Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 12 of 13
Found at i:3490589 original size:39 final size:40
Alignment explanation
Indices: 3490515--3490650 Score: 161
Period size: 39 Copynumber: 3.5 Consensus size: 40
3490505 ATTCACTTTT
* * * *
3490515 AAGCATATATCCCATTAC-ACATATAACCACCTAACATTC
1 AAGCATATATCACAATACTACATATAATCACATAACATTC
* *
3490554 AATCATAAATCACAATACT-CATATAATCACATAACATTC
1 AAGCATATATCACAATACTACATATAATCACATAACATTC
* * * *
3490593 AAGCATATATCATAATA-TACGTATAATCTCATAACATTT
1 AAGCATATATCACAATACTACATATAATCACATAACATTC
3490632 AAGCATATATCACAATACT
1 AAGCATATATCACAATACT
3490651 GAAAAACATC
Statistics
Matches: 81, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 79 0.98
40 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (40 bp):
AAGCATATATCACAATACTACATATAATCACATAACATTC
Found at i:3491286 original size:47 final size:47
Alignment explanation
Indices: 3491217--3491315 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
3491207 CATATTCACA
3491217 AACACATAAACACTTTATTCATAAGGTAACATAGGTATGAAAAAGCT
1 AACACATAAACACTTTATTCATAAGGTAACATAGGTATGAAAAAGCT
3491264 AACACATAAACACTTTATTCATAAGGTAACATAGGTATGAAAAAGCT
1 AACACATAAACACTTTATTCATAAGGTAACATAGGTATGAAAAAGCT
*
3491311 TACAC
1 AACAC
3491316 TCAAAATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.25
Consensus pattern (47 bp):
AACACATAAACACTTTATTCATAAGGTAACATAGGTATGAAAAAGCT
Found at i:3504286 original size:20 final size:20
Alignment explanation
Indices: 3504261--3504298 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3504251 TTAGCAAAGT
*
3504261 TACGGTTTTCCAACACAAGC
1 TACGGTTTTCAAACACAAGC
3504281 TACGGTTTTCAAACACAA
1 TACGGTTTTCAAACACAA
3504299 TACCATACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.26
Consensus pattern (20 bp):
TACGGTTTTCAAACACAAGC
Found at i:3505563 original size:14 final size:15
Alignment explanation
Indices: 3505544--3505575 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3505534 GTGGTTATAG
3505544 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
3505558 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
3505573 TTA
1 TTA
3505576 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:3514691 original size:70 final size:71
Alignment explanation
Indices: 3514609--3514750 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 71
3514599 ATATTTATGC
* * * *
3514609 ATTCTATCAATTTGATTTTCAAACATATATAACTAAATATAAATTTTTTTTTTTGAAAAAG-ACA
1 ATTCTATCAATTTGATTTTCAAACATATATAACTAAATATAAATTATATATTATGAAAAAGTACA
3514673 GAGCAT
66 GAGCAT
3514679 ATTCTATCAATTTGATTTTCAAACATATATAACTAAATATAAATTATATATTATGAAAAAGTACA
1 ATTCTATCAATTTGATTTTCAAACATATATAACTAAATATAAATTATATATTATGAAAAAGTACA
3514744 GAGCAT
66 GAGCAT
3514750 A
1 A
3514751 ATATTATTTA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
70 57 0.85
71 10 0.15
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (71 bp):
ATTCTATCAATTTGATTTTCAAACATATATAACTAAATATAAATTATATATTATGAAAAAGTACA
GAGCAT
Found at i:3517735 original size:25 final size:25
Alignment explanation
Indices: 3517688--3517760 Score: 114
Period size: 25 Copynumber: 3.0 Consensus size: 25
3517678 CGTATACTCT
3517688 TACGAGCTGTAA-AT-AGTAAGCTCA
1 TACGAGCTG-AATATCAGTAAGCTCA
3517712 TACGAGCTGAATATCAGTAAGCTCA
1 TACGAGCTGAATATCAGTAAGCTCA
*
3517737 TACGAGCTAAATATCAGTAAGCTC
1 TACGAGCTGAATATCAGTAAGCTC
3517761 TCTCGAGATG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
23 2 0.04
24 11 0.24
25 33 0.72
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (25 bp):
TACGAGCTGAATATCAGTAAGCTCA
Found at i:3528498 original size:50 final size:50
Alignment explanation
Indices: 3528394--3528685 Score: 336
Period size: 50 Copynumber: 5.7 Consensus size: 50
3528384 GGTAAAGGGA
3528394 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATGAGAGG
* *
3528450 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGACGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
3528500 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * **
3528550 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
3528600 TCCCATGTAAGGCCATATCTGGGATATGACATTGGCA--GTACATGATATA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
*
3528649 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3528686 TGTTATTATC
Statistics
Matches: 205, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 38 0.19
50 125 0.61
53 3 0.01
55 2 0.01
56 36 0.18
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:3534926 original size:16 final size:16
Alignment explanation
Indices: 3534905--3534935 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3534895 AGCCTAGGGG
3534905 CAAAATGTAATTTTTC
1 CAAAATGTAATTTTTC
3534921 CAAAATGTAATTTTT
1 CAAAATGTAATTTTT
3534936 GCACTAGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
CAAAATGTAATTTTTC
Found at i:3535359 original size:46 final size:43
Alignment explanation
Indices: 3535287--3535379 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 43
3535277 TACTATGTGA
*
3535287 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* *
3535330 ACCGGATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
3535376 ACCG
1 ACCG
3535380 TGTGTCTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 5 0.12
44 11 0.26
45 2 0.05
46 23 0.53
47 2 0.05
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:3535530 original size:16 final size:16
Alignment explanation
Indices: 3535509--3535540 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3535499 TGATTGAAAG
*
3535509 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
3535525 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
3535541 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:3537858 original size:82 final size:82
Alignment explanation
Indices: 3537717--3537881 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
3537707 TAGATTCCCT
3537717 TATTAATCCTTTGAGAGTTTGAAAACACTTTAGAAACAGTTTGGGACTAAATCGAGAACATTTGA
1 TATTAATCCTTTGAGAGTTTGAAAACACTTTAGAAACAGTTTGGGACTAAATCGAGAACATTTGA
3537782 AAATTTTAGAAGAAAAG
66 AAATTTTAGAAGAAAAG
* *
3537799 TATTAATCCTTTGAGAGTTTGAAAACACTTTAGAAACGGTTTGGGACTAAATCGGGAACATTTGA
1 TATTAATCCTTTGAGAGTTTGAAAACACTTTAGAAACAGTTTGGGACTAAATCGAGAACATTTGA
3537864 AAATTTTAGAAGAAAAG
66 AAATTTTAGAAGAAAAG
3537881 T
1 T
3537882 TAGAAAAATT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (82 bp):
TATTAATCCTTTGAGAGTTTGAAAACACTTTAGAAACAGTTTGGGACTAAATCGAGAACATTTGA
AAATTTTAGAAGAAAAG
Found at i:3539383 original size:16 final size:16
Alignment explanation
Indices: 3539362--3539395 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3539352 CCAGTATCCA
* *
3539362 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
3539378 ATTATCACATTTACAC
1 ATTATCACATTTACAC
3539394 AT
1 AT
3539396 ACATATTCAT
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:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:3557434 original size:43 final size:42
Alignment explanation
Indices: 3557387--3557481 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
3557377 TCCCAGAGTT
* * *
3557387 GGTCTTACATGTAATCAAATATCGATGCC-ACTGTCCTAGACAG
1 GGTCTTACACGAAATCAAATA-CGATGCCGA-TGTCCCAGACAG
** *
3557430 GGTCTTACACGAAATCGTATACGATGCCGATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAGACAG
3557472 GGTCTTACAC
1 GGTCTTACAC
3557482 ATAAATCTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 27 0.60
43 18 0.40
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.26
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATACGATGCCGATGTCCCAGACAG
Found at i:3560013 original size:42 final size:42
Alignment explanation
Indices: 3559903--3560025 Score: 131
Period size: 42 Copynumber: 2.9 Consensus size: 42
3559893 TGTGATTTCG
* * * **
3559903 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCA
1 TGTAAGACCATATCTGGGACAGTGGCATCGTATGTGATAACA
* * *
3559945 TATAAGACCCTATCTGGGACAGTGGCATCGATATGTGGTAACA
1 TGTAAGACCATATCTGGGACAGTGGCATCG-TATGTGATAACA
* * *
3559988 TGTAAGACCATATCTGAGATA-TGGCATTGTATGTGATA
1 TGTAAGACCATATCTGGGACAGTGGCATCGTATGTGATA
3560026 TATGTGTTTC
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
41 8 0.12
42 33 0.50
43 25 0.38
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.31
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGACAGTGGCATCGTATGTGATAACA
Found at i:3567208 original size:40 final size:40
Alignment explanation
Indices: 3567153--3567249 Score: 185
Period size: 40 Copynumber: 2.4 Consensus size: 40
3567143 CCAAGCACCT
*
3567153 TTGTAAAAATGTCAGCCAACTGAATGGAGGTCGGAACATA
1 TTGTAAAAATGTCAGCCAACCGAATGGAGGTCGGAACATA
3567193 TTGTAAAAATGTCAGCCAACCGAATGGAGGTCGGAACATA
1 TTGTAAAAATGTCAGCCAACCGAATGGAGGTCGGAACATA
3567233 TTGTAAAAATGTCAGCC
1 TTGTAAAAATGTCAGCC
3567250 TATCCTGAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (40 bp):
TTGTAAAAATGTCAGCCAACCGAATGGAGGTCGGAACATA
Found at i:3570288 original size:11 final size:11
Alignment explanation
Indices: 3570272--3570298 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3570262 AAGTTAGTGA
3570272 AAAAAAATTCG
1 AAAAAAATTCG
3570283 AAAAAAATTCG
1 AAAAAAATTCG
3570294 AAAAA
1 AAAAA
3570299 GAAAATTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:3573456 original size:23 final size:21
Alignment explanation
Indices: 3573410--3573461 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3573400 TGTTAATGTG
*
3573410 TGTGTTTAATAAGTGCTTACA
1 TGTGTTTAATAAGTGCTTAAA
3573431 TGTGTTTAATAAGCT-CATTTAAA
1 TGTGTTTAATAAG-TGC--TTAAA
3573454 TGTGTTTA
1 TGTGTTTA
3573462 TTGTAGGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 1 0.04
23 12 0.44
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (21 bp):
TGTGTTTAATAAGTGCTTAAA
Found at i:3576110 original size:28 final size:29
Alignment explanation
Indices: 3576070--3576129 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
3576060 CTCCAGCTTA
3576070 GGTGGGCCAAAAGGA-AAAAAAAAACTAT
1 GGTGGGCCAAAAGGAGAAAAAAAAACTAT
3576098 GGTGGGCCAAAAGGAGAAAAAAAAACTAT
1 GGTGGGCCAAAAGGAGAAAAAAAAACTAT
3576127 GGT
1 GGT
3576130 ATTGTAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.48
29 16 0.52
ACGTcount: A:0.50, C:0.10, G:0.28, T:0.12
Consensus pattern (29 bp):
GGTGGGCCAAAAGGAGAAAAAAAAACTAT
Found at i:3579876 original size:25 final size:25
Alignment explanation
Indices: 3579842--3579899 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3579832 CATATGAGCT
