TCGATA-TTTTTTATTCAGGTATCGATACTTTTATTACAGTATACTTCTCAAATAATTTGTACG-
1 TCGATACTTTAATA-T-AAGTATCGATA-TTTTATTCCAGTATGCATCTCAAACAATTTGCACGA
* * * * * * *
3798984 CAAAAAGTATCGATAAGCATATAT-A-AAGTATTGATACTTGGAGTTTCGAAACCTATTACTATA
63 AAAAAAGTATCGAT-A-CATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTA
* * * * *
3799047 AAGTAATAGGTTAATTTACAATGTAAACGGTAAATATCTACCGGTATAATGATAATAGGCGTAAA
126 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAA
*
3799112 CTTAAAGTA
191 CATAAAGTA
* * * * *
3799121 TCGATACTTAGTATATATATGTATCGATACTATTATTCTAGTATGCATCTCAAATAGTTTGCAC-
1 TCGATACTT--TA-ATATAAGTATCGATA-TTTTATTCCAGTATGCATCTCAAACAATTTGCACG
* **
3799185 ACAAAAAAGTATCGATACATATATAACAAGTATCGTTACTTAGAATTTTGAAACCTAGTACTTTA
62 A-AAAAAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTA
* * * * *
3799250 AAGTAATAGGTAAATTTACAATGTAAACGGTAAAAGTCGACCAGTTTAATGATAATAGGCGTAAA
126 AAGTAATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAA
** *
3799315 TTTCAAGTA
191 CATAAAGTA
3799324 TCGATACTTTA
1 TCGATACTTTA
3799335 GATCTAAACA
Statistics
Matches: 1170, Mismatches: 169, Indels: 143
0.79 0.11 0.10
Matches are distributed among these distances:
178 4 0.00
179 141 0.12
180 3 0.00
182 1 0.00
184 1 0.00
188 2 0.00
189 1 0.00
190 1 0.00
191 2 0.00
194 1 0.00
195 1 0.00
196 1 0.00
199 5 0.00
200 419 0.36
201 36 0.03
202 85 0.07
203 292 0.25
204 4 0.00
206 2 0.00
207 1 0.00
208 1 0.00
210 3 0.00
212 38 0.03
213 5 0.00
214 14 0.01
215 104 0.09
216 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (199 bp):
TCGATACTTTAATATAAGTATCGATATTTTATTCCAGTATGCATCTCAAACAATTTGCACGAAAA
AAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTACTTTAAAGTA
ATAGGTAAATTTACAATGTAAACAGTAAAAATCTATCGGTTTAATGATAATAGGCGTAAACATAA
AGTA
Found at i:3798505 original size:415 final size:415
Alignment explanation
Indices: 3797927--3798750 Score: 1131
Period size: 415 Copynumber: 2.0 Consensus size: 415
3797917 TAAAGTATTG
* *
3797927 ATACTTATTATATAAGTACCAATACTTTTATTCCAGTATGCATCTCAAACAATTTTCACGCAAAA
1 ATACTTATTATATAAGTACCAATACTTTTATTCAAGTATGCATCTCAAACAATTTGCACGCAAAA
* ** *
3797992 AAAAGTATCGATACATATATAACAAGTATCGATACTTAGAATTTTGAAACCTTTTAGTTTAAAGT
66 AAAAGTATCGATACATATATAAAAAGTATCGATAAATAGAATTTTGAAACCTTTTACTTTAAAGT
* * * *
3798057 AATAGGTTAATATACAATGTAAACAGTAAAAATCTACAGGTTTAATGATAATAGGCGTAAACATA
131 AATAGGTAAATATACAATGCAAACAATAAAAATCTACAGGTTTAATGATAATAGGCATAAACATA
* * **
3798122 AAGTATCGATACGT-TTA-ATATAGATATCGATATTGTTATTCCCGTACGTTTCTCAAACAATTT
196 AAGTATCGATACCTATTATATA-AG-TATCGATATTGTTATTCCAGTACGCATCTCAAACAATTT
* * ** * * * * * *
3798185 GCATGTTAAGAGCATCGATACACATGT-ACAAACTATCGATACTTGGAATTTTGAATCCTTTTAC
259 ACAGGAAAAAAGCATCGATACACATATAAC-AACTATCGATACATAGAATTTTAAAACCTTTTAC
* *
3798249 TTTAAAGTAATAGGTAAATTTACAATGGAAGCTG-TAAAAATCTATCGGTTTAATGATAATAGGC
323 TTTAAAGTAATAGATAAATTTACAATGGAAAC-GATAAAAATCTATCGGTTTAATGATAATAGGC
3798313 GTAAACATAAAGTATAGATACTTATATAA
387 GTAAACATAAAGTATAGATACTTATATAA
* *
3798342 ATACTTATTATATAAGTATCGATGA-TTTTATTCAAGTATGCATCTCAAACAATTTGCACGCAAA
1 ATACTTATTATATAAGTACCAAT-ACTTTTATTCAAGTATGCATCTCAAACAATTTGCACGCAAA
**
3798406 AAATTGT-TCGATACATATATAAAAAAGTATCGATAAATAGAATTTTGAAACCTTTTACTTTAAA
65 AAAAAGTATCGATACATATAT-AAAAAGTATCGATAAATAGAATTTTGAAACCTTTTACTTTAAA
* * *
3798470 GTAATAGGTAAATTTATAATGCAAA-AATAAAAAATCTACCGGTTTAATGATAATAGGCATAAAC
129 GTAATAGGTAAATATACAATGCAAACAAT-AAAAATCTACAGGTTTAATGATAATAGGCATAAAC
* * *
