Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007960.1 Hibiscus syriacus cultivar Beakdansim tig00110387_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: 7905731
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 39
Found at i:5360887 original size:68 final size:68
Alignment explanation
Indices: 5360791--5360943 Score: 200
Period size: 68 Copynumber: 2.2 Consensus size: 68
5360781 ACCCATTCAA
* * * *
5360791 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
5360855 GGGG
66 -GGG
* * * * *
5360859 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCATA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
5360924 GGG
66 GGG
*
5360927 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
5360944 ATGAGAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 45 0.61
69 29 0.39
ACGTcount: A:0.27, C:0.26, G:0.28, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCACA
GGG
Found at i:5361280 original size:29 final size:29
Alignment explanation
Indices: 5361246--5361317 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
5361236 CATATTATGA
** *
5361246 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
5361275 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
5361304 TACATGACATGAAT
1 TACATGACATGAAT
5361318 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:5361374 original size:30 final size:29
Alignment explanation
Indices: 5361331--5361408 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
5361321 CAGAAAAAGT
*
5361331 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
5361361 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
5361391 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
5361409 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:5361685 original size:22 final size:22
Alignment explanation
Indices: 5361611--5361677 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
5361601 TTATGGACAT
5361611 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
*
5361633 AATTCTACGGGCACATCGGTGC
1 AATTCTACGGGCACTTCGGTGC
5361655 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
5361677 A
1 A
5361678 TTTATACGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:5365279 original size:95 final size:95
Alignment explanation
Indices: 5365168--5365368 Score: 321
Period size: 95 Copynumber: 2.1 Consensus size: 95
5365158 AGATTATAAT
* * *
5365168 ATTATATATATACAATAAAGCTTGAGTTGTCCCTCTAAAGTAATTGGTTAAACGACCCGGATTTA
1 ATTATA-ATATACAATAAAGCTTGAATTGTCACTCTAAAGGAATTGGTTAAACGACCCGGATTTA
*
5365233 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTAAGCTAGCCTGATAAAGGTG
* * * *
5365264 ATTATAATATACAATAAAGCTTGAATTGTCATTCTAAAGGAATTGGTTAAATGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAATTGTCACTCTAAAGGAATTGGTTAAACGACCCGGATTTAT
5365329 GGATAAGATTAAGCTAGCCTGATAAAGGTG
66 GGATAAGATTAAGCTAGCCTGATAAAGGTG
5365359 ATTATAATAT
1 ATTATAATAT
5365369 TGAGCTGTCC
Statistics
Matches: 97, Mismatches: 8, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
95 91 0.94
96 6 0.06
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAATTGTCACTCTAAAGGAATTGGTTAAACGACCCGGATTTAT
GGATAAGATTAAGCTAGCCTGATAAAGGTG
Found at i:5366645 original size:86 final size:86
Alignment explanation
Indices: 5366498--5366716 Score: 210
Period size: 86 Copynumber: 2.5 Consensus size: 86
5366488 GGAGTCACTC
* * * ** * * *
5366498 GAAGAACATCCCATATGGTTTTCCCATGAAGAGGAGTCATCCAAAGATCGTCTCACCTGGTTTAG
1 GAAGAATATACCATATGGATTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAG
**
5366563 ACTCGTG-AAAGGG-GGCCACCT
66 A-TC-TGCAAAGGGAAACCACCT
* * * *
5366584 GAAGAATATACCATATGGCTTTCCTGTGAAGGGGAGTCATCCAAATATCATCTTACTTGGTTCAG
1 GAAGAATATACCATATGGATTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAG
*
5366649 ATCTGCTAAGGGAAACCACCT
66 ATCTGCAAAGGGAAACCACCT
* * * * *
5366670 GAGGAATATACCACATGAATTT-TTCGTGAAGGGGATTCATCCAAAGA
1 GAAGAATATACCATATGGATTTCCT-GTGAAGGGGAGTCATCCAAAGA
5366717 CCTTCGAGCT
Statistics
Matches: 109, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
84 2 0.02
85 8 0.07
86 99 0.91
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (86 bp):
GAAGAATATACCATATGGATTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAG
ATCTGCAAAGGGAAACCACCT
Found at i:5366815 original size:85 final size:85
Alignment explanation
Indices: 5366711--5366997 Score: 344
Period size: 85 Copynumber: 3.4 Consensus size: 85
5366701 GGGATTCATC
* * * * * *
5366711 CAAAGACCTTCGAGCTCGATTACATTTAGCTTAAGGGCCTATCAAATTTATAGCATAGCTCAAGG
1 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGG
5366776 CGAGAAGGGTTATCTATCAA
66 CGAGAAGGGTTATCTATCAA
* *
5366796 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGACATATCAAATTTACAGTATAACTCAAGG
1 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGG
*
5366861 CGAGAAGGGTTATCTGTCAA
66 CGAGAAGGGTTATCTATCAA
* * * * * *
5366881 CAAATACCTTCAAGTTCGATTTCATTCAGCTCAAGGGCATGTCAAATTTACAGCATAACTTAAGA
1 CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGG
* * * *
5366946 CAAGGAA-AGTTATTTGTCAA
66 CGA-GAAGGGTTATCTATCAA
* * *
5366966 CAAA-AACTATTGAGTTCGATTCCATTCAGCTC
1 CAAAGACCT-TCGAGTTCGATTACATTCAGCTC
5366998 GACGATACAT
Statistics
Matches: 176, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
84 3 0.02
85 170 0.97
86 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (85 bp):
CAAAGACCTTCGAGTTCGATTACATTCAGCTCAAGGGCATATCAAATTTACAGCATAACTCAAGG
CGAGAAGGGTTATCTATCAA
Found at i:5369003 original size:20 final size:20
Alignment explanation
Indices: 5368978--5369017 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5368968 TCGTTGCAGC
*
5368978 CAGGGTGCATGGATGCACTG
1 CAGGGTGCATCGATGCACTG
5368998 CAGGGTGCATCGATGCACTG
1 CAGGGTGCATCGATGCACTG
5369018 TGCATCGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.38, T:0.20
Consensus pattern (20 bp):
CAGGGTGCATCGATGCACTG
Found at i:5369020 original size:15 final size:15
Alignment explanation
Indices: 5369002--5369031 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5368992 GCACTGCAGG
*
5369002 GTGCATCGATGCACT
1 GTGCATCGATACACT
5369017 GTGCATCGATACACT
1 GTGCATCGATACACT
5369032 TGTGGTGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (15 bp):
GTGCATCGATACACT
Found at i:5369138 original size:20 final size:20
Alignment explanation
Indices: 5369110--5369190 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
5369100 GGTGCATCGA
* *
5369110 TGCACAGTGTATGGATACAC
1 TGCAGAGTGCATGGATACAC
5369130 TGCAGAGTGCATGGATACAC
1 TGCAGAGTGCATGGATACAC
* *
5369150 TGCAGGGTGCATGGATACAT
1 TGCAGAGTGCATGGATACAC
* * *
5369170 TGCAGGGTGTATGAATACAC
1 TGCAGAGTGCATGGATACAC
5369190 T
1 T
5369191 TTGACACCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (20 bp):
TGCAGAGTGCATGGATACAC
Found at i:5369437 original size:21 final size:19
Alignment explanation
Indices: 5369413--5369470 Score: 91
Period size: 18 Copynumber: 3.0 Consensus size: 19
5369403 ATATTTAATG
5369413 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
5369432 ACAAAATGATATCAATTGTT-
1 A-AAAA-GATATCAATTGTTA
5369452 AAAAAGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
5369471 CCAATTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.36
19 5 0.14
20 5 0.14
21 13 0.36
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTA
Found at i:5372571 original size:31 final size:31
Alignment explanation
Indices: 5372525--5372616 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
5372515 GGTCATAAAG
* *
5372525 AACCTCGA-AAACTATCCATAGGTCCCGAAA
1 AACCTAGATAAACTATCCATATGTCCCGAAA
* * *
5372555 AACCTAGATAAACTATCCATATATCCCGTAG
1 AACCTAGATAAACTATCCATATGTCCCGAAA
* * *
5372586 AACATAGGTAAACTGTCCATATGTCCCGAAA
1 AACCTAGATAAACTATCCATATGTCCCGAAA
5372617 GACAGGTAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
30 7 0.14
31 43 0.86
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (31 bp):
AACCTAGATAAACTATCCATATGTCCCGAAA
Found at i:5372624 original size:29 final size:29
Alignment explanation
Indices: 5372533--5372627 Score: 91
Period size: 31 Copynumber: 3.1 Consensus size: 29
5372523 AGAACCTCGA
* *
5372533 AAACTATCCATAGGTCCCGAAAAACCTAGAT
1 AAACTATCCATATGTCCCGAAAAA-C-AGGT
* * *
5372564 AAACTATCCATATATCCCGTAGAACATAGGT
1 AAACTATCCATATGTCCCG-A-AAAACAGGT
* *
5372595 AAACTGTCCATATGTCCCGAAAGACAGGT
1 AAACTATCCATATGTCCCGAAAAACAGGT
5372624 AAAC
1 AAAC
5372628 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
29 11 0.21
30 1 0.02
31 37 0.70
32 1 0.02
33 3 0.06
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (29 bp):
AAACTATCCATATGTCCCGAAAAACAGGT
Found at i:5373508 original size:26 final size:26
Alignment explanation
Indices: 5373474--5373526 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
5373464 CCCTTAACGA
5373474 GTGCATCGATGCACTATATATGTATC
1 GTGCATCGATGCACTATATATGTATC
5373500 GTGCATCGATGCACTATATATGTATC
1 GTGCATCGATGCACTATATATGTATC
5373526 G
1 G
5373527 GTACACAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (26 bp):
GTGCATCGATGCACTATATATGTATC
Found at i:5374609 original size:20 final size:20
Alignment explanation
Indices: 5374581--5374624 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5374571 GGTGCATCGA
*
5374581 TGCACAGTGTATGGATACAC
1 TGCACAGTGCATGGATACAC
*
5374601 TGCAGAGTGCATGGATACAC
1 TGCACAGTGCATGGATACAC
5374621 TGCA
1 TGCA
5374625 TGGTGTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (20 bp):
TGCACAGTGCATGGATACAC
Found at i:5375832 original size:13 final size:13
Alignment explanation
Indices: 5375816--5375845 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5375806 TGAATTGAAT
5375816 TTTTAAATTTTAA
1 TTTTAAATTTTAA
5375829 TTTTAAATTTTAA
1 TTTTAAATTTTAA
5375842 TTTT
1 TTTT
5375846 CGCGACTAAG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:5381048 original size:20 final size:20
Alignment explanation
Indices: 5381020--5381058 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5381010 AGAAGTAATA