*
3579842 GTAAACTCCTCCAAGCTGAATAAAG
1 GTAAGCTCCTCCAAGCTGAATAAAG
* *
3579867 GTAAGCTCCTCCGAGCTGAATAATG
1 GTAAGCTCCTCCAAGCTGAATAAAG
3579892 GTAAGCTC
1 GTAAGCTC
3579900 ATACGAGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (25 bp):
GTAAGCTCCTCCAAGCTGAATAAAG
Found at i:3579906 original size:25 final size:25
Alignment explanation
Indices: 3579855--3579927 Score: 94
Period size: 25 Copynumber: 2.9 Consensus size: 25
3579845 AACTCCTCCA
* * *
3579855 AGCTGAATAAAGGTAAGCTCCTCCG
1 AGCTGAATAATGGTAAGCTCATACG
3579880 AGCTGAATAATGGTAAGCTCATACG
1 AGCTGAATAATGGTAAGCTCATACG
*
3579905 AGCTGAGT-ATCGGTAAGCTCATA
1 AGCTGAATAAT-GGTAAGCTCATA
3579928 GGAGTTGAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 2 0.05
25 41 0.95
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (25 bp):
AGCTGAATAATGGTAAGCTCATACG
Found at i:3579936 original size:25 final size:25
Alignment explanation
Indices: 3579866--3579945 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
3579856 GCTGAATAAA
* * *
3579866 GGTAAGCTCCTCCGAGCTGAATAAT-
1 GGTAAGCTCATACGAGCTGAGT-ATC
3579891 GGTAAGCTCATACGAGCTGAGTATC
1 GGTAAGCTCATACGAGCTGAGTATC
* *
3579916 GGTAAGCTCATAGGAGTTGAGTATC
1 GGTAAGCTCATACGAGCTGAGTATC
3579941 GGTAA
1 GGTAA
3579946 CCCTATTGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
24 2 0.04
25 47 0.96
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (25 bp):
GGTAAGCTCATACGAGCTGAGTATC
Found at i:3587645 original size:25 final size:25
Alignment explanation
Indices: 3587617--3587728 Score: 116
Period size: 25 Copynumber: 4.5 Consensus size: 25
3587607 ACAAGCTGTA
*
3587617 AACGGTAAGCTCCTTCGACCTGAAT
1 AACGGTAAGCTCCTTCGAGCTGAAT
* * *
3587642 AACGGTAAACTCCTCCGAGCGGAAT
1 AACGGTAAGCTCCTTCGAGCTGAAT
* *
3587667 AACAGTAAGCTCCTTCGAGCTAAAT
1 AACGGTAAGCTCCTTCGAGCTGAAT
* * * * *
3587692 AAAGGTAAGCTCATACGAGTTGAGT
1 AACGGTAAGCTCCTTCGAGCTGAAT
*
3587717 ATCGGTAAGCTC
1 AACGGTAAGCTC
3587729 ATAAGAGCTG
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.22
Consensus pattern (25 bp):
AACGGTAAGCTCCTTCGAGCTGAAT
Found at i:3587729 original size:25 final size:25
Alignment explanation
Indices: 3587695--3587743 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3587685 GCTAAATAAA
* *
3587695 GGTAAGCTCATACGAGTTGAGTATC
1 GGTAAGCTCATAAGAGCTGAGTATC
3587720 GGTAAGCTCATAAGAGCTGAGTAT
1 GGTAAGCTCATAAGAGCTGAGTAT
3587744 TGATAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCATAAGAGCTGAGTATC
Found at i:3589366 original size:42 final size:42
Alignment explanation
Indices: 3589311--3589390 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
3589301 ATGGCCAAGC
3589311 CACACACCCGTGTGCTAGG-CAGTGTAACCTTCGAAATGGCCT
1 CACACACCCGTGTGCTAGGCCA-TGTAACCTTCGAAATGGCCT
* * * *
3589353 CACACGCCTGTGTGCTAGGCCATGTAACTTTTGAAATG
1 CACACACCCGTGTGCTAGGCCATGTAACCTTCGAAATG
3589391 AAACCTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 31 0.94
43 2 0.06
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (42 bp):
CACACACCCGTGTGCTAGGCCATGTAACCTTCGAAATGGCCT
Found at i:3594425 original size:25 final size:25
Alignment explanation
Indices: 3594405--3594461 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
3594395 TGAGCTGAAG
*
3594405 ATTGGTGTGCTCTCACAAGCTATAA
1 ATTGGTATGCTCTCACAAGCTATAA
*
3594430 ATTGGTATGCTCTCACGAGCTATAA
1 ATTGGTATGCTCTCACAAGCTATAA
*
3594455 ATCGGTA
1 ATTGGTA
3594462 ACCTTAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (25 bp):
ATTGGTATGCTCTCACAAGCTATAA
Found at i:3604997 original size:101 final size:102
Alignment explanation
Indices: 3604822--3605027 Score: 389
Period size: 101 Copynumber: 2.0 Consensus size: 102
3604812 NAGTAGCAAA
3604822 ATACCCAAAGTTGGATGATAGTGTAGATGATTGTCTGACTCCATCCCAATTTCGAGTTGATGGAA
1 ATACCCAAAGTTGGATGATAGTGTAGATGATTGTCTGACTCCATCCCAATTTCGAGTTGATGGAA
3604887 ATCACTATAATCAAGGGAAAAAT-AAAACGAGTAAGC
66 ATCACTATAATCAAGGGAAAAATAAAAACGAGTAAGC
3604923 ATACCCAAACG-TGGATGATAGTGTAGATGATTGTCTGACTCCATCCCAATTTCGAGTTGATGGA
1 ATACCCAAA-GTTGGATGATAGTGTAGATGATTGTCTGACTCCATCCCAATTTCGAGTTGATGGA
3604987 AATCACTATAATCAAGGGAAAAATAAAAACGAGTAAGC
65 AATCACTATAATCAAGGGAAAAATAAAAACGAGTAAGC
3605025 ATA
1 ATA
3605028 TAGCTTAGTA
Statistics
Matches: 103, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
101 86 0.83
102 17 0.17
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.25
Consensus pattern (102 bp):
ATACCCAAAGTTGGATGATAGTGTAGATGATTGTCTGACTCCATCCCAATTTCGAGTTGATGGAA
ATCACTATAATCAAGGGAAAAATAAAAACGAGTAAGC
Found at i:3605921 original size:27 final size:27
Alignment explanation
Indices: 3605876--3605986 Score: 105
Period size: 27 Copynumber: 3.9 Consensus size: 27
3605866 CCAATGAATC
**
3605876 GGGGAATCAGCACACAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
* *
3605903 GGGGAATCAGCACTTAGCAACAACCAATGAATA
1 GGGGAATCAGCACTTAGCAAC--CC-CT---TG
* *
3605936 GGGGAATCAGCACTTAGCAAGCCCTCG
1 GGGGAATCAGCACTTAGCAACCCCTTG
*
3605963 GGGGAATCAACACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
3605987 CTTTCACATT
Statistics
Matches: 68, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
27 41 0.60
29 2 0.03
30 2 0.03
31 2 0.03
33 21 0.31
ACGTcount: A:0.33, C:0.29, G:0.24, T:0.14
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:3605929 original size:60 final size:60
Alignment explanation
Indices: 3605852--3605983 Score: 201
Period size: 60 Copynumber: 2.2 Consensus size: 60
3605842 GGTGGATTCT
* * *
3605852 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCA
1 GCACTTAGCAACAACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
** *
3605912 GCACTTAGCAACAACCAATGAATAGGGGAATCAGCACTTAGCAAGCCCTCGGGGGAATCA
1 GCACTTAGCAACAACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
*
3605972 ACACTTAGCAAC
1 GCACTTAGCAAC
3605984 CCCCTTTCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.14
Consensus pattern (60 bp):
GCACTTAGCAACAACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCA
Found at i:3605949 original size:33 final size:33
Alignment explanation
Indices: 3605852--3605955 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
3605842 GGTGGATTCT
* *
3605852 GCACTTAGCAACCACCAATGAATCGGGGAATCA
1 GCACTTAGCAACAACCAATGAATAGGGGAATCA
* ** *
3605885 GCAC--A-CAGCAACCCCT---TGGGGGAATCA
1 GCACTTAGCAACAACCAATGAATAGGGGAATCA
3605912 GCACTTAGCAACAACCAATGAATAGGGGAATCA
1 GCACTTAGCAACAACCAATGAATAGGGGAATCA
3605945 GCACTTAGCAA
1 GCACTTAGCAA
3605956 GCCCTCGGGG
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
27 14 0.25
29 1 0.02
30 15 0.27
31 1 0.02
33 25 0.45
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (33 bp):
GCACTTAGCAACAACCAATGAATAGGGGAATCA
Found at i:3606084 original size:103 final size:103
Alignment explanation
Indices: 3605905--3606127 Score: 396
Period size: 103 Copynumber: 2.2 Consensus size: 103
3605895 ACCCCTTGGG
*
3605905 GGAATCAGCACTTAGCAACAACCAATGAATAGGGGAATCAGCACTTAGCAAGCCCTCGGGGGAAT
1 GGAATCAGCACTTAGCAACAACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
3605970 CAACACTTAGCAACCCCCTTTCACATTTAAAATACGGT
66 CAACACTTAGCAACCCCCTTTCACATTTAAAATACGGT
*
3606008 GGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
1 GGAATCAGCACTTAGCAACAACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
*
3606073 CAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
66 CAACACTTAGCAACCCCCTTTCACATTTAAAATACGGT
*
3606111 GGGATCA--ACTTAGCAAC
1 GGAATCAGCACTTAGCAAC
3606128 NNNNNNNNNN
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
101 10 0.09
103 106 0.91
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (103 bp):
GGAATCAGCACTTAGCAACAACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAAT
CAACACTTAGCAACCCCCTTTCACATTTAAAATACGGT
Found at i:3609137 original size:42 final size:42
Alignment explanation
Indices: 3609078--3609180 Score: 161
Period size: 42 Copynumber: 2.5 Consensus size: 42
3609068 TGAAACGGGC
* * *
3609078 TTGCTCACACGATCTGTGGGTCGAAATGTAAGCTATACGATA
1 TTGCTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATA
3609120 TTGCTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATA
1 TTGCTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATA
* *
3609162 CTGCTCAAACGAGCTGTGG
1 TTGCTCACACGAGCTGTGG
3609181 AGTATCCACA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (42 bp):
TTGCTCACACGAGCTGTGGGTCAAAATGTAAGCTACACGATA
Found at i:3615212 original size:13 final size:15
Alignment explanation
Indices: 3615188--3615220 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3615178 TGATTTATAT
3615188 ATTAAGATTAATTAG
1 ATTAAGATTAATTAG
3615203 -TTAA-ATTAATTAG
1 ATTAAGATTAATTAG
3615216 ATTAA
1 ATTAA
3615221 TCATGCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (15 bp):
ATTAAGATTAATTAG
Found at i:3619175 original size:29 final size:29
Alignment explanation
Indices: 3619133--3619409 Score: 197
Period size: 29 Copynumber: 9.5 Consensus size: 29
3619123 TCATCGACTA
* * *
3619133 ATGAAAAAGGATAGATTCGACAATCAATT
1 ATGAAAAGGGATAGCTTCGACCATCAATT
* * **
3619162 ATGAAAAGGGATAGCTTTGGCCATCGGTT
1 ATGAAAAGGGATAGCTTCGACCATCAATT
* *
3619191 ATGAAAAAGGGATAGCTTC-AGCTATCGATT
1 ATG-AAAAGGGATAGCTTCGA-CCATCAATT
* * * * *
3619221 ATGAAAATGGA-CGGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACCATCAATT
*
3619250 ATGAAAAGGGAT-G-TTGACAACCATCAATT
1 ATGAAAAGGGATAGCTT--CGACCATCAATT
* * *
3619279 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGACCATCAATT
* * *
3619308 ATGAAAAAGGATAGCTTC-AGCTATCGATT
1 ATGAAAAGGGATAGCTTCGA-CCATCAATT
* *
3619337 ATGAAAAGGGAT-GGTCACGACCATCAATT
1 ATGAAAAGGGATAGCT-TCGACCATCAATT
* * **
3619366 AATGAAAAGGGATGGTTTCGACCATCAAAG
1 -ATGAAAAGGGATAGCTTCGACCATCAATT
3619396 ATGAAAAGGGATAG
1 ATGAAAAGGGATAG
3619410 TTACAACCAT
Statistics
Matches: 196, Mismatches: 38, Indels: 28
0.75 0.15 0.11
Matches are distributed among these distances:
28 5 0.03
29 138 0.70
30 49 0.25
31 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACCATCAATT
Found at i:3619340 original size:87 final size:87
Alignment explanation
Indices: 3619189--3619378 Score: 231
Period size: 87 Copynumber: 2.2 Consensus size: 87
3619179 TGGCCATCGG
* * *
3619189 TTATGAAAAAGGGATAGCTTCAGCTATCGATTATGAAAATGGACGGTGACGACCATCAACTATGA
1 TTATG-AAAAGGGATAGCTTCAGCTATCGATTATGAAAAAGGAAGGTCACGACCATCAACTATGA
* *
3619254 AAAGGGATGTTGACAACCATCAA