3798534 ATAAAGTATCGATACCTATTATATAAGTATCGATATTTTTATTCTAGTATGCATCTCAAACAATT
193 ATAAAGTATCGATACCTATTATATAAGTATCGATATTGTTATTCCAGTACGCATCTCAAACAATT
* * * *
3798599 TACAGGAAAAAAGTATCGATGCATATATAACAAGTATCGATACATAGAATTTTAAAACCTTTTAC
258 TACAGGAAAAAAGCATCGATACACATATAACAACTATCGATACATAGAATTTTAAAACCTTTTAC
* * * *
3798664 TTTAAAGTTATATATAAATTTACAATGTAAACGATAAAAATCTATCGGTTTAATGATAATAGGTG
323 TTTAAAGTAATAGATAAATTTACAATGGAAACGATAAAAATCTATCGGTTTAATGATAATAGGCG
*
3798729 TAAACATAAAGTATCGATACTT
388 TAAACATAAAGTATAGATACTT
3798751 TTACTCCAAT
Statistics
Matches: 357, Mismatches: 45, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
414 16 0.04
415 330 0.92
416 8 0.02
417 3 0.01
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (415 bp):
ATACTTATTATATAAGTACCAATACTTTTATTCAAGTATGCATCTCAAACAATTTGCACGCAAAA
AAAAGTATCGATACATATATAAAAAGTATCGATAAATAGAATTTTGAAACCTTTTACTTTAAAGT
AATAGGTAAATATACAATGCAAACAATAAAAATCTACAGGTTTAATGATAATAGGCATAAACATA
AAGTATCGATACCTATTATATAAGTATCGATATTGTTATTCCAGTACGCATCTCAAACAATTTAC
AGGAAAAAAGCATCGATACACATATAACAACTATCGATACATAGAATTTTAAAACCTTTTACTTT
AAAGTAATAGATAAATTTACAATGGAAACGATAAAAATCTATCGGTTTAATGATAATAGGCGTAA
ACATAAAGTATAGATACTTATATAA
Found at i:3798863 original size:179 final size:179
Alignment explanation
Indices: 3798558--3798931 Score: 500
Period size: 179 Copynumber: 2.1 Consensus size: 179
3798548 CCTATTATAT
* * * * * * *
3798558 AAGTATCGATATTTTTATTCTAGTATGCATCTCAAACAATTTACAGGAAAAAAGTATCGATGCAT
1 AAGTATCGATATTTTTACTCCAATATGCATCTCAAACAATTTACACGAAAAAAGCATCGATACAC
* * *
3798623 ATATAACAAGTATCGATACATAGAATTTTAAAACCTTTTACTTTAAAGTTATATATAAATTTACA
66 ATATAACAAGTATCGATACATAGAATTTTAAAACCTATTACTTTAAAGTAATAGATAAATTTACA
* * *
3798688 ATGTAAACGATAAAAATCTATCGGTTTAATGATAATAGGTGTAAACATA
131 ATGGAAACGATAAAAATCTATAGGTTTAATGATAATAGGCGTAAACATA
* * * **
3798737 AAGTATCGATACTTTTACTCCAATATGCTTCTCAAACAATTTGCACGTCAAAAGCATCGATACAC
1 AAGTATCGATATTTTTACTCCAATATGCATCTCAAACAATTTACACGAAAAAAGCATCGATACAC
* * * *
3798802 ATGT-ACAATGTATCGATACTTGGAA-TTTAGAAACCTATTACTTTAAAGTAATAGGTAAATTTA
66 ATATAACAA-GTATCGATACATAGAATTTTA-AAACCTATTACTTTAAAGTAATAGATAAATTTA
* *
3798865 CAATGGAATCGGTAAAAATCTATAGGTTTAATGATAATAGGCGTAAACATA
129 CAATGGAAACGATAAAAATCTATAGGTTTAATGATAATAGGCGTAAACATA
3798916 AAGTATCGATATTTTT
1 AAGTATCGATATTTTT
3798932 TATTCAGGTA
Statistics
Matches: 168, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
178 8 0.05
179 160 0.95
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (179 bp):
AAGTATCGATATTTTTACTCCAATATGCATCTCAAACAATTTACACGAAAAAAGCATCGATACAC
ATATAACAAGTATCGATACATAGAATTTTAAAACCTATTACTTTAAAGTAATAGATAAATTTACA
ATGGAAACGATAAAAATCTATAGGTTTAATGATAATAGGCGTAAACATA
Found at i:3798962 original size:20 final size:20
Alignment explanation
Indices: 3798917--3798962 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
3798907 GTAAACATAA
*
3798917 AGTATCGATATTTTTTATTC
1 AGTATCGATATCTTTTATTC
3798937 AGGTATCGATA-CTTTTATTAC
1 A-GTATCGATATCTTTTATT-C
3798958 AGTAT
1 AGTAT
3798963 ACTTCTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (20 bp):
AGTATCGATATCTTTTATTC
Found at i:3799333 original size:582 final size:587
Alignment explanation
Indices: 3798171--3799333 Score: 1528
Period size: 582 Copynumber: 2.0 Consensus size: 587
3798161 TCCCGTACGT
* * *
3798171 TTCTCAAACAATTTGCATGTTAAGAGCATCGATACACATGTACAAACTATCGATACTTGGAATTT
1 TTCTCAAACAATTTGCACGTCAAAAGCATCGATACACATGTACAAACTATCGATACTTGGAATTT