* *
5381020 TGGTTGTTACAGTTTGTTAG
1 TGGTAGTTACAGTTAGTTAG
*
5381040 TGGTAGTTAGAGTTAGTTA
1 TGGTAGTTACAGTTAGTTA
5381059 CATGTAGTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.46
Consensus pattern (20 bp):
TGGTAGTTACAGTTAGTTAG
Found at i:5383904 original size:18 final size:19
Alignment explanation
Indices: 5383874--5383915 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5383864 TATAAAAAAG
*
5383874 TTTT-TAGTGTTTTATTTT
1 TTTTATAGTGTTTTATTAT
*
5383892 TTTTATAGT-TTTTCTTAT
1 TTTTATAGTGTTTTATTAT
5383910 TTTTAT
1 TTTTAT
5383916 GATTTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTATAGTGTTTTATTAT
Found at i:5385551 original size:16 final size:16
Alignment explanation
Indices: 5385530--5385564 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5385520 ACTAAAACAA
5385530 GGAAGCAGCATGGACC
1 GGAAGCAGCATGGACC
5385546 GGAAGCAGCATGGACC
1 GGAAGCAGCATGGACC
5385562 GGA
1 GGA
5385565 TATCACCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.23, G:0.40, T:0.06
Consensus pattern (16 bp):
GGAAGCAGCATGGACC
Found at i:5388375 original size:21 final size:21
Alignment explanation
Indices: 5388348--5388421 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
5388338 ATGTTGAGTA
5388348 GTATCGATACCGATTCAAGTG
1 GTATCGATACCGATTCAAGTG
* *
5388369 ATATCGATACTGATTCAAGTG
1 GTATCGATACCGATTCAAGTG
* *
5388390 GTATCGATACAGATTCAAATG
1 GTATCGATACCGATTCAAGTG
5388411 GTATCGATACC
1 GTATCGATACC
5388422 AAGAAGGGAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (21 bp):
GTATCGATACCGATTCAAGTG
Found at i:5389502 original size:68 final size:68
Alignment explanation
Indices: 5389186--5389480 Score: 484
Period size: 68 Copynumber: 4.3 Consensus size: 68
5389176 ATATTAATGG
*
5389186 CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5389251 GGC
66 GGC
*
5389254 CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
*
5389319 GGT
66 GGC
* * *
5389322 CTAACTGTGCATTTGAAAAAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
5389387 GGC
66 GGC
*
5389390 CTAACTGTGCATTTGACAGAAATG-TGTCAATCATGCCAGTTAGATAAAAGGCTAAGTGCCTTTG
1 CTAACTGTGCATTTGACAGAAA-GATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
5389454 AGGC
65 AGGC
* * *
5389458 CTGACTGTACATTTGATAGAAAG
1 CTAACTGTGCATTTGACAGAAAG
5389481 CTATCAATTA
Statistics
Matches: 212, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
67 1 0.00
68 210 0.99
69 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGATGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GGC
Found at i:5389596 original size:81 final size:80
Alignment explanation
Indices: 5389470--5389772 Score: 315
Period size: 81 Copynumber: 3.8 Consensus size: 80
5389460 GACTGTACAT
* * * * *
5389470 TTGATAGAAAGCTATCAATTATG-GATGTTAGATGAACGGTTAAATATCGTTGAGTAAAAGATTT
1 TTGACAGAAAGGTGTCAATTATGCCA-GTTAGATGAACGATTAAATA-CGTTGAGTAAAAGATTT
*
5389534 ATGGCCTAGTTGTTCAC
64 ATGGCCTAGTTGTGCAC
* * * *
5389551 TTGACAGAAAGGTGTCAATTTTGCCAGTTAGATGAACGATCAAATACCATTGAGTAAAAGATTAA
1 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAATA-CGTTGAGTAAAAGATTTA
*
5389616 TGGCCTAGCTGTGCAC
65 TGGCCTAGTTGTGCAC
* * *
5389632 TTGACAGAAAGGTGTCAA-TATGCCACTTAGATGAAC-AGTTAAACACTGTTGAGTAAAATATTT
1 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGA-TTAAATAC-GTTGAGTAAAAGATTT
*
5389695 AAGGCCTAGTTGTGCAC
64 ATGGCCTAGTTGTGCAC
* * * * * * * * *
5389712 TTAACAGAAATGTATCAATCATGCAAGTTAGATGAAAGGTTAAATGCCTTTGAGTAAAAGA
1 TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAT-ACGTTGAGTAAAAGA
5389773 CTAGATGTAT
Statistics
Matches: 183, Mismatches: 33, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
79 2 0.01
80 64 0.35
81 115 0.63
82 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (80 bp):
TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAATACGTTGAGTAAAAGATTTAT
GGCCTAGTTGTGCAC
Found at i:5389862 original size:45 final size:45
Alignment explanation
Indices: 5389808--5390167 Score: 422
Period size: 45 Copynumber: 8.0 Consensus size: 45
5389798 TGTATAAAAT
* *
5389808 GCATGAAAGGATGCCAGAATTGAAATGCATATGAGTGCATTAGAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTATAG
* * * *
5389853 GCATAAAAGGATGCCATAATTGAAATGCATATGGGTGCATTCTCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTATAG
* *
5389898 GCATGAAATGATGCCATAATTGAAATGCATATGTGTGCATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTATAG
* * *
5389943 GCATGAAAGGAGGCCATAATTGAAATACATAT-AGGTGCATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGA-GTGCATTATAG
*
5389988 GCATGAAAGGATGCCATAATTGAAATGCATATCGA-TGCATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATAT-GAGTGCATTATAG
* * * * *
5390033 CCATAAAAGGATGTCATAATTGAAATGCATATGGGTGAATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTATAG
* * *
5390078 GCATGAATGGATGTCATAATTGAAATGCATATGGGTGCATTATCA-
1 GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTAT-AG
* * * * *
5390123 GTATGAAAAGATGCTATAAATGAAAAGGCATGATGA-TGCATTATA
1 GCATGAAAGGATGCCATAATTG-AAATGCAT-ATGAGTGCATTATA
5390168 AATATGAATG
Statistics
Matches: 272, Mismatches: 36, Indels: 14
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.00
45 251 0.92
46 16 0.06
47 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAATTGAAATGCATATGAGTGCATTATAG
Found at i:5393711 original size:20 final size:20
Alignment explanation
Indices: 5393647--5393720 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
5393637 ATATTGAGTA
*
5393647 GTATCGATACCGATTCAAG-TG
1 GTATCGATACC-A-TAAAGATG
*
5393668 GTATCGATACCAAAAAGA-G
1 GTATCGATACCATAAAGATG
* *
5393687 AGTATCGATACCATGAGGATG
1 -GTATCGATACCATAAAGATG
5393708 GTATCGATACCAT
1 GTATCGATACCAT
5393721 TGAGCACATA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.09
20 29 0.64
21 12 0.27
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (20 bp):
GTATCGATACCATAAAGATG
Found at i:5394276 original size:55 final size:55
Alignment explanation
Indices: 5394155--5394277 Score: 135
Period size: 55 Copynumber: 2.2 Consensus size: 55
5394145 TGCAAAAAGC
* * * * *
5394155 TAATAAATTCATACTAAGTGTATGAATTTTCGTATGGGCACTATTTGTGCAGAAC
1 TAATAAATTCATACTAAGTGTATGAATTTTCATATGGGAACTATATGTACAGAAA
*
5394210 TAAGAAATTCATACTAAGTGTATGAA-TTTCTATATGGGAAAC-ATATGTACA-AATA
1 TAATAAATTCATACTAAGTGTATGAATTTTC-ATATGGG-AACTATATGTACAGAA-A
*
5394265 TAATAAGTTCATA
1 TAATAAATTCATA
5394278 ATAATTAGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
54 6 0.11
55 49 0.86
56 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (55 bp):
TAATAAATTCATACTAAGTGTATGAATTTTCATATGGGAACTATATGTACAGAAA
Found at i:5394799 original size:68 final size:68
Alignment explanation
Indices: 5394462--5394781 Score: 550
Period size: 68 Copynumber: 4.7 Consensus size: 68
5394452 ATATTAATGG
*
5394462 CTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
5394527 GGC
66 GGC
*
5394530 CTAATTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
5394595 GGC
66 GGC
* *
5394598 CTAACTGTGCATTTGACAGAAAGGTGTTAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
5394663 GGC
66 GGC
* * *
5394666 CTAACTATGCATTTGACATAAAGGTGTCAATCATGCCAGTTAGATAAAAGACTAAGTGCCTTTGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
5394731 GGC
66 GGC
* * *
5394734 CTGACTGTGCATTTGACAAAAAGCTGTCAATCATGCCAGTTAGATGAA
1 CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAA
5394782 CGGTTAAATA
Statistics
Matches: 237, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 237 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGACTAAGTGCCTTTGA
GGC
Found at i:5394972 original size:45 final size:45
Alignment explanation
Indices: 5394922--5395307 Score: 502
Period size: 45 Copynumber: 8.6 Consensus size: 45
5394912 TTGTATAAAA
*
5394922 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTTCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5394967 GGCATGAAATGATGCTATAATTGAAATGCATATGGGTTCATTATA
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * **
5395012 GGTATGAAAGGATGTCATAATTGAAATGCATATAGGTGTGTTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* *
5395057 GACATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATA
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5395102 GGCATGAAATGATGCCATAATTGAAATGCATATGGGTGTAATATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5395147 GGCATGAAATGATACCATAATTGAAATACATATAGGTGCATTATC
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * *
5395192 GGCATGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATA
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5395237 GGCATGAAAGGATGTCATAATTGTAATGTATATGGGTGCATTATT
1 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
* * * *
5395282 GGTATGAAAAGATGCTATAAATGAAA
1 GGCATGAAAGGATGCCATAATTGAAA
5395308 AGGCATGATG
Statistics
Matches: 295, Mismatches: 46, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 295 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.30
Consensus pattern (45 bp):
GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC
Found at i:5395427 original size:45 final size:45
Alignment explanation
Indices: 5395378--5395499 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 45
5395368 ATAAAGAGAA
* * *
5395378 AAATAGATATGGGCGTAATATCGGCATGAAATGATACCATAATTG
1 AAATACATATGGGCGCAATATCGGCATGAAAGGATACCATAATTG
* * **
5395423 AAATACATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTG
1 AAATACATATGGGCGCAATATCGGCATGAAAGGATACCATAATTG
* * * * *
5395468 AAATGCATATGAGTGCATTATAGGCATGAAAG
1 AAATACATATGGGCGCAATATCGGCATGAAAG
5395500 AATGTCATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.27
Consensus pattern (45 bp):
AAATACATATGGGCGCAATATCGGCATGAAAGGATACCATAATTG
Found at i:5395496 original size:90 final size:91
Alignment explanation
Indices: 5395400--5395580 Score: 217
Period size: 90 Copynumber: 2.0 Consensus size: 91
5395390 GCGTAATATC
*
5395400 GGCATGAAATG-ATACCATAATTGAAATACATATGGGTGCATTATCGGCATGAAAGGATG-TCAT