65 AAAGGGATGGTCACAACCATCAA
* * * * *
3619277 TTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGATAGCTTCA-G-CTATCGATTATG
1 TTATGAAAAGGGATAGCTTCAGCTATCGATTATGAAAAAGGA-AG-GTCACGACCATCAACTATG
*
3619340 AAAAGGGATGGTCACGACCATCAA
64 AAAAGGGATGGTCACAACCATCAA
3619364 TTAATGAAAAGGGAT
1 TT-ATGAAAAGGGAT
3619379 GGTTTCGACC
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
87 67 0.76
88 19 0.22
89 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (87 bp):
TTATGAAAAGGGATAGCTTCAGCTATCGATTATGAAAAAGGAAGGTCACGACCATCAACTATGAA
AAGGGATGGTCACAACCATCAA
Found at i:3619371 original size:117 final size:117
Alignment explanation
Indices: 3619155--3619409 Score: 379
Period size: 117 Copynumber: 2.2 Consensus size: 117
3619145 AGATTCGACA
* *
3619155 ATCAATTATGAAAAGGGATAGCTTTGGCCATCGGTTATGAAAAAGGGATAGCTTCAGCTATCGAT
1 ATCAATTATGAAAAGGGATAGCTTCGGCCATCGATTATGAAAAAGGGATAGCTTCAGCTATCGAT
* *
3619220 TATGAAAATGGACGGTGACGACCATCAACTATGAAAAGGGAT-GTTGACAACC
66 TATGAAAAGGGACGGTCACGACCATCAACTATGAAAAGGGATGGTT-ACAACC
*
3619272 ATCAATTATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAA-GGATAGCTTCAGCTATCGAT
1 ATCAATTATGAAAAGGGATAGCTTCGGCCATCGATTATGAAAAAGGGATAGCTTCAGCTATCGAT
* * * *
3619336 TATGAAAAGGGATGGTCACGACCATCAATTAATGAAAAGGGATGGTTTCGACC
66 TATGAAAAGGGACGGTCACGACCATCAACT-ATGAAAAGGGATGGTTACAACC
**
3619389 ATCAAAGATGAAAAGGGATAG
1 ATCAATTATGAAAAGGGATAG
3619410 TTACAACCAT
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
116 46 0.37
117 76 0.61
118 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (117 bp):
ATCAATTATGAAAAGGGATAGCTTCGGCCATCGATTATGAAAAAGGGATAGCTTCAGCTATCGAT
TATGAAAAGGGACGGTCACGACCATCAACTATGAAAAGGGATGGTTACAACC
Found at i:3619400 original size:146 final size:146
Alignment explanation
Indices: 3619133--3619420 Score: 341
Period size: 146 Copynumber: 2.0 Consensus size: 146
3619123 TCATCGACTA
* ** *
3619133 ATGAAAAAGGATAGATTCGACAATCAATTATGAAAAGGGATAGCTTTGGCCATCGGTTATGAAAA
1 ATGAAAAAGGATAGATTCGACAATCAATTATGAAAAAGGATAGCTTCAGCCATCGATTATGAAAA
* * * * **
3619198 AGGGATAGCTTCAGCTATCGATTATGAAAATGGACGGTGACGACCATCAACTATGAAAAGGGAT-
66 AGGGATAGCGTCAGCCATCAATTATGAAAAGGGACGGTGACGACCATCAAAGATGAAAAGGGATA
3619262 GTTGACAACCATCAATT
131 GTT-ACAACCATCAATT
* * * * * *
3619279 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGATAGCTTCAGCTATCGATTATG-AAA
1 ATGAAAAAGGATAGATTCGACAATCAATTATGAAAAAGGATAGCTTCAGCCATCGATTATGAAAA
* **
3619343 AGGGAT-G-GTCACGACCATCAATTAATGAAAAGGGATGGTTTCGACCATCAAAGATGAAAAGGG
66 AGGGATAGCGTCA-G-CCATCAATT-ATGAAAAGGGACGGTGACGACCATCAAAGATGAAAAGGG
3619406 ATAGTTACAACCATC
128 ATAGTTACAACCATC
3619421 GTTCAACACA
Statistics
Matches: 119, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
143 3 0.03
144 2 0.02
145 16 0.13
146 95 0.80
147 3 0.03
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (146 bp):
ATGAAAAAGGATAGATTCGACAATCAATTATGAAAAAGGATAGCTTCAGCCATCGATTATGAAAA
AGGGATAGCGTCAGCCATCAATTATGAAAAGGGACGGTGACGACCATCAAAGATGAAAAGGGATA
GTTACAACCATCAATT
Found at i:3622637 original size:20 final size:20
Alignment explanation
Indices: 3622604--3622642 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3622594 TTTTAAGGAC
*
3622604 ATTTTAATTCAATATAGTTTT
1 ATTTAAATTCAATA-AGTTTT
3622625 ATTTAAATT-AATAAGTTT
1 ATTTAAATTCAATAAGTTT
3622643 GCATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTAAATTCAATAAGTTTT
Found at i:3625064 original size:10 final size:10
Alignment explanation
Indices: 3625049--3625110 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
3625039 TTTGAACCAT
*
3625049 TACCAATTCG
1 TACCAATTCA
*
3625059 TACCAAATACCA
1 TACC-AAT-TCA
*
3625071 TACCATTTCA
1 TACCAATTCA
3625081 TACCAATTCCA
1 TACCAATT-CA
* *
3625092 TACCAGTTCG
1 TACCAATTCA
3625102 TACCAATTC
1 TACCAATTC
3625111 TCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (10 bp):
TACCAATTCA
Found at i:3625094 original size:21 final size:21
Alignment explanation
Indices: 3625049--3625110 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
3625039 TTTGAACCAT
*
3625049 TACCAATTCGTACCAAATACCA
1 TACCAATTCGTACC-AATTCCA
* *
3625071 TACCATTTCATACCAATTCCA
1 TACCAATTCGTACCAATTCCA
*
3625092 TACCAGTTCGTACCAATTC
1 TACCAATTCGTACCAATTC
3625111 TCAAATACCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 23 0.66
22 12 0.34
ACGTcount: A:0.34, C:0.32, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCAATTCGTACCAATTCCA
Found at i:3625881 original size:21 final size:20
Alignment explanation
Indices: 3625838--3625898 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
3625828 AATCTTGAAG
3625838 GAAATTAAGAGAAGAAA-AAAA
1 GAAA-TAAGAGAA-AAAGAAAA
*
3625859 GAAATGAGAGAAAAAGAAGAA
1 GAAATAAGAGAAAAAGAA-AA
* *
3625880 GAGATAAAAGAAAAAGAAA
1 GAAATAAGAGAAAAAGAAA
3625899 CTGAGAGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 21 0.62
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (20 bp):
GAAATAAGAGAAAAAGAAAA
Found at i:3625888 original size:15 final size:14
Alignment explanation
Indices: 3625849--3625896 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
3625839 AAATTAAGAG
*
3625849 AAGAAAAAAAGAAA
1 AAGAGAAAAAGAAA
* *
3625863 TGAGAGAAAAAGAAG
1 -AAGAGAAAAAGAAA
3625878 AAGAGATAAAAGAAA
1 AAGAGA-AAAAGAAA
3625893 AAGA
1 AAGA
3625897 AACTGAGAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.04
Consensus pattern (14 bp):
AAGAGAAAAAGAAA
Found at i:3627700 original size:40 final size:40
Alignment explanation
Indices: 3627622--3627701 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
3627612 GAGAAGCTCG
* *
3627622 ATCAGCTCACTTGAGCTCATTTAAGCTCGTTCCTGCTCAA
1 ATCAGCTCACTTGAGCACATTTAAGCTCGTTCCAGCTCAA
* **
3627662 ATCAGCTCACTTGAGCACTTTTCAA-CTCGTTTGAGCTCAA
1 ATCAGCTCACTTGAGCACATTT-AAGCTCGTTCCAGCTCAA
3627702 TTAAGCAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.33
Consensus pattern (40 bp):
ATCAGCTCACTTGAGCACATTTAAGCTCGTTCCAGCTCAA
Found at i:3631176 original size:33 final size:34
Alignment explanation
Indices: 3631111--3631184 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
3631101 TTTTACTTGG
* *
3631111 TTTCTTTCTTCACTCGTTTCTTTTGCAGACTCTT
1 TTTCTTTCTTCACTCGTTTCTTTTGCAAACTCTC
3631145 TTTCTTTC-TCACTCGATTTCTTTT-CAAACTCTC
1 TTTCTTTCTTCACTCG-TTTCTTTTGCAAACTCTC
3631178 TTTCTTT
1 TTTCTTT
3631185 TTCTTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTCTTTCTTCACTCGTTTCTTTTGCAAACTCTC
Found at i:3631189 original size:6 final size:6
Alignment explanation
Indices: 3631178--3631232 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
3631168 TCAAACTCTC
* * * *
3631178 TTTCTT TTTCTT TTTCAT TTTC-T TTTC-- TTTCAA TTTCTT TTTCAT
1 TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT TTTCAT
3631223 TTTCAT TTTC
1 TTTCAT TTTC
3631233 TCGCTCGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 4 0.09
5 5 0.12
6 34 0.79
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTCAT
Found at i:3635487 original size:14 final size:14
Alignment explanation
Indices: 3635468--3635494 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3635458 TAGTTAAATT
3635468 AGTTAATTAATTTA
1 AGTTAATTAATTTA
3635482 AGTTAATTAATTT
1 AGTTAATTAATTT
3635495 GTTAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
AGTTAATTAATTTA
Found at i:3640304 original size:43 final size:43
Alignment explanation
Indices: 3640209--3640582 Score: 301
Period size: 43 Copynumber: 8.7 Consensus size: 43
3640199 CAGGTTTATA
* *
3640209 CTTCGATTTAGCCGATGATGCACT-TATGTGCCAGTATATTTG
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATATTTG
* * * * *
3640251 CTTCAATTTATCCAATGATGCACTATCTGTGACAGTATGA-TGG
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTAT-ATTTG
* * *
3640294 CTTCGGTTTATCCAATGATGCACTATGTGTGCCAGTATATTTT
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATATTTG
** *** ** * * ** *
3640337 CTTCGATTTATCTAATGATATGCTACATATGCAAAAATATGATTA
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATAT--TTG
*
3640382 CTTCGGTTTATCCGATGATGCAC--TGTGTGCCAGTATATTTG
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATATTTG
* * * * *
3640423 CTTTGGTTTATCCGGTGATGCGCTATGTGTGTCAGTATGA-TTG
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTAT-ATTTG
* * * *
3640466 CTTCGATTTAAACCAATGATGCACTATGTTTGCTAGTATATTTG
1 CTTCGATTT-ATCCGATGATGCACTATGTGTGCCAGTATATTTG
* * * *
3640510 CTTCGATTTATCTGATGATGCACCATTTGTGCCGGTATGA-TTG
1 CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTAT-ATTTG
* * *
3640553 CTTCGGTTTATCTGATGATGCGCTATGTGT
1 CTTCGATTTATCCGATGATGCACTATGTGT
3640583 TGGATCTGGT
Statistics
Matches: 259, Mismatches: 62, Indels: 21
0.76 0.18 0.06
Matches are distributed among these distances:
41 22 0.08
42 22 0.08
43 159 0.61
44 37 0.14
45 19 0.07
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (43 bp):
CTTCGATTTATCCGATGATGCACTATGTGTGCCAGTATATTTG
Found at i:3640354 original size:86 final size:86
Alignment explanation
Indices: 3640209--3640582 Score: 378
Period size: 86 Copynumber: 4.3 Consensus size: 86
3640199 CAGGTTTATA
* * * *
3640209 CTTCGATTTAGCCGATGATGCACT-TATGTGCCAGTATATTTGCTTCAATTTATCCAATGATGCA
1 CTTCGGTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTCGATTTATCCAATGATGCA
* *
3640273 CTATCTGTGACAGTATGATGG
66 CTATATGTGACAGTATGATTG
* * *
3640294 CTTCGGTTTATCCAATGATGCACTATGTGTGCCAGTATATTTTCTTCGATTTATCTAATGATATG
1 CTTCGGTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTCGATTTATCCAATG--ATG
** * * *
3640359 CTAC-ATATGCAAAAATATGATTA
64 C-ACTATATGTGACAGTATGATTG
* * ** *
3640382 CTTCGGTTTATCCGATGATGCAC--TGTGTGCCAGTATATTTGCTTTGGTTTATCCGGTGATGCG
1 CTTCGGTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTCGATTTATCCAATGATGCA
* *
3640445 CTATGTGTGTCAGTATGATTG
66 CTATATGTGACAGTATGATTG
* * * * * **
3640466 CTTCGATTTAAACCAATGATGCACTATGTTTGCTAGTATATTTGCTTCGATTTATCTGATGATGC
1 CTTCGGTTT-ATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTCGATTTATCCAATGATGC
* * * *
3640531 ACCATTTGTGCCGGTATGATTG
65 ACTATATGTGACAGTATGATTG
* *
3640553 CTTCGGTTTATCTGATGATGCGCTATGTGT
1 CTTCGGTTTATCCGATGATGCACTATGTGT
3640583 TGGATCTGGT
Statistics
Matches: 232, Mismatches: 49, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
83 1 0.00
84 24 0.10
85 33 0.14
86 76 0.33
87 58 0.25
88 38 0.16
89 2 0.01
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (86 bp):
CTTCGGTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTCGATTTATCCAATGATGCA
CTATATGTGACAGTATGATTG
Found at i:3640506 original size:173 final size:173
Alignment explanation
Indices: 3640207--3640528 Score: 466
Period size: 173 Copynumber: 1.9 Consensus size: 173
3640197 TACAGGTTTA
3640207 TACTTCGATTTAGCCGATGATGCACTTATGTGCCAGTATATTTGCTTCAATTTATCCAATGATGC
1 TACTTCGATTTAGCCGATGATGCACTTATGTGCCAGTATATTTGCTTCAATTTATCCAATGATGC
* * *
3640272 ACTATCTGTGACAGTATGATGGCTTCGGTTTATCCAATGATGCACTATGTGTGCCAGTATATTTT
66 ACTATCTGTGACAGTATGATGGCTTCGATTTAACCAATGATGCACTATGTGTGCCAGTATATTTG
3640337 CTTCGATTTATCTAATGATATGCTACATATGCAAAAATATGAT
131 CTTCGATTTATCTAATGATATGCTACATATGCAAAAATATGAT
* * * *** **
3640380 TACTTCGGTTTATCCGATGATGCAC-TGTGTGCCAGTATATTTGCTTTGGTTTATCCGGTGATGC
1 TACTTCGATTTAGCCGATGATGCACTTATGTGCCAGTATATTTGCTTCAATTTATCCAATGATGC
* * * * * *
3640444 GCTATGTGTGTCAGTATGATTGCTTCGATTTAAACCAATGATGCACTATGTTTGCTAGTATATTT
66 ACTATCTGTGACAGTATGATGGCTTCGATTT-AACCAATGATGCACTATGTGTGCCAGTATATTT
*
3640509 GCTTCGATTTATCTGATGAT
130 GCTTCGATTTATCTAATGAT
3640529 GCACCATTTG
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
172 59 0.45
173 71 0.55
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.40
Consensus pattern (173 bp):
TACTTCGATTTAGCCGATGATGCACTTATGTGCCAGTATATTTGCTTCAATTTATCCAATGATGC
ACTATCTGTGACAGTATGATGGCTTCGATTTAACCAATGATGCACTATGTGTGCCAGTATATTTG
CTTCGATTTATCTAATGATATGCTACATATGCAAAAATATGAT
Found at i:3642382 original size:51 final size:50
Alignment explanation
Indices: 3642272--3642509 Score: 212
Period size: 51 Copynumber: 4.7 Consensus size: 50
3642262 NNNNNNGGCT
* *
3642272 CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTCCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TTTCCGATA
* * * * * *
3642323 TC-CATAGTAGCCTTCACTTAGTACCACACATGTAACCATAGTTTACCGATA
1 -CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTT-CCGATA
* * * ** *
3642374 CACGTAGTAGCTTTCGCACAGTACTACACACGTG-CTCAAAACTTCTCGGTA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGAC-CAAAGTTTC-CGATA
* * * * *
3642425 CACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATCGATA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTTT-CCGATA
*
3642476 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTG
3642510 TTCATCGATA
Statistics
Matches: 145, Mismatches: 34, Indels: 15
0.75 0.18 0.08
Matches are distributed among these distances:
50 6 0.04
51 136 0.94
52 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTTTCCGATA
Found at i:3642448 original size:102 final size:102
Alignment explanation
Indices: 3642272--3642509 Score: 340
Period size: 102 Copynumber: 2.3 Consensus size: 102
3642262 NNNNNNGGCT
* * *
3642272 CACGTAGTAGCCTTCACATAGTACTACATACGTGACCAAAGCTTTCCGGTATCCATAGTAGCCTT
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTCCGGTATCCATAGTAGCCTT
3642337 CACTTAGTACCACACATGTAACCA-TAGTTTACCGATA
66 CACTTAGTACCACACATGTAACCATTA-TTTACCGATA
* *
3642374 CACGTAGTAGCTTTCGCACAGTACTACACACGTG-CTCAAAAC-TTCTCGGTA-CACATAGTAGC
1 CACGTAGTAGCCTTCACACAGTACTACACACGTGAC-CAAAACTTTC-CGGTATC-CATAGTAGC
* * *
3642436 CTTCACTTAGTACTACACATGTGACCATTATTTATCGATA
63 CTTCACTTAGTACCACACATGTAACCATTATTTACCGATA
3642476 CACGTAGTAGCCTTCACACAGTACTACACACGTG
1 CACGTAGTAGCCTTCACACAGTACTACACACGTG
3642510 TTCATCGATA
Statistics
Matches: 122, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
101 5 0.04
102 115 0.94
103 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (102 bp):
CACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAACTTTCCGGTATCCATAGTAGCCTT
CACTTAGTACCACACATGTAACCATTATTTACCGATA
Found at i:3649604 original size:49 final size:49
Alignment explanation
Indices: 3649539--3649769 Score: 444
Period size: 49 Copynumber: 4.7 Consensus size: 49
3649529 TCATTCGATA
3649539 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
* *
3649588 CACGTAGTAGCGTTCACAAAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
3649637 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
3649686 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
3649735 CACGTAGTAGCCTTCACATAGTACTACACACGTGA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGA
3649770 NNNNNNNNNN
Statistics
Matches: 178, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 178 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (49 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAGTTTTACAGTT
Found at i:3651634 original size:3 final size:3
Alignment explanation
Indices: 3651626--3651660 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3651616 GTACCACTTA
3651626 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3651661 CCTCTATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3651672 original size:12 final size:12
Alignment explanation
Indices: 3651657--3651686 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3651647 AAGAAGAAGA
*
3651657 AGAACCTCTATT
1 AGAACCTCTATC
3651669 AGAACCTCTATC
1 AGAACCTCTATC
3651681 AGAACC
1 AGAACC
3651687 CTTCTTACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.30, G:0.10, T:0.23
Consensus pattern (12 bp):
AGAACCTCTATC
Found at i:3653494 original size:26 final size:26
Alignment explanation
Indices: 3653458--3653511 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
3653448 CAAACTTTCC
*
3653458 TATAAACATATCATCCTGGAATCACT
1 TATAAACATATCATCCCGGAATCACT
*
3653484 TATAAATATATCATCCCGGAATCACT
1 TATAAACATATCATCCCGGAATCACT
3653510 TA
1 TA
3653512 CTTTCACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.31
Consensus pattern (26 bp):
TATAAACATATCATCCCGGAATCACT
Found at i:3653912 original size:20 final size:20
Alignment explanation
Indices: 3653884--3654001 Score: 96
Period size: 20 Copynumber: 5.9 Consensus size: 20
3653874 ATAGATGTAT
*
3653884 AACAGGGGCACCGAAGTGCA
1 AACAAGGGCACCGAAGTGCA
**
3653904 AACAAGGGCA-TAAATGTGCA
1 AACAAGGGCACCGAA-GTGCA
* * * *
3653924 AACAGGGGCACCGTAGTACG
1 AACAAGGGCACCGAAGTGCA
* *
3653944 AAC-AGGGACACCAAAGTGTA
1 AACAAGGG-CACCGAAGTGCA
* * *
3653964 TACAGGGGCACCTAAGTGCA
1 AACAAGGGCACCGAAGTGCA
3653984 AACAAGGGCACCGAAGTG
1 AACAAGGGCACCGAAGTG
3654002 AATATCCCGT
Statistics
Matches: 72, Mismatches: 22, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
19 5 0.07
20 63 0.88
21 4 0.06
ACGTcount: A:0.37, C:0.22, G:0.31, T:0.10
Consensus pattern (20 bp):
AACAAGGGCACCGAAGTGCA
Found at i:3653928 original size:40 final size:40
Alignment explanation
Indices: 3653884--3654001 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
3653874 ATAGATGTAT
*
3653884 AACAGGGGCACCGAAGTGCAAACAAGGGCA-TAAATGTGCA
1 AACAGGGGCACCGAAGTGCAAACAAGGGCACCAAA-GTGCA
* * * *
3653924 AACAGGGGCACCGTAGTACGAAC-AGGGACACCAAAGTGTA
1 AACAGGGGCACCGAAGTGCAAACAAGGG-CACCAAAGTGCA
* * *
3653964 TACAGGGGCACCTAAGTGCAAACAAGGGCACCGAAGTG
1 AACAGGGGCACCGAAGTGCAAACAAGGGCACCAAAGTG
3654002 AATATCCCGT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
39 4 0.06
40 53 0.83
41 7 0.11
ACGTcount: A:0.37, C:0.22, G:0.31, T:0.10
Consensus pattern (40 bp):
AACAGGGGCACCGAAGTGCAAACAAGGGCACCAAAGTGCA
Found at i:3655038 original size:15 final size:16
Alignment explanation
Indices: 3655016--3655062 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
3655006 GCAGAAATCG
3655016 AGAGAAAAAGAAAAAA
1 AGAGAAAAAGAAAAAA
3655032 A-AGAAAAA-AATAGAAA
1 AGAGAAAAAGAA-A-AAA
3655048 AGAGCAAAAAGAAAA
1 AGAG-AAAAAGAAAA
3655063 TTGATGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.08
15 8 0.31
16 5 0.19
17 3 0.12
18 6 0.23
19 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (16 bp):
AGAGAAAAAGAAAAAA
Found at i:3660833 original size:32 final size:30
Alignment explanation
Indices: 3660735--3660851 Score: 83
Period size: 32 Copynumber: 3.6 Consensus size: 30
3660725 CAAAAAAGGG
*
3660735 AAGAAAAAGAAAAATCAAAATCAAAGTCAAAATGAA
1 AAGAAAAAGAAAAA--AAAATCAAAAT--AAA--AA
**
3660771 AATGAAAAA-AATCAAAAATCAAAATAAAAA
1 AA-GAAAAAGAAAAAAAAATCAAAATAAAAA
* *
3660801 AAGAAGAAAGAAGAAAAAAATCAGAATGAAAA
1 AAGAA-AAAGAA-AAAAAAATCAAAATAAAAA
*
3660833 AGGAAAAAGAAAAAGAAAA
1 AAGAAAAAGAAAAA-AAAA
3660852 GGAGAGGCCA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
29 3 0.04
30 10 0.15
31 12 0.18
32 22 0.32
34 10 0.15
36 5 0.07
37 6 0.09
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.09
Consensus pattern (30 bp):
AAGAAAAAGAAAAAAAAATCAAAATAAAAA
Found at i:3662990 original size:43 final size:43
Alignment explanation
Indices: 3662940--3663162 Score: 365
Period size: 43 Copynumber: 5.2 Consensus size: 43
3662930 AAGATTGCGG
* * * *
3662940 ATCTTATCTTCCCTAGGAATAGGGAAACAGATCTAAGCTACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
3662983 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
*
3663026 ATCTTATCTTCCCCAAGAGTAAGGAAACAGATCCAAGCTACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
*
3663069 ATCTTATCTTCCCCAAGAGTAAGGAAACAGATCCAAGCTACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
* *
3663112 ATCTTATCTTCCCCAGGAGTAGGGAAACAGATCCAAGCCACGA
1 ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
*
3663155 GTCTTATC
1 ATCTTATC
3663163 CCCCTGAGGT
Statistics
Matches: 171, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 171 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (43 bp):
ATCTTATCTTCCCCAAGAGTAGGGAAACAGATCCAAGCTACGA
Found at i:3663282 original size:50 final size:50
Alignment explanation
Indices: 3663216--3663766 Score: 411
Period size: 50 Copynumber: 11.0 Consensus size: 50
3663206 CTCCCTAAGG
* * * *
3663216 TTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
* * * * *
3663266 TTGCAGTTCAAAAGATTAAAGCTACATCAGCGAATCTTACCTT-CCAGGCGA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTT-GCTTCCCTGAC-A
* * * *
3663317 -TGCAGTGGAACAGATTAAAGCCACATCGGCGAATCTTGCTTCCCTTACA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
* * * * * * *
3663366 TTGTAGTTCAAAAGATTAAAGCTACATCAGTGAATCTTACCTT-CCAGGCGA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTT-GCTTCCCTGAC-A
* * **
3663417 -TGCAGTGGAATAGATTAAAGCCACATCAATGAATCTTGCTTCCCTGACA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
* * * * * * *
3663466 TTACAGTTCAAAAGATTAAAGCTACATCAGCAAATCTTACCTT-CCAGGCGA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTT-GCTTCCCTGAC-A
* * * * *
3663517 -TGCAGTGGAACAA-ATTAAAGCCACATCGGTGAATCTTGCTTCCTTAACA
1 TTGCAGTTGAA-AAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