* * * * *
3798236 TGAATCCTTTTACTTTAAAGTAATAGGTAAATTTACAATGGAAGCTGTAAAAATCTATCGGTTTA
66 AGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGGAAGCGGTAAAAATCTATAGGTTTA
*
3798301 ATGATAATAGGCGTAAACATAAAGTATAGATACTTATATAAATACTTATTATATAAGTATCGATG
131 ATGATAATAGGCGTAAACATAAAGTATAGATAC-TATAT--ATA-TTATTATACAAGTATCGATG
*
3798366 ATTTTATTCAAGTATGCATCTCAAACAATTTGCACGCAAAAAATTGTTCGATACATATATAAAAA
192 ATTTTATTCAAGTATACATCTCAAACAATTTGCACGCAAAAAA-TGTTCGATACATATAT--AAA
* * * *
3798431 AGTATCGATAAATAGAATTTTGAAACCTTTTACTTTAAAGTAATAGGTAAATTTATAATGCAAAA
254 AGTATCGATAAATAGAATTTCGAAACCTATTACTATAAAGTAATAGGTAAATTTACAATGCAAAA
*
3798496 ATAAAAAATCTACCGGTTTAATGATAATAGGCATAAACATAAAGTATCGATACCTATTATATAAG
319 ATAAAAAATCTACCGGTATAATGATAATAGGCATAAACATAAAGTATCGATACCTATTATATAAG
* * * *
3798561 TATCGATATTTTTATTCTAGTATGCATCTCAAACAATTTACAGGAAAAAAGTATCGATGCATATA
384 TATCGATACTATTATTCTAGTATGCATCTCAAACAATTTACAGCAAAAAAGTATCGATACATATA
** * *
3798626 TAACAAGTATCGATACATAGAATTTTAAAACCTTTTACTTTAAAGTTATATATAAATTTACAATG
449 TAACAAGTATCGATACATAGAATTTTAAAACCTAGTACTTTAAAGTAATAGATAAATTTACAATG
* * * *
3798691 TAAACGATAAAAATCTATCGGTTTAATGATAATAGGTGTAAACATAAAGTATCGATACTTTTACT
514 TAAACGATAAAAATCGACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTACT
3798756 CCAATATGC
579 CCAATATGC
**
3798765 TTCTCAAACAATTTGCACGTCAAAAGCATCGATACACATGTACAATGTATCGATACTTGGAATTT
1 TTCTCAAACAATTTGCACGTCAAAAGCATCGATACACATGTACAAACTATCGATACTTGGAATTT
*
3798830 AGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGGAATCGGTAAAAATCTATAGGTTTA
66 AGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGGAAGCGGTAAAAATCTATAGGTTTA
* *
3798895 ATGATAATAGGCGTAAACATAAAGTATCGATA-T-T-T-T-TTA-T-T-CAGGTATCGAT-ACTT
131 ATGATAATAGGCGTAAACATAAAGTATAGATACTATATATATTATTATACAAGTATCGATGA-TT
* * *
3798951 TTATT-ACAGTATACTTCTCAAATAATTTGTACGC-AAAAA-GTATCGATAAGCATATAT-AAAG
195 TTATTCA-AGTATACATCTCAAACAATTTGCACGCAAAAAATGT-TCGAT-A-CATATATAAAAG
* ** * * * * **
3799012 TATTGATACTTGGAGTTTCGAAACCTATTACTATAAAGTAATAGGTTAATTTACAATGTAAACGG
256 TATCGATAAATAGAATTTCGAAACCTATTACTATAAAGTAATAGGTAAATTTACAATGCAAA-AA
* * * * *
3799077 T-AAATATCTACCGGTATAATGATAATAGGCGTAAACTTAAAGTATCGATACTTAGTATATATAT
320 TAAAAAATCTACCGGTATAATGATAATAGGCATAAACATAAAGTATCGATACCTA-T-TATATAA
* *
3799141 GTATCGATACTATTATTCTAGTATGCATCTCAAATAGTTTGCACA-CAAAAAAGTATCGATACAT
383 GTATCGATACTATTATTCTAGTATGCATCTCAAACAATTT--ACAGCAAAAAAGTATCGATACAT
* * * *
3799205 ATATAACAAGTATCGTTACTTAGAATTTTGAAACCTAGTACTTTAAAGTAATAGGTAAATTTACA
446 ATATAACAAGTATCGATACATAGAATTTTAAAACCTAGTACTTTAAAGTAATAGATAAATTTACA
* * ** *
3799270 ATGTAAACGGTAAAAGTCGACCAGTTTAATGATAATAGGCGTAAATTTCAAGTATCGATACTTT
511 ATGTAAACGATAAAAATCGACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTT
3799334 AGATCTAAAC
Statistics
Matches: 499, Mismatches: 60, Indels: 32
0.84 0.10 0.05
Matches are distributed among these distances:
579 105 0.21
580 7 0.01
581 50 0.10
582 175 0.35
583 4 0.01
584 1 0.00
585 3 0.01
587 1 0.00
590 1 0.00
591 1 0.00
592 1 0.00
594 150 0.30
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (587 bp):
TTCTCAAACAATTTGCACGTCAAAAGCATCGATACACATGTACAAACTATCGATACTTGGAATTT
AGAAACCTATTACTTTAAAGTAATAGGTAAATTTACAATGGAAGCGGTAAAAATCTATAGGTTTA
ATGATAATAGGCGTAAACATAAAGTATAGATACTATATATATTATTATACAAGTATCGATGATTT
TATTCAAGTATACATCTCAAACAATTTGCACGCAAAAAATGTTCGATACATATATAAAAGTATCG
ATAAATAGAATTTCGAAACCTATTACTATAAAGTAATAGGTAAATTTACAATGCAAAAATAAAAA