1 GGCATGAAA-GAATACCATAATTGAAATACATATGGGTGCATTATCGGCATGAAAAGATGCT-AT
* *
5395463 AATTG-AAATGCAT-ATGAGTGCATTATA
64 AAATGAAAAGGCATGATGA-TGCATTATA
** * ** * *
5395490 GGCATGAAAGAATGTCATAATTGTAATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAA
1 GGCATGAAAGAATACCATAATTGAAATACATATGGGTGCATTATCGGCATGAAAAGATGCTATAA
5395555 ATGAAAAGGCATGATGATGCATTATA
66 ATGAAAAGGCATGATGATGCATTATA
5395581 AATATGAATG
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
89 1 0.01
90 55 0.71
91 17 0.22
92 4 0.05
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (91 bp):
GGCATGAAAGAATACCATAATTGAAATACATATGGGTGCATTATCGGCATGAAAAGATGCTATAA
ATGAAAAGGCATGATGATGCATTATA
Found at i:5395505 original size:45 final size:45
Alignment explanation
Indices: 5395415--5395543 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 45
5395405 GAAATGATAC
* * *
5395415 CATAATTGAAATACATATGGGTGCATTATCGGCATGAAAGGATGT
1 CATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGAATGT
*
5395460 CATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGAATGT
1 CATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGAATGT
* * * *
5395505 CATAATTGTAATGTATATGGGTGCATTATTGGTATGAAA
1 CATAATTGAAATGCATATGGGTGCATTATAGGCATGAAA
5395544 AGATGCTATA
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (45 bp):
CATAATTGAAATGCATATGGGTGCATTATAGGCATGAAAGAATGT
Found at i:5395579 original size:253 final size:253
Alignment explanation
Indices: 5395131--5395637 Score: 978
Period size: 253 Copynumber: 2.0 Consensus size: 253
5395121 ATTGAAATGC
*
5395131 ATATGGGTGTAATATCGGCATGAAATGATACCATAATTGAAATACATATAGGTGCATTATCGGCA
1 ATATGGGCGTAATATCGGCATGAAATGATACCATAATTGAAATACATATAGGTGCATTATCGGCA
*
5395196 TGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGGATGTCATAATTGT
66 TGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGAATGTCATAATTGT
5395261 AATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAAATGAAAAGGCATGATGATGCATTA
131 AATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAAATGAAAAGGCATGATGATGCATTA
5395326 TAAATATGAATGGATGTTATCAATGAAAATAATGAATAATGAATAAAGAGAAAAATAG
196 TAAATATGAATGGATGTTATCAATGAAAATAATGAATAATGAATAAAGAGAAAAATAG
*
5395384 ATATGGGCGTAATATCGGCATGAAATGATACCATAATTGAAATACATATGGGTGCATTATCGGCA
1 ATATGGGCGTAATATCGGCATGAAATGATACCATAATTGAAATACATATAGGTGCATTATCGGCA
5395449 TGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGAATGTCATAATTGT
66 TGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGAATGTCATAATTGT
5395514 AATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAAATGAAAAGGCATGATGATGCATTA
131 AATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAAATGAAAAGGCATGATGATGCATTA
*
5395579 TAAATATGAATGGATGTTATCAATGAAAATAATGAATAATGAATAAAGAGACAAATAG
196 TAAATATGAATGGATGTTATCAATGAAAATAATGAATAATGAATAAAGAGAAAAATAG
5395637 A
1 A
5395638 AAAGAAAAAT
Statistics
Matches: 250, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
253 250 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (253 bp):
ATATGGGCGTAATATCGGCATGAAATGATACCATAATTGAAATACATATAGGTGCATTATCGGCA
TGAAAGGATGTCATAATTGAAATGCATATGAGTGCATTATAGGCATGAAAGAATGTCATAATTGT
AATGTATATGGGTGCATTATTGGTATGAAAAGATGCTATAAATGAAAAGGCATGATGATGCATTA
TAAATATGAATGGATGTTATCAATGAAAATAATGAATAATGAATAAAGAGAAAAATAG
Found at i:5396291 original size:24 final size:24
Alignment explanation
Indices: 5396263--5396312 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5396253 TATCCTAAAC
5396263 ACTCCAATATGCATATATAAGTTA
1 ACTCCAATATGCATATATAAGTTA
5396287 ACTCCAATATGCATATATAAGTTA
1 ACTCCAATATGCATATATAAGTTA
5396311 AC
1 AC
5396313 CCCATTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (24 bp):
ACTCCAATATGCATATATAAGTTA
Found at i:5397298 original size:20 final size:21
Alignment explanation
Indices: 5397259--5397300 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5397249 TTGATTTTAT
*
5397259 AATAATTTATATATTTTTTAAA
1 AATAATTTATATA-TCTTTAAA
5397281 AATAATTTATATA-CTTTAAA
1 AATAATTTATATATCTTTAAA
5397301 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTTATATATCTTTAAA
Found at i:5397395 original size:31 final size:29
Alignment explanation
Indices: 5397358--5397703 Score: 227
Period size: 30 Copynumber: 11.6 Consensus size: 29
5397348 TCAAATTACA
*
5397358 TTAAAATATATATTTTATTCTTATTTTAGC
1 TTAAAA-ATATATTTTATTCTTATTTTAAC
* * * *
5397388 TTTAAAATATTTTTTTATTTTTA-TCTAAC
1 TTAAAAATA-TATTTTATTCTTATTTTAAC
*
5397417 TTAAAAATATATTTTATATC--ATCTTAAC
1 TTAAAAATATATTTTAT-TCTTATTTTAAC
* *
5397445 TTTTAAAAATATAATTTTATTATCATTTTAAC
1 --TTAAAAATAT-ATTTTATTCTTATTTTAAC
* * * *
5397477 TTTTAAAGATTTATTTTATTCTTACTTTAAA
1 --TTAAAAATATATTTTATTCTTATTTTAAC
* * *
5397508 TTATTAAATATGTTTTATT-TATATATTAAC
1 TTA-AAAATATATTTTATTCT-TATTTTAAC
* * * *
5397538 ATAAAAA-AAATTTTAATCTTATTTTAGC
1 TTAAAAATATATTTTATTCTTATTTTAAC
* * * * *
5397566 TTAAACAGTATACTTTATTATTGTCTTAAC
1 TTAAA-AATATATTTTATTCTTATTTTAAC
5397596 TTAAAAAATATATTTTATTCTTATTTTAAC
1 TT-AAAAATATATTTTATTCTTATTTTAAC
*
5397626 TTAAAAATGCATATTTTATTCTTATCTTGATAC
1 TTAAAAAT--ATATTTTATTCTTAT-TTTA-AC
** * * *
5397659 AAAAAAAATATATTTTATTTTTATCTTAAT
1 -TTAAAAATATATTTTATTCTTATTTTAAC
5397689 TTAAAAATAT-TTTTA
1 TTAAAAATATATTTTA
5397704 ACATATATTT
Statistics
Matches: 242, Mismatches: 55, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.00
28 34 0.14
29 39 0.16
30 84 0.35
31 42 0.17
32 34 0.14
33 2 0.01
34 6 0.02
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATTTTAAC
Found at i:5397453 original size:30 final size:30
Alignment explanation
Indices: 5397417--5397495 Score: 113
Period size: 32 Copynumber: 2.6 Consensus size: 30
5397407 TTTATCTAAC
5397417 TTAAAAATATATTTTATATCATCTTAACTT
1 TTAAAAATATATTTTATATCATCTTAACTT
*
5397447 TTAAAAATATAATTTTATTATCATTTTAACTT
1 TTAAAAATAT-ATTTTA-TATCATCTTAACTT
* *
5397479 TTAAAGATTTATTTTAT
1 TTAAAAATATATTTTAT
5397496 TCTTACTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 11 0.25
31 12 0.27
32 21 0.48
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.53
Consensus pattern (30 bp):
TTAAAAATATATTTTATATCATCTTAACTT
Found at i:5397676 original size:63 final size:61
Alignment explanation
Indices: 5397533--5397696 Score: 172
Period size: 63 Copynumber: 2.7 Consensus size: 61
5397523 TATTTATATA
* * * * * *
5397533 TTAACATAAAAAA-A-ATTTTAATCTTATTTTAGCTTAAACA-GTATACTTTATTATTGTC
1 TTAACAAAAAAAATATATTTTATTCTTATTTTAACTTAAAAATGCATACTTTATTATTATC
** * *
5397591 TTAACTTAAAAAATATATTTTATTCTTATTTTAACTTAAAAATGCATATTTTATTCTTATC
1 TTAACAAAAAAAATATATTTTATTCTTATTTTAACTTAAAAATGCATACTTTATTATTATC
* * *
5397652 TTGATACAAAAAAAATATATTTTATTTTTATCTTAATTTAAAAAT
1 TT-A-ACAAAAAAAATATATTTTATTCTTATTTTAACTTAAAAAT
5397697 ATTTTTAACA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
58 12 0.14
59 1 0.01
60 23 0.26
61 16 0.18
62 1 0.01
63 35 0.40
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.48
Consensus pattern (61 bp):
TTAACAAAAAAAATATATTTTATTCTTATTTTAACTTAAAAATGCATACTTTATTATTATC
Found at i:5397695 original size:32 final size:32
Alignment explanation
Indices: 5397598--5397695 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 32
5397588 GTCTTAACTT
* *
5397598 AAAAAATATATTTTATTCTTATTTTAACTT-A
1 AAAAAATATATTTTATTCTTATCTTAATTTAA
*** * **
5397629 AAAATGCATATTTTATTCTTATCTTGATACAA
1 AAAAAATATATTTTATTCTTATCTTAATTTAA
*
5397661 AAAAAATATATTTTATTTTTATCTTAATTTAA
1 AAAAAATATATTTTATTCTTATCTTAATTTAA
5397693 AAA
1 AAA
5397696 TATTTTTAAC
Statistics
Matches: 51, Mismatches: 15, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
31 22 0.43
32 29 0.57
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (32 bp):
AAAAAATATATTTTATTCTTATCTTAATTTAA
Found at i:5397739 original size:29 final size:31
Alignment explanation
Indices: 5397706--5397771 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 31
5397696 TATTTTTAAC
5397706 ATATATTTAATAAGTTAA-GTAAGAATA-AA
1 ATATATTTAATAAGTTAATGTAAGAATATAA
* *
5397735 ATATATTTAATAAGTTAATGTAATAATATAT
1 ATATATTTAATAAGTTAATGTAAGAATATAA
5397766 ATATAT
1 ATATAT
5397772 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 18 0.55
30 8 0.24
31 7 0.21
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.41
Consensus pattern (31 bp):
ATATATTTAATAAGTTAATGTAAGAATATAA
Found at i:5397804 original size:2 final size:2
Alignment explanation
Indices: 5397760--5397794 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5397750 TAATGTAATA
5397760 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5397795 CAGAATATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5397886 original size:29 final size:28
Alignment explanation
Indices: 5397854--5398012 Score: 93
Period size: 27 Copynumber: 5.9 Consensus size: 28
5397844 GATAAGAACA
*
5397854 AAATATATTTTTTAGTTAA-AATAAAAAT
1 AAATATATTTTTAAGTTAAGAAT-AAAAT
* *
5397882 GAAATATAGTTGTAAGTTAAGAATAAAAT
1 -AAATATATTTTTAAGTTAAGAATAAAAT
* *
5397911 -AA-ATATTTTTAAATTAAAAATAATAAT
1 AAATATATTTTTAAGTTAAGAATAA-AAT
*** *
5397938 AAA-ATAAAATTAAGTTTAGAATAAAAT
1 AAATATATTTTTAAGTTAAGAATAAAAT
** * *
5397965 --ATAT-TTAATAATTTAAG-ATAAAAA
1 AAATATATTTTTAAGTTAAGAATAAAAT
*
5397989 ATAATAT-TTTTTAAGTTGAGAATA
1 A-AATATATTTTTAAGTTAAGAATA
5398013 TAAAATATTA
Statistics
Matches: 99, Mismatches: 23, Indels: 17
0.71 0.17 0.12
Matches are distributed among these distances:
24 6 0.06
25 9 0.09
26 19 0.19
27 21 0.21
28 20 0.20
29 21 0.21
30 3 0.03
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.38
Consensus pattern (28 bp):
AAATATATTTTTAAGTTAAGAATAAAAT
Found at i:5397920 original size:54 final size:53
Alignment explanation
Indices: 5397846--5397970 Score: 128
Period size: 54 Copynumber: 2.3 Consensus size: 53
5397836 AAATAAAAGA
* * * * **
5397846 TAAGAACAAAATATATTTTTT-AGTT-AAAATAAAAATGAAATATAGTTGTAAGT
1 TAAGAATAAAATAAATTTTTTAAATTAAAAATAAAAATAAAATA-AAAT-TAAGT
*
5397899 TAAGAATAAAATAAATATTTTTAAATTAAAAATAATAATAAAATAAAATTAAGT
1 TAAGAATAAAATAAAT-TTTTTAAATTAAAAATAAAAATAAAATAAAATTAAGT