* * * * * *
3663566 TTGCAGTTCAAAAGACTAAAGCTACATCAGCGAATCTTACCTT-CCAGGCA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTT-GCTTCCCTGACA
* * * * *
3663616 GTGCAG-TGAAGCAGATTAAAGCCACATCGGTGAATCTTGATT-CCTCGACA
1 TTGCAGTTGAA-AAGATTAAAGCCACATCAGCGAATCTTGCTTCCCT-GACA
* * * * * * *
3663666 TTGTAGTTGAGAAGATTAAAGCTACAACAGCGAATCTTACTTCCCAGATA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
* * * * *
3663716 GTGCAGTGGAACAGATTAAAGCCACAGCGGCGAATCTTGCTTCCCTGACA
1 TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
3663766 T
1 T
3663767 CAAAGTTATG
Statistics
Matches: 375, Mismatches: 107, Indels: 38
0.72 0.21 0.07
Matches are distributed among these distances:
49 21 0.06
50 332 0.89
51 22 0.06
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (50 bp):
TTGCAGTTGAAAAGATTAAAGCCACATCAGCGAATCTTGCTTCCCTGACA
Found at i:3663374 original size:100 final size:100
Alignment explanation
Indices: 3663217--3663766 Score: 822
Period size: 100 Copynumber: 5.5 Consensus size: 100
3663207 TCCCTAAGGT
3663217 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
3663282 TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
66 TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
* * *
3663317 TGCAGTGGAACAGATTAAAGCCACATCGGCGAATCTTGCTTCCCTTACATTGTAGTTCAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
*
3663382 TAAAGCTACATCAGTGAATCTTACCTTCCAGGCGA
66 TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
* ** *
3663417 TGCAGTGGAATAGATTAAAGCCACATCAATGAATCTTGCTTCCCTGACATTACAGTTCAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
*
3663482 TAAAGCTACATCAGCAAATCTTACCTTCCAGGCGA
66 TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
* * * *
3663517 TGCAGTGGAACAAATTAAAGCCACATCGGTGAATCTTGCTTCCTTAACATTGCAGTTCAAAAGAC
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
3663582 TAAAGCTACATCAGCGAATCTTACCTTCCAGGC-A
66 TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
* * * *
3663616 GTGCAGT-GAAGCAGATTAAAGCCACATCGGTGAATCTTGATT-CCTCGACATTGTAGTTGAGAA
1 -TGCAGTGGAA-CAGATTAAAGCCACATCGGTGAATCTTGCTTCCCT-GACATTGCAGTTCAAAA
* **
3663679 GATTAAAGCTACAACAGCGAATCTTA-CTTCCCA-GATA
63 GATTAAAGCTACATCAGCGAATCTTACCTT-CCAGGCGA
* *
3663716 GTGCAGTGGAACAGATTAAAGCCACAGCGGCGAATCTTGCTTCCCTGACAT
1 -TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACAT
3663767 CAAAGTTATG
Statistics
Matches: 408, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
99 10 0.02
100 392 0.96
101 6 0.01
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.25
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTCAAAAGAT
TAAAGCTACATCAGCGAATCTTACCTTCCAGGCGA
Found at i:3664337 original size:15 final size:15
Alignment explanation
Indices: 3664299--3664343 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
3664289 GCAGAAATCG
*
3664299 AGAGAAAAATAAAAA
1 AGAGAAAAATAGAAA
*
3664314 AGAAAAAAATAGAAA
1 AGAGAAAAATAGAAA
*
3664329 AGAGCAAAA-AGAAA
1 AGAGAAAAATAGAAA
3664343 A
1 A
3664344 ATGATGTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (15 bp):
AGAGAAAAATAGAAA
Found at i:3673053 original size:20 final size:21
Alignment explanation
Indices: 3673021--3673069 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3673011 TATAGCTTTC
3673021 TTTAAATATTTTTTAT-ATTTT
1 TTTAAA-ATTTTTTATGATTTT
3673042 TTTAAAA-TTTTTATGATTTT
1 TTTAAAATTTTTTATGATTTT
*
3673062 TTAAAAAT
1 TTTAAAAT
3673070 ATAAATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 7 0.28
20 12 0.48
21 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTAAAATTTTTTATGATTTT
Found at i:3673156 original size:20 final size:20
Alignment explanation
Indices: 3673039--3673146 Score: 109
Period size: 19 Copynumber: 5.3 Consensus size: 20
3673029 TTTTTTATAT
3673039 TTTTTTAAAATT-TTTATG-A
1 TTTTTTAAAATTATTT-TGAA
3673058 TTTTTTAAAAATATAAATTTTGAA
1 TTTTTT-AAAAT-T--ATTTTGAA
*
3673082 -TTTATATAAA-TATTTTGAA
1 TTTTTTA-AAATTATTTTGAA
3673101 -TTTTTAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
3673120 TTTTTTAAAATTATTTTGAA
1 TTTTTTAAAATTATTTTGAA
3673140 TTATTTT
1 TT-TTTT
3673147 GTAATTTTTT
Statistics
Matches: 77, Mismatches: 2, Indels: 18
0.79 0.02 0.19
Matches are distributed among these distances:
18 3 0.04
19 28 0.36
20 26 0.34
21 6 0.08
22 1 0.01
23 9 0.12
24 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTTTAAAATTATTTTGAA
Found at i:3673157 original size:11 final size:10
Alignment explanation
Indices: 3673092--3673156 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
3673082 TTTATATAAA
3673092 TATTTTGAAT
1 TATTTTGAAT
**
3673102 T-TTTAAAAT
1 TATTTTGAAT
3673111 TATTTTGAAT
1 TATTTTGAAT
*
3673121 T-TTTTAAAAT
1 TATTTT-GAAT
3673131 TATTTTGAAT
1 TATTTTGAAT
3673141 TATTTTGTAAT
1 TATTTTG-AAT
3673152 T-TTTT
1 TATTTT
3673157 TAGAGAGACC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 11 0.24
10 26 0.58
11 8 0.18
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (10 bp):
TATTTTGAAT
Found at i:3677930 original size:19 final size:20
Alignment explanation
Indices: 3677897--3677935 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3677887 CTTTATATAA
3677897 ATTTATATATATTTTTAAAT
1 ATTTATATATATTTTTAAAT
*
3677917 ATTT-TATATTTTTTTAAAT
1 ATTTATATATATTTTTAAAT
3677936 NNNNNNNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTATATATATTTTTAAAT
Found at i:3678880 original size:17 final size:18
Alignment explanation
Indices: 3678849--3678896 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
3678839 AAAAAATACA
*
3678849 TATTT-ATATTAAATATT
1 TATTTAATATTTAATATT
3678866 T-TGTTAA-ATTTAATATT
1 TAT-TTAATATTTAATATT
3678883 TATTTAATATTTAA
1 TATTTAATATTTAA
3678897 ATTATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 17 0.65
18 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTAATATTTAATATT
Found at i:3681864 original size:21 final size:21
Alignment explanation
Indices: 3681838--3681898 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
3681828 TAACTTAATA
* *
3681838 ATAAAAGATCAAAAATCTATG
1 ATAAAAGATTAAGAATCTATG
3681859 ATAAAAGATTAAGAATCTATG
1 ATAAAAGATTAAGAATCTATG
3681880 ATAAAAGATTAAGAATCTA
1 ATAAAAGATTAAGAATCTA
3681899 ATCACATCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (21 bp):
ATAAAAGATTAAGAATCTATG
Found at i:3682937 original size:30 final size:30
Alignment explanation
Indices: 3682903--3682961 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3682893 ATCTTCAACT
3682903 CCATGGCCGAATTTCACAAGGGGAAACCAC
1 CCATGGCCGAATTTCACAAGGGGAAACCAC
* *
3682933 CCATGGCTGAATTTGACAAGGGGAAACCA
1 CCATGGCCGAATTTCACAAGGGGAAACCA
3682962 TGGCTAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.15
Consensus pattern (30 bp):
CCATGGCCGAATTTCACAAGGGGAAACCAC
Found at i:3683825 original size:50 final size:50
Alignment explanation
Indices: 3683744--3684024 Score: 298
Period size: 50 Copynumber: 5.6 Consensus size: 50
3683734 ATTTGGGTAA
*
3683744 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
3683794 ATAGGTCCCATGTAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
3683844 AGAGGTCCCATGTAAGACCATGTGTTGGG-CATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGT-CTGGGACATGGCATTGGCACCGAGATG
** * * *
3683894 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
3683944 AGAACTCTCATGTAATACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
3683993 AAACATCCCATGTAAGACTATGTCTGGGACAT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACAT
3684025 AACTTTGGCA
Statistics
Matches: 191, Mismatches: 37, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
49 31 0.16
50 157 0.82
51 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:3686639 original size:49 final size:50
Alignment explanation
Indices: 3686560--3686802 Score: 202
Period size: 50 Copynumber: 4.8 Consensus size: 50
3686550 TGAATATAAC
* * * ** * *
3686560 ATGCCAAAGCTATGTCCCAGACATAATCTTACATGGGATGTT-TCTTGT-G
1 ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGA-GTTCTCATATAG
* * *
3686609 CTGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAG
1 ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
* ** * *
3686659 ATGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCG
1 ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
* * * * *
3686709 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATATCAATG
1 ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGA-GT-TC-TCATAT--A-G
* * *
3686765 ATGCCAATGCCATGTGCCAGACATGGTCTTACATGGGA
1 ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGA
3686803 TCTCTTTACT
Statistics
Matches: 157, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
48 3 0.02
49 35 0.22
50 77 0.49
51 1 0.01
52 2 0.01
53 4 0.03
56 35 0.22
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAACGCCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATAG
Found at i:3686735 original size:100 final size:105
Alignment explanation
Indices: 3686610--3686799 Score: 255
Period size: 100 Copynumber: 1.8 Consensus size: 105
3686600 TTTCTTGTGC
* * * * *
3686610 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA-GT-TC-TCATAT-A-GATGCCAACGCC
1 TGCCAACGCCATATCCCAAACATGGTCTTACATGGGACCTCTCATAATATAATGATGCCAACGCC
3686670 ATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
66 ATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
* *
3686710 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATATCAATGATGCCAATGC
1 TGCCAACGCCATATCCCAAACATGGTCTTACATGGGACCTCTCATAATAT-AATGATGCCAACGC
* *
3686775 CATGTGCCAGACATGGTCTTACATG
65 CATATCCCAGACATGGTCTTACATG
3686800 GGATCTCTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
100 33 0.44
101 1 0.01
102 2 0.03
103 5 0.07
105 1 0.01
106 33 0.44
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (105 bp):
TGCCAACGCCATATCCCAAACATGGTCTTACATGGGACCTCTCATAATATAATGATGCCAACGCC
ATATCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
Found at i:3686777 original size:56 final size:52
Alignment explanation
Indices: 3686610--3686807 Score: 215
Period size: 50 Copynumber: 3.8 Consensus size: 52
3686600 TTTCTTGTGC
* * **
3686610 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTC-ATAT-AGA
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCTATATCAGA
* * *
3686660 TGCCAACGCCATATCCCAGACATGGTCTTACATGAGACCTCTC-ATCTC-GG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCTATATCAGA
* *