ATCTACCGGTATAATGATAATAGGCATAAACATAAAGTATCGATACCTATTATATAAGTATCGAT
ACTATTATTCTAGTATGCATCTCAAACAATTTACAGCAAAAAAGTATCGATACATATATAACAAG
TATCGATACATAGAATTTTAAAACCTAGTACTTTAAAGTAATAGATAAATTTACAATGTAAACGA
TAAAAATCGACCAGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTTACTCCAATAT
GC
Found at i:3799892 original size:18 final size:19
Alignment explanation
Indices: 3799841--3799886 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
3799831 AACCAAAACC
3799841 TTCTTCTCAACCAAGGTCA
1 TTCTTCTCAACCAAGGTCA
3799860 -TCTTCTCAACCAAGGT-A
1 TTCTTCTCAACCAAGGTCA
3799877 TTCTTCTCAA
1 TTCTTCTCAA
3799887 GTAAGGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.26, C:0.30, G:0.09, T:0.35
Consensus pattern (19 bp):
TTCTTCTCAACCAAGGTCA
Found at i:3799898 original size:18 final size:18
Alignment explanation
Indices: 3799826--3799886 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
3799816 GACGCAGTTA
***
3799826 TTCTCAACCAAAACCTTC
1 TTCTCAACCAAGGTCTTC
*
3799844 TTCTCAACCAAGGTCATC
1 TTCTCAACCAAGGTCTTC
*
3799862 TTCTCAACCAAGGTATTC
1 TTCTCAACCAAGGTCTTC
3799880 TTCTCAA
1 TTCTCAA
3799887 GTAAGGGCTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.31
Consensus pattern (18 bp):
TTCTCAACCAAGGTCTTC
Found at i:3805537 original size:19 final size:21
Alignment explanation
Indices: 3805513--3805564 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3805503 CGGCCAAGAG
*
3805513 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
3805532 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
3805553 CATGTATTTTCA
1 CATGTATTTTCA
3805565 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:3805941 original size:13 final size:12
Alignment explanation
Indices: 3805921--3805954 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3805911 ATCTTTATTT
3805921 CATCATCAAGATC
1 CATCATCAAGA-C
*
3805934 CTTCATCAAGAC
1 CATCATCAAGAC
3805946 CATCATCAA
1 CATCATCAA
3805955 TCCCATAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24
Consensus pattern (12 bp):
CATCATCAAGAC
Found at i:3809494 original size:19 final size:21
Alignment explanation
Indices: 3809466--3809515 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3809456 GCCAAGAGCT
* *
3809466 TGTATCTTCA-TT-AAAATCA
1 TGTATTTTCATTTAAAAATAA
3809485 TGTATTTTCATTTAAAAATAA
1 TGTATTTTCATTTAAAAATAA
3809506 TGTATTTTCA
1 TGTATTTTCA
3809516 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 16 0.59
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (21 bp):
TGTATTTTCATTTAAAAATAA
Found at i:3812910 original size:20 final size:21
Alignment explanation
Indices: 3812885--3812924 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3812875 CAAACAATTT
3812885 CCCATA-ACAAAGTATCGATA
1 CCCATATACAAAGTATCGATA
*
3812905 CCCATATATAAAGTATCGAT
1 CCCATATACAAAGTATCGAT
3812925 TCTTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.25
Consensus pattern (21 bp):
CCCATATACAAAGTATCGATA
Found at i:3813171 original size:202 final size:197
Alignment explanation
Indices: 3812827--3814736 Score: 1488
Period size: 200 Copynumber: 9.7 Consensus size: 197
3812817 TGTCCAAGTT
** * **
3812827 TTGATACTTTTTATATTCGTATCGATACTTTTATTCTAGTATGGTTCTCAAACAATTTCCCATAA
1 TTGATAC-TTTTATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAATTTCCCGCAA
* **
3812892 CAAAGTATCGATACCCATATATA-AAGTATCGATTCTTGGAATTTCAAAACCTATTACTTTAAAG
65 -AAAGTATCGATA--CATATATACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAG
* *
3812956 TAATAGGTAAATTTACAATGGAAACGGTAAAAATCTATCAGTTTAATGATAATAGGTGTAAACAT
127 TAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACAT
*
3813021 AAATTA
192 AAAATA
* *
3813027 TTGATACTTATTATATAAGTATCGATACTTTTTATTCCAGTATGCATCTCAAACAATTTCCACGC
1 TTGATACTT-TTATATAAGTATCGATAC-TTTTATTCTAGTATGCTTCTCAAACAATTTCC-CGC
* ** *
3813092 AAAAAAGTATCGATACATATATAACAAGTATTGATACTTATAATTTTGAAACCTTTTACTTTAAA
63 -AAAAAGTATCGATACATATAT-ACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAA
*
3813157 GTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAAAGATAATAGGTGTAAACA
126 GTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACA
3813222 TAAAATA
191 TAAAATA
* * * *
3813229 TCGATATCTTTAATATAGGTATCGATACTTTTATTATAGTATGCTTCTCAAACAATTT---GC--
1 TTGATA-CTTTTATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAATTTCCCGCAA
* * * * *
3813289 -ACGTATCGATACACATGTACAAAGTATCGATGCTTGGAATTTTGAAACCTATTACTCTAAAGTA
65 AAAGTATCGATACATATATAC-AAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGTA
* * * *
3813353 ATAGGAAAATTTACAATGTAAACGGTAAAAATCTACCGGTTTAATGATAATGGGCGTAAACAT--
129 ATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACATAA
3813416 -A-A
194 AATA
* * * * * * ** *
3813418 --G----------GT-A-TAT--ATACTGTTATTCCAGTATGCATCTCACACAGTTTGTTCACAA
1 TTGATACTTTTATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAATTT-CCCGCAA
* * * * * *
3813467 AAAGTATCGCTACACATATAACAAGTATCGATTCTTGGACTTTCGAAACCTATTACTTTAAGGTA
65 AAAGTATCGATACATATAT-ACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGTA
* * *
3813532 ATACGTAAATTTAAAATGTAAACGGTAAAAATCTA-C----T-A-GATAATAGGCGTAAACATAA
129 ATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACATAA
*
3813590 AGTA
194 AATA
* * * * * *
3813594 CCT-ATAGTTATTATATAGGTATCGATA-TTATCATTCCAGTATG-TATCTCAAACAATTTGCAC
1 -TTGATACTT-TTATATAAGTATCGATACTT-TTATTCTAGTATGCT-TCTCAAACAATTT-CCC
* * * * *
3813656 GCAAAAAGTATTGATACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTGTTACTTTAA
61 GCAAAAAGTATCGATACATATAT-ACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAA
** * *
3813721 AGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTA-TTGATTTAATGATAATGGGCGTAAA
125 AGTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAG-TTTAATGATAATAGGTGTAAA
*
3813785 CATAAAGTA
189 CATAAAATA
* * ** * * *
3813794 TTGATACTTATTATATAGGTATCGATACTATTATTCCGGTATGCATCTCAAACAATTTTCTCGTA
1 TTGATACTT-TTATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAA-TTTCCCGCA
* * * *
3813859 AAAAGTATCGCTACACATATAACAAGTATCGATACTTGGACTTTCGAAACCTATTACTTTAAAGT
64 AAAAGTATCGATACATATAT-ACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGT
* * * * *
3813924 AATAGGCAAATTTACAATGTAAACGGTAAAATTCTACCGGTTCAATGATAATTGGTGTAAACATA
128 AATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACATA
*
3813989 AAGTA
193 AAATA
*** * * * * * **
3813994 CCAATACTTATTATATAGGTATCGATACTGTTATAATC-GGTATGCATCTCAAAAAATTTGAACG
1 TTGATACTT-TTATATAAGTATCGATACT-TT-TATTCTAGTATGCTTCTCAAACAATTT-CCCG
* * * ** *
3814058 CAAAAAGTCTCGATACACATATAACAA-TATCGATACTTGGACTTTCAAAACCTGTTACTTTAAA
62 CAAAAAGTATCGATACATATAT-ACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAA
* * **** **
3814122 GTAATAGGTAAATTAACAATGTAAACGTTAAAAATCTTTTGGTTTAATGATAATAGGCCTAAACA
126 GTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACA
*
3814187 TAAAGTA
191 TAAAATA
* * *
3814194 TTGATACGTTTA-ATATAGATATCGATACTTATT-TTCCAGTATGCTTCTCAAACAATTTGCACG