* *
5397953 TTAGAATAAAATATATTT
1 TAAGAATAAAATAAATTT
5397971 AATAATTTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
53 16 0.27
54 24 0.40
55 5 0.08
56 15 0.25
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (53 bp):
TAAGAATAAAATAAATTTTTTAAATTAAAAATAAAAATAAAATAAAATTAAGT
Found at i:5398215 original size:19 final size:20
Alignment explanation
Indices: 5398191--5398231 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
5398181 TTTCAACCTC
*
5398191 TTAAAATAAA-TATATTAAT
1 TTAAAATAAATTAAATTAAT
5398210 TTAAAATAAATTAAATTAAT
1 TTAAAATAAATTAAATTAAT
5398230 TT
1 TT
5398232 TAACCCTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAATAAATTAAATTAAT
Found at i:5403163 original size:21 final size:20
Alignment explanation
Indices: 5403130--5403192 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 20
5403120 TGACTGTTGC
5403130 AGTAGG-GGTTTAGAAATCA
1 AGTAGGAGGTTTAGAAATCA
*
5403149 GGTAGGAGGATTTAGAAATCA
1 AGTAGGAGG-TTTAGAAATCA
*
5403170 AGTAGGATGGTTTAGAAACCA
1 AGTAGGA-GGTTTAGAAATCA
5403191 AG
1 AG
5403193 CAAGGGAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 5 0.13
20 2 0.05
21 29 0.76
22 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.24
Consensus pattern (20 bp):
AGTAGGAGGTTTAGAAATCA
Found at i:5403689 original size:23 final size:24
Alignment explanation
Indices: 5403645--5403689 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5403635 AATTAAAAAA
* *
5403645 TAAAATAAATTCCACCTGTCTTAT
1 TAAAATAAAATCCACCTCTCTTAT
5403669 TAAAA-AAAATCCACCTCTCTT
1 TAAAATAAAATCCACCTCTCTT
5403690 CCTCCTCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.33
Consensus pattern (24 bp):
TAAAATAAAATCCACCTCTCTTAT
Found at i:5415627 original size:23 final size:24
Alignment explanation
Indices: 5415574--5415627 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
5415564 CATAATATAT
*
5415574 ATGATAAGAGCATAAGAGATAATA
1 ATGATAAGAGCATAAGAAATAATA
* *
5415598 TTAATAAGAG-ATAAGAAAT-ATGA
1 ATGATAAGAGCATAAGAAATAAT-A
5415621 ATGATAA
1 ATGATAA
5415628 TAGTATATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 2 0.08
23 14 0.58
24 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.19, T:0.24
Consensus pattern (24 bp):
ATGATAAGAGCATAAGAAATAATA
Found at i:5415713 original size:21 final size:22
Alignment explanation
Indices: 5415688--5415728 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5415678 ATGCATTCTG
5415688 TTATATGAGATGTTT-TATGAT
1 TTATATGAGATGTTTATATGAT
* *
5415709 TTATATTATATGTTTATATG
1 TTATATGAGATGTTTATATG
5415729 CCTCACTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (22 bp):
TTATATGAGATGTTTATATGAT
Found at i:5416090 original size:22 final size:21
Alignment explanation
Indices: 5416046--5416090 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5416036 TGCCGAGGTA
* * *
5416046 CTGTAGTAGGGTATCGGTTCC
1 CTGTAGTAGGGAATCGATACC
5416067 CTGTAGTAGAGGAATCGATACC
1 CTGTAGTAG-GGAATCGATACC
5416089 CT
1 CT
5416091 TTAAGTAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
CTGTAGTAGGGAATCGATACC
Found at i:5420351 original size:21 final size:23
Alignment explanation
Indices: 5420303--5420353 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5420293 TTCCCCTGTG
5420303 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
5420326 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
5420347 GGGGGGA
1 GGGGGGA
5420354 TCAATTCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:5430601 original size:23 final size:24
Alignment explanation
Indices: 5430541--5430601 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
5430531 AATGAGACAT
5430541 AATATATATGATAAGAGCATAAGAG
1 AATATA-ATGATAAGAGCATAAGAG
* * *
5430566 ATTATATTAATAAGAG-ATAAGA-
1 AATATAATGATAAGAGCATAAGAG
5430588 AATATGAATGATAA
1 AATAT-AATGATAA
5430602 TAGTGTATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 4 0.14
23 12 0.41
24 8 0.28
25 5 0.17
ACGTcount: A:0.54, C:0.02, G:0.16, T:0.28
Consensus pattern (24 bp):
AATATAATGATAAGAGCATAAGAG
Found at i:5430694 original size:21 final size:22
Alignment explanation
Indices: 5430668--5430708 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5430658 ATGCATTCTG
5430668 TTATATGAGATGTTT-TATGAT
1 TTATATGAGATGTTTATATGAT
* *
5430689 TTATATTATATGTTTATATG
1 TTATATGAGATGTTTATATG
5430709 CCTCACTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (22 bp):
TTATATGAGATGTTTATATGAT
Found at i:5434252 original size:11 final size:10
Alignment explanation
Indices: 5434222--5434248 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5434212 AAATTATCAA
5434222 TAAAAAATAT
1 TAAAAAATAT
5434232 TAAAAAATAT
1 TAAAAAATAT
5434242 TAAAAAA
1 TAAAAAA
5434249 ATATATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:5434867 original size:60 final size:60
Alignment explanation
Indices: 5434784--5434938 Score: 179
Period size: 60 Copynumber: 2.6 Consensus size: 60
5434774 CAATTGTCCT
* * ** * * * *
5434784 CAAAGTATGAACT-TCATTTTAAATTGGTTTTTAAATTTTTAAATGTTTCAATTTCATCCC
1 CAAACTATG-ACTATCATTCTAAATTGGTCCTCAAACTTTTAAATATTTAAATTTCATCCC
* *
5434844 TAAACTATGACTATCATTCTAAATTGGTCCTCAAACTTTTGAATATTTAAATTTCATCCC
1 CAAACTATGACTATCATTCTAAATTGGTCCTCAAACTTTTAAATATTTAAATTTCATCCC
*
5434904 CAAACTATGA-TATTCATTCTAAATTGGTCCCCAAA
1 CAAACTATGACTA-TCATTCTAAATTGGTCCTCAAA
5434939 TAGTTTGGAC
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 5 0.06
60 76 0.94
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (60 bp):
CAAACTATGACTATCATTCTAAATTGGTCCTCAAACTTTTAAATATTTAAATTTCATCCC
Found at i:5434928 original size:32 final size:31
Alignment explanation
Indices: 5434833--5434928 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 31
5434823 TAAATGTTTC
*
5434833 AATTTCATCCCTAAACTATGACTATCATTCTA
1 AATTTCATCCCCAAACTATGA-TATCATTCTA
** * *
5434865 AA-TTGGTCCTCAAACTTTTGA-AT-ATT-TA
1 AATTTCATCCCCAAAC-TATGATATCATTCTA
5434893 AATTTCATCCCCAAACTATGATATTCATTCTA
1 AATTTCATCCCCAAACTATGATA-TCATTCTA
5434925 AATT
1 AATT
5434929 GGTCCCCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
28 8 0.16
29 14 0.29
30 3 0.06
31 12 0.24
32 12 0.24
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTTCATCCCCAAACTATGATATCATTCTA
Found at i:5434936 original size:31 final size:30
Alignment explanation
Indices: 5434840--5434938 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 30
5434830 TTCAATTTCA
*
5434840 TCCCTAAACTATGACTATCATTCTAAATTGG
1 TCCCCAAACTATGA-TATCATTCTAAATTGG
* * **
5434871 TCCTCAAACTTTTGA-AT-ATT-TAAATTTCA
1 TCCCCAAAC-TATGATATCATTCTAAA-TTGG
5434900 TCCCCAAACTATGATATTCATTCTAAATTGG
1 TCCCCAAACTATGATA-TCATTCTAAATTGG
5434931 TCCCCAAA
1 TCCCCAAA
5434939 TAGTTTGGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
28 8 0.15
29 14 0.26
30 3 0.06
31 20 0.38
32 8 0.15
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.36
Consensus pattern (30 bp):
TCCCCAAACTATGATATCATTCTAAATTGG
Found at i:5434966 original size:60 final size:59
Alignment explanation
Indices: 5434832--5434971 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 59
5434822 TTAAATGTTT
* * *
5434832 CAATTTCATCCCTAAACTATGACTATCATTCTAAATTGGTCCTCAAACTTTTGAATATTT
1 CAATTTCATCCC-AAACTATGACTATCATTCTAAATTGGTCCCCAAACTTTTGAACATTC
* *
5434892 AAATTTCATCCCCAAACTATGA-TATTCATTCTAAATTGGTCCCCAAA-TAGTTTGGACATTC
1 CAATTTCAT-CCCAAACTATGACTA-TCATTCTAAATTGGTCCCCAAACT--TTTGAACATTC
5434953 CAATTTCATCCCAAACTAT
1 CAATTTCATCCCAAACTAT
5434972 ACATACATAC
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
59 3 0.04
60 48 0.69
61 19 0.27
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (59 bp):
CAATTTCATCCCAAACTATGACTATCATTCTAAATTGGTCCCCAAACTTTTGAACATTC
Found at i:5435733 original size:31 final size:31
Alignment explanation
Indices: 5435691--5435872 Score: 298
Period size: 31 Copynumber: 6.0 Consensus size: 31
5435681 CCTCTTTCTC
*
5435691 CTTCTTATTCTTCAAGAGCTTAAACCCATAT
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
5435722 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
5435753 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
5435784 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
5435815 CTTCTTCTTCTTCAAGAGCTTAAA--CATAT
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
** * *
5435844 -AGCTTCTTCTTCAAAAGCTTAAACTCATA
1 CTTCTTCTTCTTCAAGAGCTTAAACCCATA
5435873 GCAATTAAAA
Statistics
Matches: 145, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
28 20 0.14
29 5 0.03
30 4 0.03
31 116 0.80
ACGTcount: A:0.28, C:0.27, G:0.07, T:0.38
Consensus pattern (31 bp):
CTTCTTCTTCTTCAAGAGCTTAAACCCATAT
Found at i:5437193 original size:20 final size:20
Alignment explanation
Indices: 5437168--5437216 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5437158 TTCACTTTTT
5437168 TTAAAAATAAAAAAAATACA
1 TTAAAAATAAAAAAAATACA
* * *
5437188 TTAAAAATGAATAAAATTCA
1 TTAAAAATAAAAAAAATACA
*
5437208 ATAAAAATA
1 TTAAAAATA
5437217 TAATGTAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
TTAAAAATAAAAAAAATACA
Found at i:5440147 original size:23 final size:22
Alignment explanation
Indices: 5440117--5440198 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
5440107 GCATGGCCTT
5440117 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
5440139 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
5440161 GTGTATCGATGCATATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
5440184 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
5440199 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 19 0.41
24 11 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:5448512 original size:16 final size:18
Alignment explanation
Indices: 5448483--5448522 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5448473 TATTAAATTG
*
5448483 ATTTA-AAAATATAA-AT
1 ATTTATAAAATATAATAA
5448499 ATTTATAAAA-ATAATAA
1 ATTTATAAAATATAATAA
5448516 ATTTATA
1 ATTTATA
5448523 TATCAAATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTTATAAAATATAATAA
Found at i:5448524 original size:19 final size:19
Alignment explanation
Indices: 5448470--5448524 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
5448460 TAACAAATAT
* * *
5448470 AAATATTAAATTGATTTAA
1 AAATAATAAATTTATATAA
5448489 AAAT-ATAAATATT-TATAA
1 AAATAATAAAT-TTATATAA
5448507 AAATAATAAATTTATATA
1 AAATAATAAATTTATATA
5448525 TCAAATTGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAATAATAAATTTATATAA
Found at i:5450124 original size:2 final size:2
Alignment explanation
Indices: 5450117--5450175 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
5450107 TTACTTTCAA
* * *
5450117 AT AT AT AT AT AT AT AT AT TT GAA AG AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
5450160 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5450176 GAGATAGAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5455369 original size:13 final size:13
Alignment explanation
Indices: 5455340--5455392 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
5455330 AATGATAAAT
*
5455340 AATATAAAAATTAC
1 AATA-AAAAAGTAC
*
5455354 AATAAAAAAGTCC
1 AATAAAAAAGTAC
5455367 AATAAACAAA-TAC
1 AATAAA-AAAGTAC
5455380 AATAAAAAAGTAC
1 AATAAAAAAGTAC
5455393 TAAATACAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 3 0.09
13 24 0.71
14 7 0.21
ACGTcount: A:0.66, C:0.11, G:0.04, T:0.19
Consensus pattern (13 bp):
AATAAAAAAGTAC
Found at i:5462109 original size:20 final size:19
Alignment explanation
Indices: 5462084--5462137 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
5462074 GCGAAATAAA
5462084 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
5462104 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
5462124 AATCGCAACGCGAT
1 AATCGCAACGCGAT
5462138 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:5462148 original size:21 final size:20
Alignment explanation
Indices: 5462124--5462236 Score: 77
Period size: 21 Copynumber: 5.5 Consensus size: 20
5462114 CAGTTCCCAG
5462124 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
5462144 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * *
5462165 AATTCGCATTGCGATTTTCCAA
1 AA-TCGCAACGCGATTAT-GAA
* *
5462187 AATTGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
* *
5462207 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
5462227 TATCGCAACG
1 AATCGCAACG
5462237 AGTATCCGTA
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.01
20 32 0.45
21 33 0.46
22 4 0.06
23 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:5462214 original size:20 final size:20
Alignment explanation
Indices: 5462185--5462422 Score: 146
Period size: 20 Copynumber: 11.8 Consensus size: 20
5462175 GCGATTTTCC
* *
5462185 AAAATTGCAACGCGAATATG
1 AAAATCGCAACGCGAATACG
*
5462205 AAAATCGCAACGCG-ATTCTG
1 AAAATCGCAACGCGAATAC-G
** * * *
5462225 ACTATCGCAACGAGTATCCG
1 AAAATCGCAACGCGAATACG
* *
5462245 TAAAATCGCAACGCGTATCCG
1 -AAAATCGCAACGCGAATACG
*
5462266 TAAATCGCAACGAC-AATACG
1 AAAATCGCAACG-CGAATACG
* *
5462286 TAAAATCGCAACAC--ATATCC
1 -AAAATCGCAACGCGAATA-CG
*
5462306 ATAAATCGCAACGAGAATACG
1 A-AAATCGCAACGCGAATACG
* *
5462327 TAAATCGCAACGCGTAT-CTG
1 AAAATCGCAACGCGAATAC-G
* *
5462347 TAAATCGCAACGAGAATACG
1 AAAATCGCAACGCGAATACG
* * * *
5462367 TAAATCGCAATGCGTATCCG
1 AAAATCGCAACGCGAATACG
*
5462387 TAAATCGCAACGAC-AATACG
1 AAAATCGCAACG-CGAATACG
5462407 TAAAATCGCAACGCGA
1 -AAAATCGCAACGCGA
5462423 TCGATAATTA
Statistics
Matches: 172, Mismatches: 32, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
19 7 0.04
20 116 0.67
21 46 0.27
22 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGAATACG
Found at i:5462351 original size:40 final size:41
Alignment explanation
Indices: 5462186--5462421 Score: 293
Period size: 40 Copynumber: 5.8 Consensus size: 41
5462176 CGATTTTCCA
* * * *
5462186 AAATTGCAACGCGAATATG-AAAATCGCAACGCG-ATTC-T
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
* * *
5462224 GACTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGT
1 -A-AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
* * * *
5462267 AAATCGCAACGACAATACGTAAAATCGCAACACATATCCAT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
*
5462308 AAATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
*
5462348 AAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
*
5462388 AAATCGCAACGACAATACGTAAAATCGCAACGCG
1 AAATCGCAACGAGAATACGTAAAATCGCAACGCG
5462422 ATCGATAATT
Statistics
Matches: 169, Mismatches: 23, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 85 0.50
41 78 0.46
42 4 0.02
43 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AAATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGT
Found at i:5462530 original size:20 final size:20
Alignment explanation
Indices: 5462507--5462575 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
5462497 TGCAATAGGA
5462507 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
5462527 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
5462547 AAATCGCAATGCGAAT-CTGT
1 AAATCGCAATGCGAATAC-GT
5462567 AAATCGCAA
1 AAATCGCAA
5462576 CGAGATTCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 1 0.02
20 47 0.98
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:5462552 original size:40 final size:39
Alignment explanation
Indices: 5462490--5462575 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 39
5462480 GATTATGACT
* *
5462490 ATCGCATTGCAATAGGAAAATCGCAATGCGAATAC-GTAA
1 ATCGCAATGCAATACGAAAATCGCAATGCGAAT-CTGTAA
*
5462529 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAA
1 ATCGCAATGC-AATACGAAAATCGCAATGCGAATCTGTAA
5462569 ATCGCAA
1 ATCGCAA
5462576 CGAGATTCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 10 0.24
40 32 0.76
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (39 bp):
ATCGCAATGCAATACGAAAATCGCAATGCGAATCTGTAA
Found at i:5462902 original size:20 final size:20
Alignment explanation
Indices: 5462877--5462957 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
5462867 CAACACGGAA
5462877 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAAT-TGACT
*
5462897 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAATTGACT
*
5462917 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAATTGACT
* *
5462937 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCGGAATTGACT
5462957 A
1 A
5462958 ATTTCGCGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
20 52 0.93
21 4 0.07
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGGAATTGACT
Found at i:5462984 original size:20 final size:20
Alignment explanation
Indices: 5462959--5463060 Score: 86
Period size: 20 Copynumber: 5.8 Consensus size: 20
5462949 AAATGACTAA
*
5462959 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
5462979 TTTCGCATTGCGA--TTCA-
1 TTTCGCATTGCGATTTTCAT
*
5462996 -CTCG--TTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
5463013 TTTCGCATTGCGA--TTCA-
1 TTTCGCATTGCGATTTTCAT
*
5463030 -CTCG--TTGCGATTTTCA-
1 TTTCGCATTGCGATTTTCAT
5463046 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
5463061 ATCTCGTTGC
Statistics
Matches: 66, Mismatches: 5, Indels: 23
0.70 0.05 0.24
Matches are distributed among these distances:
14 12 0.18
16 14 0.21
17 3 0.05
18 11 0.17
19 8 0.12
20 18 0.27
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:5463055 original size:33 final size:34
Alignment explanation
Indices: 5462964--5463093 Score: 201
Period size: 34 Copynumber: 3.9 Consensus size: 34
5462954 ACTAATTTCG
5462964 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
5462998 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
5463032 CGTTGCGATTTTCA-TTTCGCATTGCGATT-ATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CT
** * *
5463065 CGTTGCGATAGTCATTTCCGCTTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
5463094 AGTCTGTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
32 1 0.01
33 29 0.32
34 60 0.67
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:5463073 original size:67 final size:68
Alignment explanation
Indices: 5462964--5463093 Score: 201
Period size: 67 Copynumber: 1.9 Consensus size: 68
5462954 ACTAATTTCG
** *
5462964 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTTCGCATTGCGATTC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGCGATTC
5463029 ACT
66 ACT
*
5463032 CGTTGCGATTTTCA-TTTCGCATTGCGATT-ATCTCGTTGCGATAGTCATTTCCGCTTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CTCGTTGCGATAGTCATTTCCGCATTGCGAT
5463094 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
66 1 0.02
67 42 0.74
68 14 0.25
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (68 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCCGCATTGCGATTC
ACT
Found at i:5463214 original size:14 final size:14
Alignment explanation
Indices: 5463195--5463231 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5463185 CATCAATTAA
5463195 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5463209 ACAAATCATCTTTT
1 ACAAATCAACATTT
5463223 ACAAATCAA
1 ACAAATCAA
5463232 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5464681 original size:42 final size:42
Alignment explanation
Indices: 5464602--5464694 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
5464592 CCTCTTCAAT
* * *
5464602 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
5464644 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
5464686 GATGACAGG
1 GATGACAGG
5464695 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:5465199 original size:20 final size:20
Alignment explanation
Indices: 5465174--5465261 Score: 124
Period size: 20 Copynumber: 4.5 Consensus size: 20
5465164 GAACCTTAAA
5465174 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
5465194 ATCGCAATGCGAAAATAACT
1 ATCGCAACGCGAAAATGACT
*
5465214 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
5465234 ATCGCAACGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
5465253 ATCGCAACG
1 ATCGCAACG