3686710 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAATATCAATGA
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTC-T-ATATC-A-GA
* * * *
3686766 TGCCAATGCCATGTGCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCT
3686808 TTACTCATAT
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
50 82 0.66
53 4 0.03
56 39 0.31
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (52 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCTATATCAGA
Found at i:3687426 original size:17 final size:17
Alignment explanation
Indices: 3687406--3687440 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3687396 ATATTCTACC
3687406 ATAAAACATAAAAATAA
1 ATAAAACATAAAAATAA
3687423 ATAAAACATAAAAATAA
1 ATAAAACATAAAAATAA
3687440 A
1 A
3687441 CACATTTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
ATAAAACATAAAAATAA
Found at i:3697580 original size:18 final size:18
Alignment explanation
Indices: 3697557--3697592 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3697547 GTTATGGCTG
3697557 AATCTGATAATTTTACGA
1 AATCTGATAATTTTACGA
3697575 AATCTGATAATTTTACGA
1 AATCTGATAATTTTACGA
3697593 TAAAGGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (18 bp):
AATCTGATAATTTTACGA
Found at i:3698198 original size:24 final size:23
Alignment explanation
Indices: 3698171--3698216 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
3698161 ATACAGAATC
*
3698171 CTACCCCCATCCTCTACACACCAA
1 CTACCACCATCCTCT-CACACCAA
* *
3698195 CTACGAGCATCCTCTCACACCA
1 CTACCACCATCCTCTCACACCA
3698217 TGTGGGGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.28, C:0.50, G:0.04, T:0.17
Consensus pattern (23 bp):
CTACCACCATCCTCTCACACCAA
Found at i:3702986 original size:24 final size:26
Alignment explanation
Indices: 3702932--3703000 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
3702922 ATAATAAGAA
3702932 AGGAT-GAAATTGGCTAAGTGAAATG
1 AGGATGGAAATTGGCTAAGTGAAATG
* *
3702957 ATGATGGAAA-TGGCTAGGTG-AATG
1 AGGATGGAAATTGGCTAAGTGAAATG
*
3702981 AGGATGGAGATTTGGCTAAG
1 AGGATGGA-AATTGGCTAAG
3703001 GTTTTGAAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 11 0.31
25 14 0.39
26 11 0.31
ACGTcount: A:0.35, C:0.04, G:0.36, T:0.25
Consensus pattern (26 bp):
AGGATGGAAATTGGCTAAGTGAAATG
Found at i:3704328 original size:30 final size:30
Alignment explanation
Indices: 3704289--3704379 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
3704279 ATAAAATAGC
3704289 ATCGAGCTCAATGAGCTAAGATTGAGCTGA
1 ATCGAGCTCAATGAGCTAAGATTGAGCTGA
* * **
3704319 ATTGAGCTCAAGGAATTGAA-ATTCGAGCTGA
1 ATCGAGCTCAATGAGCT-AAGATT-GAGCTGA
* * *
3704350 ATCAAGCTCAATAAGCTAGGATTGAGCTGA
1 ATCGAGCTCAATGAGCTAAGATTGAGCTGA
3704380 TCAACTAGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
30 24 0.51
31 23 0.49
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.24
Consensus pattern (30 bp):
ATCGAGCTCAATGAGCTAAGATTGAGCTGA
Found at i:3715115 original size:42 final size:42
Alignment explanation
Indices: 3715056--3715194 Score: 242
Period size: 42 Copynumber: 3.3 Consensus size: 42
3715046 TACTCCCCAG
* *
3715056 CTCGTATGAGCAGCATCGTGTAGCTTACATTCTGACCCACAA
1 CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAA
3715098 CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAA
1 CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAA
*
3715140 CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAG
1 CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAA
*
3715182 CTCGTGTGAGTAG
1 CTCGTATGAGTAG
3715195 ACCAATTCCC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 93 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (42 bp):
CTCGTATGAGTAGCATCGTATAGCTTACATTCTGACCCACAA
Found at i:3720984 original size:15 final size:15
Alignment explanation
Indices: 3720936--3720987 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3720926 TCCATTGAGC
3720936 AAGAAAAAGAAAAAGAGA
1 AAGAAAAAG--AAAGA-A
* **
3720954 AACAAAAAGAGTGAA
1 AAGAAAAAGAAAGAA
3720969 AAGAAAAAGAAAGAA
1 AAGAAAAAGAAAGAA
3720984 AAGA
1 AAGA
3720988 CTGACGAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 17 0.61
16 3 0.11
18 8 0.29
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAAGAA
Found at i:3720997 original size:26 final size:26
Alignment explanation
Indices: 3720967--3721034 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
3720957 AAAAAGAGTG
3720967 AAAAGAAAAAGAAAGAA-AAGACTGAC
1 AAAAGAAAAAGAAA-AACAAGACTGAC
* ** * * *
3720993 GAAAGTGAGATAAAAACAAGAGTGAC
1 AAAAGAAAAAGAAAAACAAGACTGAC
3721019 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
3721035 GAGTGTGAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 2
0.70 0.26 0.05
Matches are distributed among these distances:
25 2 0.07
26 28 0.93
ACGTcount: A:0.68, C:0.06, G:0.21, T:0.06
Consensus pattern (26 bp):
AAAAGAAAAAGAAAAACAAGACTGAC
Found at i:3728438 original size:19 final size:19
Alignment explanation
Indices: 3728414--3728470 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
3728404 ATGCACGTCC
3728414 AAATGCATGTCTCTCCATT
1 AAATGCATGTCTCTCCATT
3728433 AAATGCA-G----TCCATT
1 AAATGCATGTCTCTCCATT
*
3728447 -GA-GCATGTCTCTCCATT
1 AAATGCATGTCTCTCCATT
3728464 AAATGCA
1 AAATGCA
3728471 GTCCATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 14
0.64 0.04 0.31
Matches are distributed among these distances:
12 3 0.10
13 2 0.07
14 6 0.21
17 6 0.21
18 2 0.07
19 10 0.34
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.32
Consensus pattern (19 bp):
AAATGCATGTCTCTCCATT
Found at i:3728453 original size:31 final size:31
Alignment explanation
Indices: 3728418--3728479 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3728408 ACGTCCAAAT
3728418 GCATGTCTCTCCATTAAATGCAGTCCATTGA
1 GCATGTCTCTCCATTAAATGCAGTCCATTGA
3728449 GCATGTCTCTCCATTAAATGCAGTCCATTGA
1 GCATGTCTCTCCATTAAATGCAGTCCATTGA
3728480 ATATACTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (31 bp):
GCATGTCTCTCCATTAAATGCAGTCCATTGA
Found at i:3741834 original size:52 final size:52
Alignment explanation
Indices: 3741751--3742060 Score: 602
Period size: 52 Copynumber: 6.0 Consensus size: 52
3741741 TAAGGAAACG
* *
3741751 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
3741803 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
3741855 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
3741907 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
3741959 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
3742011 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAAC
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAAC
3742061 GGAGGTTGTC
Statistics
Matches: 256, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 256 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:3755508 original size:21 final size:22
Alignment explanation
Indices: 3755482--3755522 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3755472 TTTTTCCACT
*
3755482 ATTTCTTTTTC-CTCTCTTTCA
1 ATTTCTTTTTCAATCTCTTTCA
3755503 ATTTCTTTTTCAATCTCTTT
1 ATTTCTTTTTCAATCTCTTT
3755523 TTGCTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTCTTTTTCAATCTCTTTCA
Found at i:3760294 original size:45 final size:46
Alignment explanation
Indices: 3760239--3760331 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 46
3760229 CAAAGAAAAG
* *
3760239 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTAGTATATGATGA
1 ACCTCGACCCACTACCAATG-ACGATAGGAACCTTAGTATATGATGA
* *
3760285 ACCTC-ACCCACTACCAATGACGATAGGATCCTTGGTATATGATGA
1 ACCTCGACCCACTACCAATGACGATAGGAACCTTAGTATATGATGA
3760330 AC
1 AC
3760332 GCCACACTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 36 0.86
46 6 0.14
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTACCAATGACGATAGGAACCTTAGTATATGATGA
Found at i:3764458 original size:46 final size:46
Alignment explanation
Indices: 3764406--3764498 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
3764396 CAAAGAAAAG
3764406 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
*
3764452 ACCTCGACCCACTATCAAGGATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
3764498 A
1 A
3764499 TGCCACACTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:3772512 original size:22 final size:22
Alignment explanation
Indices: 3772457--3772524 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
3772447 CATCTTTTTA
*
3772457 TTTTCTCACTTTCTTTTCAT-TTT
1 TTTTCTCAATTT-TTTT-ATCTTT
*
3772480 CTTTTGT-AATTTTTTTATCTTT
1 -TTTTCTCAATTTTTTTATCTTT
3772502 TTTTCTCAATTTTCTTT-TCTTT
1 TTTTCTCAATTTT-TTTATCTTT
3772524 T
1 T
3772525 GGATTTTTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 7 0.18
22 19 0.50
23 7 0.18
24 5 0.13
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.72
Consensus pattern (22 bp):
TTTTCTCAATTTTTTTATCTTT
Found at i:3774635 original size:16 final size:16
Alignment explanation
Indices: 3774599--3774638 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3774589 CTTTTTTTTG
3774599 TTTTTTTAAATCACAA
1 TTTTTTTAAATCACAA
*
3774615 ATTTTTTAAATCAC--
1 TTTTTTTAAATCACAA
3774629 TTTTTTTAAA
1 TTTTTTTAAA
3774639 AATTTCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
16 13 0.59
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTTTTAAATCACAA
Found at i:3777444 original size:20 final size:20
Alignment explanation
Indices: 3777430--3777488 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
3777420 ATGAGCTTAA
*
3777430 TTGAGCTCGTGTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
*
3777450 TTGAGCTCGAATGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
3777470 TTGAGCTCGAGTGAGCTGA
1 TTGAGCTCGAGTGAGCTGA
3777489 ACCGCATGGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.34, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:3779430 original size:7 final size:6
Alignment explanation
Indices: 3779410--3779463 Score: 63
Period size: 6 Copynumber: 9.0 Consensus size: 6
3779400 TCACTTGCAC
* * * **
3779410 TTTCTT TTTCTT TTTCGT TTTCTA TTTCCT TTTCAC TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
3779458 TTTCTT
1 TTTCTT
3779464 CCTCTTCGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:3779431 original size:18 final size:18
Alignment explanation
Indices: 3779392--3779461 Score: 77
Period size: 18 Copynumber: 3.9 Consensus size: 18
3779382 CTTTTTTCGA
** *
3779392 TTTCTTTTTCACTTGCAC
1 TTTCTTTTTCTTTTTCAC