1 TTGATACTTTTATATA-AG-TATCGATACTT-TTATTCTAGTATGCTTCTCAAACAATTT-CCCG
* * * * * *
3814257 TC-AAAAGCATCGATACACATGTTCAAAGTATCGATGCTTGGAATTTTGAAACCTATTACTATAA
62 -CAAAAAGTATCGATACATATATAC-AAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAA
* * * * * ** * * *
3814321 AGCAATAGGTAAATTAACAATGTAAAAGGTAAAAGTTTTACTGGTATAATGATAATAGGCGTATA
125 AGTAATAGGTAAATTTACAATGTAAACGGTAAAA-ATCTACCAGTTTAATGATAATAGGTGTAAA
* ** * *
3814386 TACCAAGTG
189 CATAAAATA
* * * * * *
3814395 TCGATAC-TTTATATACATGTATCGAT-GTTGTTAGTCCAGTATGTTTCTC-AACAATTTGCACG
1 TTGATACTTTTATATA-A-GTATCGATACTT-TTATTCTAGTATGCTTCTCAAACAATTT-CCCG
* * * * ** * * *
3814457 CTAAATGTATCGATACACATGTACAAAGTATCGATACCCGTAATTTTGAAACCGATTTCTTTAAA
62 CAAAAAGTATCGATACATATATAC-AAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAA
* ** * * ** **
3814522 GTAATAGGTAAATTTACAATGTAAACGGTAAAAGTCTACTGGTATATTGATAATAGACGTAAATG
126 GTAATAGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACA
** *
3814587 CCAAGTA
191 TAAAATA
* * ** * * * * * *
3814594 TCGATA-TTGTCTATATATGTATAAATACATTCATTCAAGTATGTTTCTCAAGCAATTTGCACGC
1 TTGATACTT-T-TATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAATTT-CCCGC
* * * **
3814658 AAAAGGCATTGATACACGTATATA-AAGTATCGAATACTTATAATTTTGAAACCTATTACTTT-A
63 AAAAAGTATCGATACA--TATATACAAGTATCG-ATACTTGGAATTTTGAAACCTATTACTTTAA
*
3814721 AGTAATAGGTTAATTT
125 AGTAATAGGTAAATTT
3814737 TGAAAACGAT
Statistics
Matches: 1433, Mismatches: 202, Indels: 150
0.80 0.11 0.08
Matches are distributed among these distances:
172 45 0.03
173 1 0.00
174 4 0.00
176 3 0.00
178 1 0.00
179 85 0.06
180 2 0.00
187 1 0.00
189 2 0.00
190 1 0.00
191 3 0.00
192 3 0.00
193 234 0.16
197 2 0.00
198 7 0.00
199 113 0.08
200 582 0.41
201 195 0.14
202 144 0.10
203 5 0.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (197 bp):
TTGATACTTTTATATAAGTATCGATACTTTTATTCTAGTATGCTTCTCAAACAATTTCCCGCAAA
AAGTATCGATACATATATACAAGTATCGATACTTGGAATTTTGAAACCTATTACTTTAAAGTAAT
AGGTAAATTTACAATGTAAACGGTAAAAATCTACCAGTTTAATGATAATAGGTGTAAACATAAAA
TA
Found at i:3814892 original size:20 final size:20
Alignment explanation
Indices: 3814867--3814905 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3814857 CGTTTCTACC
3814867 GGTAAATTAACAATGTACAT
1 GGTAAATTAACAATGTACAT
3814887 GGTAAATTAACAATGTACA
1 GGTAAATTAACAATGTACA
3814906 AGTATCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (20 bp):
GGTAAATTAACAATGTACAT
Found at i:3815449 original size:215 final size:215
Alignment explanation
Indices: 3815078--3815468 Score: 595
Period size: 215 Copynumber: 1.8 Consensus size: 215
3815068 AGCTTTAAAC
* * * * *
3815078 AGGCGCTACCTATTTCATTAATTAAGCGCTACTTGTTATGTTATTATGGCTAATAATATTTCTAG
1 AGGCGCTACCTATTACATTAAATAAGCACTACTTGTTATATTATTATAGCTAATAATATTTCTAG
* * *
3815143 TAATTAACATATTTTGTTAACGTCTGATTTCTAAGGCTCCATCAGCTTAAACTTTGGAAACGTTT
66 TAATTAACATATTTTGATAACGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGAAACATTT
3815208 TAGACACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAAACGATTTTGTTATTG
131 TAGACACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAAACGATTTTGTTATTG
3815273 TCAAATTTCTAAAGCCTTAT
196 TCAAATTTCTAAAGCCTTAT
* * *
3815293 AGGCGCTACCTATTACATTAAATAAGCACTACTTGTTATATTATTATAGTTGATAATGTTTCCT-
1 AGGCGCTACCTATTACATTAAATAAGCACTACTTGTTATATTATTATAGCTAATAATATTT-CTA
* * * *
3815357 GTAATTAACATATTTTGATATCGTCGGATTTTTAAGGTTCCATCAGCTTAAACTTTGGTAACATT
65 GTAATTAACATATTTTGATAACGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGAAACATT
*** *
3815422 TTAGGTGCTACCTAATATGTTGATAATATTGATAACAAATCAAGTAA
130 TTAGACACTACCTAATATATTGATAATATTGATAACAAATCAAGTAA
3815469 ATAACCTCTT
Statistics
Matches: 156, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
215 154 0.99
216 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (215 bp):
AGGCGCTACCTATTACATTAAATAAGCACTACTTGTTATATTATTATAGCTAATAATATTTCTAG
TAATTAACATATTTTGATAACGTCGGATTTCTAAGGCTCCATCAGCTTAAACTTTGGAAACATTT
TAGACACTACCTAATATATTGATAATATTGATAACAAATCAAGTAATTAAACGATTTTGTTATTG
TCAAATTTCTAAAGCCTTAT
Found at i:3821328 original size:27 final size:28
Alignment explanation
Indices: 3821281--3821333 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
3821271 AAACAATTGA
*
3821281 AGCACTCCAAAAGAAAGAAAG-AAATCC
1 AGCACTCAAAAAGAAAGAAAGCAAATCC
3821308 AGCACTCAAAAAG-AAGAAAAGCAAAT
1 AGCACTCAAAAAGAAAG-AAAGCAAAT
3821334 AAAAGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 16 0.70
28 4 0.17
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (28 bp):
AGCACTCAAAAAGAAAGAAAGCAAATCC
Found at i:3822673 original size:24 final size:24
Alignment explanation
Indices: 3822606--3822673 Score: 57
Period size: 24 Copynumber: 2.8 Consensus size: 24
3822596 GACATGTCCT
* * *
3822606 TTGAGGTTCCAACAA-TTATGTCTC
1 TTGAAGTTCC-ACAAGTTGTGTCAC
* * * *
3822630 TAGAAGTTCAAAAAGATGTGTCAC
1 TTGAAGTTCCACAAGTTGTGTCAC
3822654 TTGAAGTTCCACAAGTTGTG
1 TTGAAGTTCCACAAGTTGTG
3822674 ATTATTGAGG
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
23 3 0.09
24 29 0.91
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (24 bp):
TTGAAGTTCCACAAGTTGTGTCAC
Found at i:3826408 original size:113 final size:113
Alignment explanation
Indices: 3826246--3826454 Score: 276
Period size: 113 Copynumber: 1.8 Consensus size: 113
3826236 AGTATCGATC
* * * *
3826246 TTGACTCTCTTAGGACTTGTATCATAGAAATCTCAATCTAGTATTTCTTAAGATTATTTCTCTAG
1 TTGACTCTCTTAGGACTTATATCATAGAAAGCTCAAGCTAGTATTTCTTAAGATCATTTCTCTAG
3826311 AAACCTCAATTCGGTCTTTCTAAAGATTGTTCTCTAAGGAACCTCAAT
66 AAACCTCAATTCGGTCTTTCTAAAGATTGTTCTCTAAGGAACCTCAAT
* * * * * *
3826359 TTGATTCTCTTAGGACTTATATCCTAGAAAGCT-TAGCATAGTCTTTCTTAAGATCATTTTTGTA
1 TTGACTCTCTTAGGACTTATATCATAGAAAGCTCAAGC-TAGTATTTCTTAAGATCATTTCTCTA
* * **
3826423 GAATCCTTAATTTTGTCTTTCTAAAGATTGTT
65 GAAACCTCAATTCGGTCTTTCTAAAGATTGTT
3826455 TCCCAAGGGA
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
112 2 0.02
113 79 0.98
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (113 bp):
TTGACTCTCTTAGGACTTATATCATAGAAAGCTCAAGCTAGTATTTCTTAAGATCATTTCTCTAG
AAACCTCAATTCGGTCTTTCTAAAGATTGTTCTCTAAGGAACCTCAAT
Found at i:3829033 original size:41 final size:41
Alignment explanation
Indices: 3828976--3829057 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3828966 TTGAACCCTT
3828976 GGACATCAATGAATTCATTCCCCCAAAATCATCATTATAGC
1 GGACATCAATGAATTCATTCCCCCAAAATCATCATTATAGC
3829017 GGACATCAATGAATTCATTCCCCCAAAATCATCATTATAGC
1 GGACATCAATGAATTCATTCCCCCAAAATCATCATTATAGC
3829058 ATGCACCTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (41 bp):
GGACATCAATGAATTCATTCCCCCAAAATCATCATTATAGC
Found at i:3831592 original size:12 final size:12
Alignment explanation
Indices: 3831552--3831584 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3831542 GCACGAGTTG
3831552 TTTATT-TTTAT
1 TTTATTCTTTAT
3831563 TTTATTCTTTAT
1 TTTATTCTTTAT
3831575 TTTATTCTTT