5465262 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
19 15 0.24
20 47 0.76
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:5465341 original size:33 final size:33
Alignment explanation
Indices: 5465304--5465383 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
5465294 GCGATTATAG
* * *
5465304 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
5465337 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
5465370 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
5465384 AGTCATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:5465347 original size:19 final size:19
Alignment explanation
Indices: 5465323--5465421 Score: 82
Period size: 19 Copynumber: 5.3 Consensus size: 19
5465313 GCGATTTTGT
5465323 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
5465342 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
5465356 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
** *
5465375 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA--TTTCG
*
5465396 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
5465416 TGTTGC
1 CGTTGC
5465422 AAAAGTAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
14 10 0.16
16 3 0.05
17 3 0.05
19 22 0.35
20 9 0.15
21 15 0.24
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:5465712 original size:94 final size:94
Alignment explanation
Indices: 5465471--5465851 Score: 595
Period size: 94 Copynumber: 4.1 Consensus size: 94
5465461 ATAGATTGCA
* * *
5465471 TTAC-TTCAACCAAATGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
5465535 TTAGCAGAATTGACAACAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
5465564 TTACTTTTCAACCAAAAGACAAAACAAAGATAAATACTAACTTCATAGTGTTAAAGAATACACAG
1 TTAC-TTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
*
5465629 TTTAGCAAAATTGGCAGCAACCGAACAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
*
5465659 TTACTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
5465724 TTAGTAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
5465753 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATATTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
5465817 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
5465847 TTACT
1 TTACT
5465852 AAGCAATCTA
Statistics
Matches: 268, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
93 23 0.09
94 159 0.59
95 86 0.32
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.23
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:5467681 original size:40 final size:40
Alignment explanation
Indices: 5467623--5467714 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
5467613 GTTGCGATTA
** *
5467623 TCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCATTT
1 TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
*
5467662 CTCTCGTTGCGATAGTCATTTTCGTATTGCGATTTTCATTT
1 -TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
5467703 TCAT-GTTGCGAT
1 TC-TCGTTGCGAT
5467715 TTTAAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTTCGCATTGCGATTTTCATTT
Found at i:5467715 original size:20 final size:20
Alignment explanation
Indices: 5467627--5467717 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
5467617 CGATTATCTC
*
5467627 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
5467646 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
5467666 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
* *
5467687 ATTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
5467707 GTTGCGATTTT
1 GTTGCGATTTT
5467718 AAGTTTAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.22
20 30 0.50
21 17 0.28
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:5468312 original size:20 final size:20
Alignment explanation
Indices: 5468278--5468473 Score: 186
Period size: 20 Copynumber: 9.7 Consensus size: 20
5468268 TTAAAAATCG
5468278 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTGT
* *
5468299 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
* *
5468319 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTGT
* *
5468339 CTTTGCGATTTACAG-ATACG-
1 CGTTGCGATTTAC-GTAT-TGT
*
5468359 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTGT
* *
5468379 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
5468399 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTGT
* *
5468420 CGTTGCGATTTACGGATACG-
1 CGTTGCGATTTACGTAT-TGT
5468440 CGTTGCGATTTTACGTATTGT
1 CGTTGCGA-TTTACGTATTGT
5468461 CGTTGCGATTTAC
1 CGTTGCGATTTAC
5468474 AGATACGCGT
Statistics
Matches: 142, Mismatches: 21, Indels: 25
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 98 0.69
21 43 0.30
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTGT
Found at i:5468424 original size:41 final size:41
Alignment explanation
Indices: 5468276--5468510 Score: 375
Period size: 41 Copynumber: 5.8 Consensus size: 41
5468266 CTTTAAAAAT
*
5468276 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * *
5468317 CGCATTGCGA-TTTACGTATTCTCTTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
5468357 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
5468397 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
5468438 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* *
5468479 CGCGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGAT
5468511 AGTCAGAATC
Statistics
Matches: 181, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 74 0.41
41 107 0.59
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:5468484 original size:20 final size:20
Alignment explanation
Indices: 5468299--5468571 Score: 204
Period size: 20 Copynumber: 13.5 Consensus size: 20
5468289 TACGTATTGT
*
5468299 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATACG
* * *
5468319 CATTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATACG
*
5468339 CTTTGCGATTTACAGATACG
1 CGTTGCGATTTACAGATACG
* *
5468359 CGTTGCGATTTAC-GTATTCT
1 CGTTGCGATTTACAG-ATACG
*
5468379 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACAGATACG
*
5468399 CGTTGCGATTTTAC-G-TATTG
1 CGTTGCGA-TTTACAGATA-CG
*
5468419 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACAGATACG
*
5468440 CGTTGCGATTTTAC-G-TATTG
1 CGTTGCGA-TTTACAGATA-CG
5468460 TCGTTGCGATTTACAGATACG
1 -CGTTGCGATTTACAGATACG
* *
5468481 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACAGATACG
*
5468502 CGTTGCGATAGT-CAGA-ATCG
1 CGTTGCGAT-TTACAGATA-CG
* *
5468522 CGTTGCGATTTATATG-TTCG
1 CGTTGCGATTTACA-GATACG
* * *
5468542 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACAGATACG
5468562 CGTTGCGATT
1 CGTTGCGATT
5468572 ATGTAAAATC
Statistics
Matches: 206, Mismatches: 26, Indels: 42
0.75 0.09 0.15
Matches are distributed among these distances:
19 8 0.04
20 142 0.69
21 52 0.25
22 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTACAGATACG
Found at i:5468582 original size:61 final size:61
Alignment explanation
Indices: 5468341--5468583 Score: 139
Period size: 61 Copynumber: 4.0 Consensus size: 61
5468331 CGTATTCTCT
* * * **
5468341 TTGCGATTTACAGATACGCGTTGCGA-TTTAC-GTATTCTCGTTGCGAT--TTACGGATACGCG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACAG-ATACGCGTTGCGATAGTCA-AAAT-CGCG
* * * * ** *
5468401 TTGCGATTTTAC-G-TATTGTCGTTGCGA-TTTACGGATACGCGTTGCGAT-TTTACGTATTGTC
1 TTGCGA-TTTACAGATA-CG-CGTTGCGATTTTACAGATACGCGTTGCGATAGTCA-AAATCG-C
5468462 G
61 G
* * *
5468463 TTGCGATTTACAGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTTACAGATACGCGTTGCGATTTTACAGATACGCGTTGCGATAGTCAAAATCGCG
* * * *
5468524 TTGCGATTTATATG-TTCGCGTTGCGATTTT-CATATTCGCGTTGCGATTATGT-AAAATCGC
1 TTGCGATTTACA-GATACGCGTTGCGATTTTACAGATACGCGTTGCGA-TA-GTCAAAATCGC
5468584 AATGCTAATT
Statistics
Matches: 152, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
59 2 0.01
60 20 0.13
61 81 0.53
62 45 0.30
63 4 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (61 bp):
TTGCGATTTACAGATACGCGTTGCGATTTTACAGATACGCGTTGCGATAGTCAAAATCGCG
Found at i:5472191 original size:10 final size:10
Alignment explanation
Indices: 5472169--5472201 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
5472159 TATTTTTAAT
5472169 AAAATAT-TA
1 AAAATATCTA
5472178 AAAATATCTA
1 AAAATATCTA
5472188 AAAATATCTA
1 AAAATATCTA
5472198 AAAA
1 AAAA
5472202 AACCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATCTA
Found at i:5472211 original size:20 final size:19
Alignment explanation
Indices: 5472168--5472211 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5472158 TTATTTTTAA
* *
5472168 TAAAATATTAAAAATATCT
1 TAAAATATTAAAAAAACCT
*
5472187 AAAAATATCTAAAAAAACCT
1 TAAAATAT-TAAAAAAACCT
5472207 TAAAA
1 TAAAA
5472212 ACATGTGAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAATATTAAAAAAACCT
Found at i:5473838 original size:25 final size:25
Alignment explanation
Indices: 5473805--5473853 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5473795 AATTATGTTA
* *
5473805 AAAAATTTAAGGGGTGTGAAATTAT
1 AAAAATTTAAGAGGTGAGAAATTAT
*
5473830 AAAATTTTAAGAGGTGAGAAATTA
1 AAAAATTTAAGAGGTGAGAAATTA
5473854 GATAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (25 bp):
AAAAATTTAAGAGGTGAGAAATTAT
Found at i:5473860 original size:25 final size:25
Alignment explanation
Indices: 5473805--5473860 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
5473795 AATTATGTTA
* * * *
5473805 AAAAATTTAAGGGGTGTGAAATTAT
1 AAAATTTTAAGAGGTGAGAAATTAG
5473830 AAAATTTTAAGAGGTGAGAAATTAG
1 AAAATTTTAAGAGGTGAGAAATTAG
*
5473855 ATAATT
1 AAAATT
5473861 AATAAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.32
Consensus pattern (25 bp):
AAAATTTTAAGAGGTGAGAAATTAG
Found at i:5474221 original size:10 final size:10
Alignment explanation
Indices: 5474206--5474239 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
5474196 TTTATCACAC
5474206 CAAATTCTCT
1 CAAATTCTCT
5474216 CAAATTCTCT
1 CAAATTCTCT
5474226 -AAATTTCTCT
1 CAAA-TTCTCT
5474236 CAAA
1 CAAA
5474240 AACTCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.14
10 16 0.73