**
3779410 TTTCTTTTTCTTTTTCGT
1 TTTCTTTTTCTTTTTCAC
* *
3779428 TTTCTATTTCCTTTTCAC
1 TTTCTTTTTCTTTTTCAC
3779446 TTTCTTTTTCTTTTTC
1 TTTCTTTTTCTTTTTC
3779462 TTCCTCTTCG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.06, C:0.23, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTCTTTTTCTTTTTCAC
Found at i:3779432 original size:36 final size:36
Alignment explanation
Indices: 3779384--3779461 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
3779374 TTCTCTCACT
*
3779384 TTTTTCGATTTCTTTTTCAC-TTGCACTTTCTTTTTC
1 TTTTTCGATTTCTATTTC-CTTTGCACTTTCTTTTTC
* *
3779420 TTTTTCGTTTTCTATTTCCTTTTCACTTTCTTTTTC
1 TTTTTCGATTTCTATTTCCTTTGCACTTTCTTTTTC
3779456 TTTTTC
1 TTTTTC
3779462 TTCCTCTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 1 0.03
36 37 0.97
ACGTcount: A:0.06, C:0.22, G:0.04, T:0.68
Consensus pattern (36 bp):
TTTTTCGATTTCTATTTCCTTTGCACTTTCTTTTTC
Found at i:3780249 original size:24 final size:24
Alignment explanation
Indices: 3780221--3780266 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3780211 GTCTTTGCTA
* *
3780221 AAGCAAGCCTAGACAGCATTAAAG
1 AAGCAAGCATAGACAACATTAAAG
*
3780245 AAGCAAGCATGGACAACATTAA
1 AAGCAAGCATAGACAACATTAA
3780267 TGGAGCTGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.13
Consensus pattern (24 bp):
AAGCAAGCATAGACAACATTAAAG
Found at i:3781607 original size:14 final size:14
Alignment explanation
Indices: 3781590--3781626 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3781580 GAAAAAAAAT
*
3781590 AAAAAAAAGTGAGC
1 AAAAAAAAGTGAGA
*
3781604 AAAAAAAATTGAGA
1 AAAAAAAAGTGAGA
3781618 AAAAAAAAG
1 AAAAAAAAG
3781627 AGTTGAAAGT
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:0.73, C:0.03, G:0.16, T:0.08
Consensus pattern (14 bp):
AAAAAAAAGTGAGA
Found at i:3782582 original size:15 final size:15
Alignment explanation
Indices: 3782558--3782593 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3782548 ATTGAGAGAC
3782558 GAAA-AAAAAGAAAT
1 GAAAGAAAAAGAAAT
3782572 GAAAGAAAAAGAAAT
1 GAAAGAAAAAGAAAT
*
3782587 CAAAGAA
1 GAAAGAA
3782594 GTGAGAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.75, C:0.03, G:0.17, T:0.06
Consensus pattern (15 bp):
GAAAGAAAAAGAAAT
Found at i:3782617 original size:24 final size:24
Alignment explanation
Indices: 3782564--3782609 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3782554 AGACGAAAAA
3782564 AAAGAAATGAAAGAAAAAGAAATC
1 AAAGAAATGAAAGAAAAAGAAATC
* *
3782588 AAAGAAGTGAGAGAAAAAGAAA
1 AAAGAAATGAAAGAAAAAGAAA
3782610 ATGAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.07
Consensus pattern (24 bp):
AAAGAAATGAAAGAAAAAGAAATC
Found at i:3782636 original size:18 final size:18
Alignment explanation
Indices: 3782613--3782655 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3782603 AAAGAAAATG
3782613 AAGAAA-AGAGAATTGAAA
1 AAGAAATAGAG-ATTGAAA
* *
3782631 AAGAAATTGAGATTGAGA
1 AAGAAATAGAGATTGAAA
3782649 AAGAAAT
1 AAGAAAT
3782656 TGAAAAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.16
Consensus pattern (18 bp):
AAGAAATAGAGATTGAAA
Found at i:3782656 original size:18 final size:18
Alignment explanation
Indices: 3782624--3782658 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3782614 AGAAAAGAGA
3782624 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAATTGAG
*
3782642 ATTGAGAAAGAAATTGA
1 ATTGAAAAAGAAATTGA
3782659 AAAAGAGAGA
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:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
ATTGAAAAAGAAATTGAG
Found at i:3801155 original size:22 final size:23
Alignment explanation
Indices: 3801110--3801155 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3801100 AAATTCTACT
* *
3801110 AGTAAAAATGCAGACAAGTTGCC
1 AGTAAAAATGCAGACAAATCGCC
*
3801133 AGTAAAAATGC-GATAAATCGCC
1 AGTAAAAATGCAGACAAATCGCC
3801155 A
1 A
3801156 TTCTGCTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (23 bp):
AGTAAAAATGCAGACAAATCGCC
Found at i:3805263 original size:22 final size:22
Alignment explanation
Indices: 3805238--3805288 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
3805228 TTTGGCACGT
3805238 AATGGTTTAAGTTTAAGTACGA
1 AATGGTTTAAGTTTAAGTACGA
** *
3805260 AATGGTTTTTGGTTTAGGTACGA
1 AATGG-TTTAAGTTTAAGTACGA
3805283 AATGGT
1 AATGGT
3805289 ATGGTTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.29, C:0.04, G:0.27, T:0.39
Consensus pattern (22 bp):
AATGGTTTAAGTTTAAGTACGA
Found at i:3811535 original size:18 final size:17
Alignment explanation
Indices: 3811493--3811810 Score: 138
Period size: 17 Copynumber: 17.6 Consensus size: 17
3811483 ACGAGGATTT
3811493 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* **
3811510 TTTATGAAACACGGTCAA
1 TTTTTGAAACAC-GAAAA
*
3811528 TTTTTGAAAACACAAAAA
1 TTTTTG-AAACACGAAAA
* * *
3811546 TTTTTGAAAGATGAGAATTT
1 TTTTTGAAACACGA-AA--A
*
3811566 TTTTTAAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * *
3811583 TTTATGAAACATGGAAATCT
1 TTTTTGAAACA-CGAAA--A
*
3811603 TTTTTGAAAACAAGAAAA
1 TTTTTG-AAACACGAAAA
* * *
3811621 TTTTCGAAATACGAGAA
1 TTTTTGAAACACGAAAA
* * *
3811638 TTTTAGAAAAACGGGAAA
1 TTTTTGAAACAC-GAAAA
3811656 -TTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* *
3811673 TTTTGGAAACAC-AGGAA
1 TTTTTGAAACACGA-AAA
** *
3811690 TTTTAAAAACACGAAGAT
1 TTTTTGAAACACGAA-AA
* * *
3811708 TTTTTGAAGCATGAGAA
1 TTTTTGAAACACGAAAA
**
3811725 TTTTTGAAAACACGAATTT
1 TTTTTG-AAACACGAA-AA
* * *
3811744 TTTTTAAAAAACAAGGAAA
1 TTTTT--GAAACACGAAAA
*
3811763 TTTTTGAAGCACGAGAAA
1 TTTTTGAAACACGA-AAA
3811781 TTTTTTGAAAACACG-AAA
1 -TTTTTG-AAACACGAAAA
3811799 TCTTTTGAAACA
1 T-TTTTGAAACA
3811811 TGATTTTTTT
Statistics
Matches: 218, Mismatches: 60, Indels: 46
0.67 0.19 0.14
Matches are distributed among these distances:
16 1 0.00
17 87 0.40
18 68 0.31
19 24 0.11
20 33 0.15
21 5 0.02
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:3811539 original size:36 final size:36
Alignment explanation
Indices: 3811478--3811798 Score: 157
Period size: 37 Copynumber: 8.8 Consensus size: 36
3811468 GATAAAAAAC
*
3811478 GAAACACGAGGATTTTTTTTG-AAACACGAAAATTTAT
1 GAAACACGA-GA-ATTTTTTGAAAACACGAAAATTTAT
* *
3811515 GAAACACG-GTCAA-TTTTTGAAAACACAAAAATTTTT
1 GAAACACGAG--AATTTTTTGAAAACACGAAAATTTAT
* * *
3811551 GAAAGATGAGAATTTTTTTTAAAACACGAAAATTTAT
1 GAAACACGAGAA-TTTTTTGAAAACACGAAAATTTAT
* *
3811588 GAAACATG-GAAATCTTTTTTGAAAACAAGAAAATTT-T
1 GAAACACGAG-AA--TTTTTTGAAAACACGAAAATTTAT
* * *
3811625 CGAAATACGAGAA-TTTTAGAAAA-ACGGGAAATTT-T
1 -GAAACACGAGAATTTTTTGAAAACAC-GAAAATTTAT
* * * *
3811660 GAAAACACGA-AA-ATTTTGGAAACACAGGAATTTTA-
1 G-AAACACGAGAATTTTTTGAAAACAC-GAAAATTTAT
* * * * *
3811695 AAAACACGA-AGATTTTTTG-AAGCATGAGAATTTTT
1 GAAACACGAGA-ATTTTTTGAAAACACGAAAATTTAT
* * * * *
3811730 GAAAACACGA-ATTTTTTTTAAAAAACAAGGAAATTTTT
1 G-AAACACGAGA-ATTTTTT-GAAAACACGAAAATTTAT
*
3811768 GAAGCACGAGAAATTTTTTGAAAACACGAAA
1 GAAACACGAG-AATTTTTTGAAAACACGAAA
3811799 TCTTTTGAAA
Statistics
Matches: 218, Mismatches: 44, Indels: 44
0.71 0.14 0.14
Matches are distributed among these distances:
34 25 0.11
35 47 0.22
36 41 0.19
37 56 0.26
38 47 0.22
39 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (36 bp):
GAAACACGAGAATTTTTTGAAAACACGAAAATTTAT
Found at i:3811576 original size:73 final size:73
Alignment explanation
Indices: 3811477--3811641 Score: 208
Period size: 73 Copynumber: 2.2 Consensus size: 73
3811467 TGATAAAAAA
* * *
3811477 CGAAACACGAGGATTTTTTTTGAAACACGAAAATTTATGAAACACGG-TCAATTTTTGAAAACAC
1 CGAAAGACGAGAATTTTTTTTAAAACACGAAAATTTATGAAACACGGATC-ATTTTTGAAAACA-
3811541 A-AAAATTTT
64 AGAAAATTTT
* * * *
3811550 TGAAAGATGAGAATTTTTTTTAAAACACGAAAATTTATGAAACATGGAAATCTTTTTTGAAAACA
1 CGAAAGACGAGAATTTTTTTTAAAACACGAAAATTTATGAAACACGG--ATCATTTTTGAAAACA
3811615 AGAAAATTTT
64 AGAAAATTTT
*
3811625 CGAAATACGAGAATTTT
1 CGAAAGACGAGAATTTT
3811642 AGAAAAACGG
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
73 41 0.53
74 1 0.01
75 34 0.44
76 2 0.03
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (73 bp):
CGAAAGACGAGAATTTTTTTTAAAACACGAAAATTTATGAAACACGGATCATTTTTGAAAACAAG
AAAATTTT
Found at i:3811804 original size:19 final size:18
Alignment explanation
Indices: 3811492--3811808 Score: 110
Period size: 18 Copynumber: 17.6 Consensus size: 18
3811482 CACGAGGATT
3811492 TTTTTTG-AAACACGAAA
1 TTTTTTGAAAACACGAAA
* * *
3811509 ATTTATG-AAACACGGTCAA
1 TTTTTTGAAAACAC-G-AAA
*
3811528 -TTTTTGAAAACACAAAA
1 TTTTTTGAAAACACGAAA
* * *
3811545 ATTTTTGAAAGATGA-GAAT
1 TTTTTTGAAA-A-CACGAAA
*
3811564 TTTTTTTAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* * *
3811582 ATTTATG-AAACATGGAAA
1 TTTTTTGAAAACA-CGAAA
*
3811600 TCTTTTTTGAAAACAAGAAA
1 --TTTTTTGAAAACACGAAA
* * *
3811620 ATTTTCG-AAATACGAGAA
1 TTTTTTGAAAACACGA-AA
*
3811638 -TTTTAGAAAA-ACGGGAAA
1 TTTTTTGAAAACAC--GAAA
3811656 --TTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
* * *
3811672 -ATTTTGGAAACACAGGAA
1 TTTTTTGAAAACAC-GAAA
*
3811690 --TTTTAAAAACACGAAGA
1 TTTTTTGAAAACACGAA-A
* *
3811707 TTTTTTG-AAGCATGAGAA
1 TTTTTTGAAAACACGA-AA
*
3811725 -TTTTTGAAAACACGAATT
1 TTTTTTGAAAACACGAA-A
* *
3811743 TTTTTTAAAAAACAAGGAAA
1 TTTTTT-GAAAAC-ACGAAA
*
3811763 -TTTTTG-AAGCACGAGAAA
1 TTTTTTGAAAACAC--GAAA
3811781 TTTTTTGAAAACACGAAA
1 TTTTTTGAAAACACGAAA
*
3811799 TCTTTTGAAA
1 TTTTTTGAAA
3811809 CATGATTTTT
Statistics
Matches: 224, Mismatches: 45, Indels: 61
0.68 0.14 0.18
Matches are distributed among these distances:
16 7 0.03
17 72 0.32
18 74 0.33
19 42 0.19
20 20 0.09
21 9 0.04
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (18 bp):
TTTTTTGAAAACACGAAA
Found at i:3811946 original size:15 final size:16
Alignment explanation
Indices: 3811930--3811961 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3811920 TGATTCTATT
3811930 AAAACACGAGAATTTAA
1 AAAACACGAGAATTT-A
3811947 AAAACACGAGAATTT
1 AAAACACGAGAATTT
3811962 TAGAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
AAAACACGAGAATTTA
Found at i:3812121 original size:17 final size:16
Alignment explanation
Indices: 3812101--3812144 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3812091 TTCGAATTTA
3812101 AAAAAATAAAATAAAAT
1 AAAAAATAAAAT-AAAT
* *
3812118 AAAAAAGAACATAAAT
1 AAAAAATAAAATAAAT
*
3812134 ACAAAATAAAA
1 AAAAAATAAAA
3812145 ATACTTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
AAAAAATAAAATAAAT