1 TTTATTCTTT
3831585 TTTATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTCTTTAT
Found at i:3844584 original size:29 final size:30
Alignment explanation
Indices: 3844538--3844599 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
3844528 AAATTTTAGC
* *
3844538 TAGTAACCAAAATGTAAATTTTGAAA-GTT
1 TAGTAACCAAAATATAAATTTGGAAATGTT
*
3844567 TAGTAACCAAAGTATAAATTTGGAAATGTT
1 TAGTAACCAAAATATAAATTTGGAAATGTT
3844597 TAG
1 TAG
3844600 GGATCACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (30 bp):
TAGTAACCAAAATATAAATTTGGAAATGTT
Found at i:3845617 original size:41 final size:38
Alignment explanation
Indices: 3845547--3845623 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
3845537 AGTTGAAAAG
* *
3845547 AATAATAAAATAAATATATTATACTAAATAAAAGGGAA
1 AATAATAAAATAAAAATAATATACTAAATAAAAGGGAA
*
3845585 AATAATAAAATAATAAATAATAGTATTAAAATAAAAGGG
1 AATAATAAAATAA-AAATAATA-TACT-AAATAAAAGGG
3845624 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 13 0.39
39 6 0.18
40 3 0.09
41 11 0.33
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (38 bp):
AATAATAAAATAAAAATAATATACTAAATAAAAGGGAA
Found at i:3846336 original size:64 final size:63
Alignment explanation
Indices: 3846267--3846388 Score: 201
Period size: 64 Copynumber: 1.9 Consensus size: 63
3846257 TAAAACATCT
3846267 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATACCTAAAAAA-AATATAATATTC
* *
3846331 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAA
1 TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAA
3846389 AATATAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 12 0.22
64 43 0.78
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (63 bp):
TAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAATATTC
Found at i:3846358 original size:19 final size:19
Alignment explanation
Indices: 3846302--3846364 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
3846292 CTATTTAAAC
**
3846302 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
3846322 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
3846342 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
3846361 TAAA
1 TAAA
3846365 CTAAAATACC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:3846389 original size:25 final size:24
Alignment explanation
Indices: 3846342--3846389 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
3846332 AAATCCTAAT
** *
3846342 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
3846366 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
3846390 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:3846461 original size:76 final size:74
Alignment explanation
Indices: 3846338--3846485 Score: 199
Period size: 76 Copynumber: 2.0 Consensus size: 74
3846328 TTCTAAATCC
* *
3846338 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAATATT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATA-CAAAAAAAAATATAAAAT-TAAAAATATT
3846403 ATCCTAAAACT
64 ATCCTAAAACT
* ** *
3846414 TAATTAAAATACTAAACCCTATTTAAACTAAAATA-AAAAGATAAAATATAATGTTTAAAATATT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAA-A-AAAATATAAAATTAAAAATATT
3846478 ATCCTAAA
64 ATCCTAAA
3846486 CTTGAGTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
74 3 0.05
75 18 0.28
76 43 0.67
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.30
Consensus pattern (74 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAAAAAAATATAAAATTAAAAATATTAT
CCTAAAACT
Done.