11 3 0.14
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:5474325 original size:17 final size:18
Alignment explanation
Indices: 5474288--5474328 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
5474278 CTATTATGTA
*
5474288 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
5474306 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
5474323 TTTACT
1 TTTACT
5474329 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:5474584 original size:111 final size:111
Alignment explanation
Indices: 5474398--5474722 Score: 605
Period size: 111 Copynumber: 2.9 Consensus size: 111
5474388 ATATATCTAT
*
5474398 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
5474463 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
*
5474509 ACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
5474574 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
* *
5474620 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATCAGTAATAATTAGT
1 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
5474685 TGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
5474723 TTTTTGTAAT
Statistics
Matches: 208, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 208 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:5476255 original size:18 final size:18
Alignment explanation
Indices: 5476232--5476289 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
5476222 CCAGCAGCCA
5476232 CCGCATCCATATATGATG
1 CCGCATCCATATATGATG
5476250 CCGCATCCATATATGATG
1 CCGCATCCATATATGATG
*
5476268 CCGCAGCCATATATGATG
1 CCGCATCCATATATGATG
5476286 CCGC
1 CCGC
5476290 CATCACCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (18 bp):
CCGCATCCATATATGATG
Found at i:5476664 original size:21 final size:21
Alignment explanation
Indices: 5476640--5476679 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5476630 GGACGACGAC
5476640 GACGACGAAGATGACGATGGT
1 GACGACGAAGATGACGATGGT
* *
5476661 GACGACGACGATGATGATG
1 GACGACGAAGATGACGATG
5476680 ACAGCGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.15, G:0.38, T:0.15
Consensus pattern (21 bp):
GACGACGAAGATGACGATGGT
Found at i:5478112 original size:34 final size:32
Alignment explanation
Indices: 5478059--5478128 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
5478049 CCTTACAAAC
*
5478059 TCCCTAGTTTTTCCGGGCTAAACTATAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTATAACCTT
*
5478091 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTATAACCTT
5478125 TCCC
1 TCCC
5478129 CTTTACACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTATAACCTT
Found at i:5478513 original size:20 final size:21
Alignment explanation
Indices: 5478476--5478518 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5478466 CCATTAGACA
5478476 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
5478497 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
5478518 G
1 G
5478519 CAATCTGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.28, G:0.42, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:5480876 original size:30 final size:32
Alignment explanation
Indices: 5480812--5480876 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
5480802 CTAGTTTTTT
5480812 CGGGCTAAACTAGAACATTTCCCTAGCTTTTACA
1 CGGGCTAAACTAGAACATTTCCC-A-CTTTTACA
* *
5480846 CGGGCTAAGCTAGAACCTTTCCC-C-TTTACA
1 CGGGCTAAACTAGAACATTTCCCACTTTTACA
5480876 C
1 C
5480877 AAGGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 7 0.24
31 1 0.03
34 21 0.72
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (32 bp):
CGGGCTAAACTAGAACATTTCCCACTTTTACA
Found at i:5481177 original size:21 final size:21
Alignment explanation
Indices: 5481151--5481210 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
5481141 GGAGCGTGGA
5481151 GGGAATCGGTACCCCCTGGGG
1 GGGAATCGGTACCCCCTGGGG
5481172 GGGAATCGGTACCCCCT-GGG
1 GGGAATCGGTACCCCCTGGGG
*
5481192 GGGAATCTGTA-CCCCTGGG
1 GGGAATCGGTACCCCCTGGG
5481211 CAATCTGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 5 0.14
20 15 0.41
21 17 0.46
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTGGGG
Found at i:5484111 original size:21 final size:21
Alignment explanation
Indices: 5484085--5484138 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
5484075 GTTTCCAGAT
*
5484085 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
5484106 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
5484127 TCGCAATGCGAA
1 TCGCAATGCGAA
5484139 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:5484600 original size:51 final size:50
Alignment explanation
Indices: 5484491--5484620 Score: 129
Period size: 51 Copynumber: 2.5 Consensus size: 50
5484481 CCCCTACGTG
* * *
5484491 GCATATAGCGCGG-AGCAGAGGGCGCGCTATACCCCATGTGTAACCCAATTA
1 GCATATAGCGCGGTA-CAG-GGGCGCGCTATACCCCACGTGTAACCAAATCA
* * *
5484542 GCGTATAGCGCGGTACATGGGGCGCGCTATACTCCACGTG-ATGCCAAATCA
1 GCATATAGCGCGGTACA-GGGGCGCGCTATACCCCACGTGTA-ACCAAATCA
* *
5484593 GCATATAGCGCAGTTCAGGAGGCGCGCT
1 GCATATAGCGCGGTACAGG-GGCGCGCT
5484621 TTATTGCTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
50 3 0.05
51 61 0.92
52 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (50 bp):
GCATATAGCGCGGTACAGGGGCGCGCTATACCCCACGTGTAACCAAATCA
Found at i:5485412 original size:28 final size:27
Alignment explanation
Indices: 5485381--5485438 Score: 84
Period size: 25 Copynumber: 2.2 Consensus size: 27
5485371 GAAGTAGTAG
*
5485381 AATAAAAGGAGCGAAAGACATGCATAAC
1 AATAAAA-CAGCGAAAGACATGCATAAC
5485409 AAT--AACAGCGAAAGACATGCATAAC
1 AATAAAACAGCGAAAGACATGCATAAC
5485434 AATAA
1 AATAA
5485439 CAGCGTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 22 0.81
26 2 0.07
28 3 0.11
ACGTcount: A:0.55, C:0.16, G:0.17, T:0.12
Consensus pattern (27 bp):
AATAAAACAGCGAAAGACATGCATAAC
Found at i:5485419 original size:25 final size:25
Alignment explanation
Indices: 5485390--5485443 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
5485380 GAATAAAAGG
5485390 AGCGAAAGACATGCATAACAATAAC
1 AGCGAAAGACATGCATAACAATAAC
5485415 AGCGAAAGACATGCATAACAATAAC
1 AGCGAAAGACATGCATAACAATAAC
5485440 AGCG
1 AGCG
5485444 TTATTGCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.50, C:0.20, G:0.19, T:0.11
Consensus pattern (25 bp):
AGCGAAAGACATGCATAACAATAAC
Found at i:5486608 original size:23 final size:22
Alignment explanation
Indices: 5486572--5486615 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
5486562 AAGACATTTA
5486572 GATTAAAATCATATACTTTTTTG
1 GATTAAAATCATATA-TTTTTTG
* *
5486595 GATTAAAGTTATATATTTTTT
1 GATTAAAATCATATATTTTTT
5486616 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (22 bp):
GATTAAAATCATATATTTTTTG
Found at i:5488213 original size:23 final size:26
Alignment explanation
Indices: 5488165--5488219 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
5488155 TGAGAAAAAA
5488165 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
5488190 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
5488213 AGAAATA
1 AGAAATA
5488220 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:5488407 original size:107 final size:108
Alignment explanation
Indices: 5488210--5488409 Score: 246
Period size: 107 Copynumber: 1.9 Consensus size: 108
5488200 TATTTATTTA
* * * *
5488210 TTTAGAAATATCAGAAAATGACTTCTAGGTGTCTTAAGACAGCTCTTTTCTTCGATATTAATAAA
1 TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCCCTTTTCTTCGATATTAATAAA
* *
5488275 TATTAATATAATAATAAAATTATAATTTTTTATAATATTTAAT
66 TATAAATATAATAATAAAATAATAATTTTTTATAATATTTAAT
* * * *
5488318 TTTA-AAATACCAGAATATGACATCTAGTTTTATTAAGACTGCCCTTTTCTTCGATATTGAA-AA
1 TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCCCTTTTCTTCGATATT-AATAA
*
5488381 ATAAATAAATA-AATATTAAAA-AATAATTT
65 AT--ATAAATATAATAATAAAATAATAATTT
5488410 ATGTAAAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
107 57 0.73
108 15 0.19
109 6 0.08
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (108 bp):
TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCCCTTTTCTTCGATATTAATAAA
TATAAATATAATAATAAAATAATAATTTTTTATAATATTTAAT
Found at i:5489778 original size:3 final size:3
Alignment explanation
Indices: 5489770--5489836 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
5489760 GGCCCGTTTG
* *
5489770 TAA TAA TAA -AA AAA TAA TAA -AA TAA TAA TAA TAA TCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5489816 TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TAA TA
5489837 GTAAATGGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5489827 original size:34 final size:34
Alignment explanation
Indices: 5489772--5489836 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
5489762 CCCGTTTGTA
5489772 ATAATAAAAAAATAATAAAATAATAATAATAATC
1 ATAATAAAAAAATAATAAAATAATAATAATAATC
*
5489806 ATAATAATAATAATAAT-AAATAATAATAATA
1 ATAATAA-AAAAATAATAAAATAATAATAATA
5489837 GTAAATGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 21 0.72
35 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (34 bp):
ATAATAAAAAAATAATAAAATAATAATAATAATC
Found at i:5490168 original size:84 final size:82
Alignment explanation
Indices: 5490002--5490185 Score: 210
Period size: 84 Copynumber: 2.2 Consensus size: 82
5489992 TCAGATGAGT
* * * * *
5490002 TCTTCTCATTATGAACTTTCTGCTGGGGATGATGTTGACCTATTTCCTTCTGTGATAGAGTCATT
1 TCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATCTCCTTCTGTGATAGAATCATC
*
5490067 AAAAAGGTTAAATAAGC
66 AAAAAGGTTAAACAAGC
* * *
5490084 TCTTCTCATTATGAACTTTCT-CTGGAAAGGTTGATGCTAATCTATCTCCTTCTGTGATAGAATT
1 TCTTCTCATTATGAACTTTCTGCTGG---GGATGATGCTAACCTATCTCCTTCTGTGATAGAATC
*
5490148 ATGCAAAAA-GTTGAACAAGC
63 AT-CAAAAAGGTTAAACAAGC
* *
5490168 TCTTCTTATTGTGAACTT
1 TCTTCTCATTATGAACTT
5490186 CTTCTTCTTC
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
81 4 0.05
82 21 0.24
84 56 0.65
85 5 0.06
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (82 bp):
TCTTCTCATTATGAACTTTCTGCTGGGGATGATGCTAACCTATCTCCTTCTGTGATAGAATCATC
AAAAAGGTTAAACAAGC
Found at i:5490481 original size:225 final size:221
Alignment explanation
Indices: 5490151--5490671 Score: 678
Period size: 225 Copynumber: 2.3 Consensus size: 221
5490141 TAGAATTATG
** *
5490151 CAAAAAGTTGAACAAGCTCTTCTTATTGTGAACTTCTTCTT-CTTCAGATGAGTTCTTCTCATTA
1 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTA
* *
5490215 TGAACTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
66 TGAACTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
* *
5490280 CTCATTATGAA-T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGC
131 CTCATTATGAATTCTTCTTCCTTCTTCAGATGA--A-TTCTTCTCATTACGAACT-TACTCTGGA
5490341 AA-TGTTAATCCATCAAATGATGAATTTAAA
192 AAGT-TTAATCCATCAAATGATGAATTTAAA
* *
5490371 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTTA
1 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCC---TTCAGATGAGTTCTTCTCA
5490436 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
63 TTATGAAC-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAAT
*
5490501 TCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTCCTCTGG
127 TCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTACTCTGG
** * * ** *
5490566 AAAGTTTGTTCCATCGAGTGATGGTTTTGAA
191 AAAGTTTAATCCATCAAATGATGAATTTAAA
* * * *
5490597 TAAAAAGTTGAACAAATTCTTCTCATTATGAATTTATTCTT-CTTCAGATGACGAGTTCTTCTCA
1 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCAGAT---GAGTTCTTCTCA
*
5490661 TTACGAACTTC
63 TTATGAACTTC
5490672 CTCTTTCTTC
Statistics
Matches: 263, Mismatches: 24, Indels: 24
0.85 0.08 0.08
Matches are distributed among these distances:
220 37 0.14
221 1 0.00
222 7 0.03
224 29 0.11
225 90 0.34
226 78 0.30
227 3 0.01
228 5 0.02
229 13 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (221 bp):
CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCAGATGAGTTCTTCTCATTA
TGAACTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
CTCATTATGAATTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTACGAACTTACTCTGGAAAGT
TTAATCCATCAAATGATGAATTTAAA
Found at i:5490488 original size:113 final size:113
Alignment explanation
Indices: 5490150--5490675 Score: 578
Period size: 113 Copynumber: 4.7 Consensus size: 113
5490140 ATAGAATTAT
* ** * *
5490150 GCAAAAAGTTGAACAAGCTCTTCTTATTGTGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
5490211 ATTATGAAC-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
5490258 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * * * *
5490319 CTCATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* * * *
5490370 ACAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTATTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
5490435 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
* *
5490483 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * * * *
5490548 ATTACGAACTTCCTCTGG-AAAGTTTGTTCCATCGAGTGATGGTTTTGA
66 ATTATGAACTTTCTCTGGAAAAG-CTGATCCATCAAATGATGGATTTGA
** * *
5490596 ATAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTATT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* *
5490657 CTCATTACGAACTTCCTCT
63 CTCATTATGAACTTTCTCT
5490676 TTCTTCTTCA
Statistics
Matches: 360, Mismatches: 43, Indels: 26
0.84 0.10 0.06
Matches are distributed among these distances:
108 44 0.12
109 11 0.03
110 4 0.01
111 21 0.06
112 89 0.25
113 175 0.49
114 1 0.00
115 5 0.01
116 10 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
Found at i:5491585 original size:93 final size:93
Alignment explanation
Indices: 5491443--5491990 Score: 902
Period size: 93 Copynumber: 5.9 Consensus size: 93
5491433 TTCATCTTTT
* * * *
5491443 AATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACACTTCCA
1 AATT-CAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCA
5491507 GAAGATGCTATGAGCACATTCATCTTCCA
65 GAAGATGCTATGAGCACATTCATCTTCCA
* *
5491536 AATTCAATGATTAGTTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
5491601 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
*
5491629 AATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
5491694 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
* *
5491722 AATTCAATGATTGGTTTTTTAGGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 AATTCAATGATTGG-TTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCA
** *
5491787 GAAGATGCTATGAGCAC-TTGTTCTACCA
65 GAAGATGCTATGAGCACATTCATCTTCCA
*
5491815 AATTCAATGATTGGTTTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
1 AATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
5491880 AAGATGCTATGAGCACATTCATCTTCCA
66 AAGATGCTATGAGCACATTCATCTTCCA
* * *
5491908 AATTCAATGATTGGTTTTTTTAGAGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCC
1 AATTCAATGATTGG--TTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCC
5491973 AGAAGATGCTATGAGCAC
64 AGAAGATGCTATGAGCAC
5491991 TTGTTCTACT
Statistics
Matches: 425, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
92 73 0.17
93 225 0.53
94 64 0.15
95 63 0.15
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (93 bp):
AATTCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATGAGCACATTCATCTTCCA
Found at i:5492974 original size:1 final size:1
Alignment explanation
Indices: 5492970--5493027 Score: 71
Period size: 1 Copynumber: 58.0 Consensus size: 1
5492960 CTTGACCCCC
* * * * *
5492970 TTTTTTCTTTTTTCTCTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5493028 CTCTTCAAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:5492992 original size:10 final size:9
Alignment explanation
Indices: 5492970--5493032 Score: 85
Period size: 9 Copynumber: 7.0 Consensus size: 9
5492960 CTTGACCCCC
5492970 TTTTTTCTT
1 TTTTTTCTT
*
5492979 TTTTCTCTTT
1 TTTTTTC-TT
5492989 TTTTTTCTT
1 TTTTTTCTT
5492998 TTTTTT-TT
1 TTTTTTCTT
5493006 TTTTTT-TT
1 TTTTTTCTT
5493014 TTTTTTCTT
1 TTTTTTCTT
5493023 TTTTTCTCTT
1 TTTTT-TCTT
5493033 CAAACATAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
8 16 0.33
9 21 0.43
10 12 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:5492999 original size:25 final size:25
Alignment explanation
Indices: 5492971--5493025 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
5492961 TTGACCCCCT
5492971 TTTTTCTTTTTTCTCTTTTTTTTTC
1 TTTTTCTTTTTTCTCTTTTTTTTTC
* * *
5492996 TTTTTTTTTTTTTTTTTTTTTTTTC
1 TTTTTCTTTTTTCTCTTTTTTTTTC
5493021 TTTTT
1 TTTTT
5493026 TTCTCTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (25 bp):
TTTTTCTTTTTTCTCTTTTTTTTTC
Found at i:5504130 original size:23 final size:26
Alignment explanation
Indices: 5504082--5504136 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 26
5504072 TGAGAAAAAA
5504082 AGAAA-AAAATAATTTATATATATTT
1 AGAAATAAAATAATTTATATATATTT
*
5504107 ATAAATAAAAT-ATTTAT-T-TATTT
1 AGAAATAAAATAATTTATATATATTT
5504130 AGAAATA
1 AGAAATA
5504137 TCAGAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 1 0.04
25 10 0.37
26 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AGAAATAAAATAATTTATATATATTT
Found at i:5504326 original size:107 final size:108
Alignment explanation
Indices: 5504127--5504326 Score: 239
Period size: 107 Copynumber: 1.9 Consensus size: 108
5504117 TATTTATTTA
* * *
5504127 TTTAGAAATATCAGAAAATGACTTCTAGGTGTCTTAAGACAGCTCTTTTCTTCGATATTAATAAA
1 TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCTCTTTTCTTCGATATTAATAAA
* *
5504192 TATTAATATAATAATAAAATTACAATTTTTTATAATATTTAAT
66 TATAAATATAATAATAAAATAACAATTTTTTATAATATTTAAT
* * *
5504235 TTTA-AAATACCAGAATATGACATCTAGTTGTATTAAGACTG-TCCTTTTCTTCGATATTGAA-A
1 TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCT-CTTTTCTTCGATATT-AATA
* *
5504297 AATAAATAAAT-TAATATTAAAA-AATAATTT
64 AAT--ATAAATATAATAATAAAATAACAATTT
5504327 ATGTAAAAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
106 1 0.01
107 56 0.72
108 16 0.21
109 5 0.06
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (108 bp):
TTTAGAAATACCAGAAAATGACATCTAGGTGTATTAAGACAGCTCTTTTCTTCGATATTAATAAA
TATAAATATAATAATAAAATAACAATTTTTTATAATATTTAAT
Found at i:5505723 original size:3 final size:3
Alignment explanation
Indices: 5505715--5505779 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
5505705 GGCCCGTTTG
* *
5505715 TAA TAA TAA -AA TAA TAA TAA AAA TAA TAA TAA TAA TCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5505762 TAA TAAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TA
5505780 GTAAATGGAG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5506044 original size:3 final size:3
Alignment explanation
Indices: 5506036--5506068 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
5506026 TTGTCCGGGA
5506036 TAT TAT TAT TA- TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5506069 ATAATAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5506051 original size:11 final size:11
Alignment explanation
Indices: 5506035--5506068 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
5506025 TTTGTCCGGG
5506035 ATATTATTATT
1 ATATTATTATT
5506046 ATATTATTATT
1 ATATTATTATT
*
5506057 ATTTTATTATT
1 ATATTATTATT
5506068 A
1 A
5506069 ATAATAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTATTATT
Found at i:5506055 original size:14 final size:14
Alignment explanation
Indices: 5506036--5506068 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5506026 TTGTCCGGGA
5506036 TATTATTATTATAT
1 TATTATTATTATAT
*
5506050 TATTATTATTTTAT
1 TATTATTATTATAT
5506064 TATTA
1 TATTA
5506069 ATAATAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATTATAT
Found at i:5509911 original size:31 final size:31
Alignment explanation
Indices: 5509876--5509936 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5509866 TGAATACAAC
*
5509876 TTAATTAAATAAAAATGAAAGTGATCATATT
1 TTAATTAAATAAAAATGAAAGTAATCATATT
5509907 TTAATTAAATAAAAATGAAAGTAATCATAT
1 TTAATTAAATAAAAATGAAAGTAATCATAT
5509937 ATTATGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.34
Consensus pattern (31 bp):
TTAATTAAATAAAAATGAAAGTAATCATATT
Done.