Found at i:3812473 original size:21 final size:20
Alignment explanation
Indices: 3812433--3812480 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
3812423 CTTGATTTTG
*
3812433 GGCTGCTCTCTGGGCTGCTA
1 GGCTGCTCTCTGGCCTGCTA
*
3812453 GGCTGCTACTGTGGCCTGCTA
1 GGCTGCT-CTCTGGCCTGCTA
*
3812474 AGCTGCT
1 GGCTGCT
3812481 GGTGCTGTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.08, C:0.29, G:0.33, T:0.29
Consensus pattern (20 bp):
GGCTGCTCTCTGGCCTGCTA
Found at i:3812598 original size:10 final size:10
Alignment explanation
Indices: 3812570--3812609 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
3812560 CTTTCCCCCT
*
3812570 TTCTTCTTCC
1 TTCTTCTTTC
3812580 TTCTTCTTTC
1 TTCTTCTTTC
3812590 TTCTTCTTT-
1 TTCTTCTTTC
3812599 TT-TTCTTTC
1 TTCTTCTTTC
3812608 TT
1 TT
3812610 TTTTCTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 6 0.21
9 4 0.14
10 18 0.64
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:3812618 original size:10 final size:10
Alignment explanation
Indices: 3812569--3812618 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
3812559 TCTTTCCCCC
*
3812569 TTTCTTCTTC
1 TTTCTTCTTT
*
3812579 CTTCTTCTTT
1 TTTCTTCTTT
*
3812589 CTTCTTCTTTT
1 TTTCTTC-TTT
3812600 TTTCTTTCTTT
1 TTTC-TTCTTT
3812611 TTTCTTCT
1 TTTCTTCT
3812619 CCTTTGTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 19 0.54
11 13 0.37
12 3 0.09
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTCTTT
Found at i:3812729 original size:14 final size:15
Alignment explanation
Indices: 3812706--3812748 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3812696 TCTCCTCCCA
*
3812706 TTTTCCTTTTCTT-C
1 TTTTCTTTTTCTTCC
3812720 TTTTCTTTTTCTTCC
1 TTTTCTTTTTCTTCC
*
3812735 TTTGTCTTTCTCTT
1 TTT-TCTTTTTCTT
3812749 TTATTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 4 0.16
16 9 0.36
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTCTTTTTCTTCC
Found at i:3812785 original size:24 final size:24
Alignment explanation
Indices: 3812752--3812802 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
3812742 TTCTCTTTTA
3812752 TTTTTGTTTG-TTACTTGCTTCTTG
1 TTTTTGTTTGCTT-CTTGCTTCTTG
* * *
3812776 TTTTTTTTTGCTTCTTGGTTGTTG
1 TTTTTGTTTGCTTCTTGCTTCTTG
3812800 TTT
1 TTT
3812803 GCTTTACTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.02, C:0.10, G:0.18, T:0.71
Consensus pattern (24 bp):
TTTTTGTTTGCTTCTTGCTTCTTG
Found at i:3812788 original size:17 final size:18
Alignment explanation
Indices: 3812766--3812806 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3812756 TGTTTGTTAC
* *
3812766 TTGCTTCTT-GTTTTTTT
1 TTGCTTCTTGGTTGTTGT
3812783 TTGCTTCTTGGTTGTTGT
1 TTGCTTCTTGGTTGTTGT
3812801 TTGCTT
1 TTGCTT
3812807 TACTAGGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.00, C:0.12, G:0.20, T:0.68
Consensus pattern (18 bp):
TTGCTTCTTGGTTGTTGT
Found at i:3813215 original size:59 final size:60
Alignment explanation
Indices: 3813152--3813268 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 60
3813142 TCAAGGGTCC
* **
3813152 AAATGTAATTTTGAGAAAGTTTAGGGGTTAAAATTTAA-TTTAGAAAAGTTTAGGGGTTG
1 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTTG
3813211 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGT
1 AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGT
3813269 CAAAATGCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 35 0.65
60 19 0.35
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (60 bp):
AAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTTAGAAAAGTTTAGGGGTTG
Found at i:3813266 original size:89 final size:89
Alignment explanation
Indices: 3813106--3813274 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
3813096 TAATGGCAGC
* * *
3813106 AAAACTTTTGGGGTCGAAACGTAATTTTGAGAAAGTTCAAGGGTCCAAATGTAATTTTGAGAAAG
1 AAAACTTTAGGGGTCGAAACGTAATTTTGAGAAAGTTCAAGGGTCAAAATGCAATTTTGAGAAAG
*
3813171 TTTAGGGGTTAAAATTTAATTTAG
66 TTTAGGGGTCAAAATTTAATTTAG
* * * * *
3813195 AAAAGTTTAGGGGTTGAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGCAATTTT-AGAAAA
1 AAAACTTTAGGGGTCGAAACGTAATTTTGAGAAAGTTCAAGGGTCAAAATGCAATTTTGAG-AAA
3813259 GTTTAGGGGTCAAAAT
65 GTTTAGGGGTCAAAAT
3813275 GCAAAAAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
88 2 0.03
89 68 0.97
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (89 bp):
AAAACTTTAGGGGTCGAAACGTAATTTTGAGAAAGTTCAAGGGTCAAAATGCAATTTTGAGAAAG
TTTAGGGGTCAAAATTTAATTTAG
Found at i:3813278 original size:30 final size:30
Alignment explanation
Indices: 3813115--3813275 Score: 200
Period size: 30 Copynumber: 5.4 Consensus size: 30
3813105 CAAAACTTTT
* * *
3813115 GGGGTCGAAACGTAATTTTGAGAAAGTTCA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
* *
3813145 AGGGTCCAAATGTAATTTTGAGAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
* * *
3813175 GGGGTTAAAATTTAATTTAGA-AAAGTTTA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
**
3813204 GGGGTTGAAATGTAATTTTGAGAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAGAAAGTTTA
*
3813234 GGGGTCAAAATGCAATTTT-AGAAAAGTTTA
1 GGGGTCAAAATGTAATTTTGAG-AAAGTTTA
3813264 GGGGTCAAAATG
1 GGGGTCAAAATG
3813276 CAAAAAAATA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
29 28 0.25
30 86 0.75
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.32
Consensus pattern (30 bp):
GGGGTCAAAATGTAATTTTGAGAAAGTTTA
Found at i:3814057 original size:153 final size:153
Alignment explanation
Indices: 3813471--3817138 Score: 5111
Period size: 153 Copynumber: 23.9 Consensus size: 153
3813461 TCGAGAACAG
* * * *
3813471 CTCGGCGTGCGACCCGAGGCTCAACTCA-CCTA-TC-GTAAT-AGTTGATTTTTG-AAAACTAGA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGT-ATGAGTTGATTTTTGAAAAACAAG-
** * ** * * * *
3813531 AATTGAAAAATACCTCACGATGTGACCTGATCCTCAACTCATCTCTCGCACTATGAGTTTATTTT
64 AATTGAAAAATACCT--CGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTT
* * *
3813596 TTGAAAGAATAGAA-ATTGAAA-AATAC
127 TTGAAA-AACAGAATTTTAAAAGAATAC
* * * * * * *
3813622 CTCAGG-ATGTGACCCAAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACATGA
1 CTC-GGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGA
* * * * *
3813686 ATTTAAAAGAAATACCTCGGCATAGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
65 A-TT-GAA-AAATACCTCGGC---GTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGAT
* *
3813749 TTTTTGAAAAAAATAGAA-ATT-AAA-AATAC
124 TTTTTG--AAAAACAGAATTTTAAAAGAATAC
* * * * * * * *
3813778 CTCGGTATGTGCCCCGAGGCTCAACTCACCTCTA-ACAATATGAGTTAATTTTTGAAAAACAAAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACC-CCACGCAGTATGAGTTGATTTTTGAAAAACAAGA
* * ** * *
3813842 ATTTAAAAGAAATACCTCGGCATGGTCCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTT
65 A-TT-GAA-AAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTT
3813907 TTGAAAAACAGAATTTTAAAAGAATAC
127 TTGAAAAACAGAATTTTAAAAGAATAC
3813934 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
*
3813999 TTGAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814064 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814087 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814152 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814217 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814240 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814305 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814370 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814393 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814458 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814523 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814546 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814611 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814676 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814699 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814764 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814829 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3814852 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3814917 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3814982 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815005 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815070 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815135 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815158 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815223 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815288 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815311 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815376 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815441 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815464 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815529 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815594 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815617 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815682 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815747 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815770 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
3815835 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
3815900 AAAACAGAATTTTAAAAGAATAC
131 AAAACAGAATTTTAAAAGAATAC
3815923 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
* *
3815988 TTGAAAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTTGCAATATGAGTT-AATTTTTGA
66 TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
* * *
3816052 AAAATATAAATTTAAAAGAAATAC
131 AAAACAGAATTTTAAAAG-AATAC
* * * * ** *
3816076 CTCAGCATG-G-TCCAAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAAA-ACAGA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACA-AG-
* * * * * * *
3816138 AATTAAAAAAAATACCTCGGCATGACCCAAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTT
64 AATT--GAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTT
* * *
3816202 TTGAAAAAACAGAAATTTAAAAAAAGAC
127 TTG-AAAAACAGAATTTTAAAAGAATAC
* * * * ** * *
3816230 CTCAGC--GTGACTCGAGGCTCAACTCACCTCTTGCAATATGAGGTGATTTTTGAAAAA-ACAGA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACA-AG-
* * * * * *
3816292 AATTTAAAAAAAGACCTCAGCGTGACTCGAGGCTCAACTCACCTCTTGCAATATGAGGTGA-TTT
64 AA-TT-GAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTT
* * *
3816356 TTGAAAAAACAGAAATTTAAAAAAAGAC
127 TTG-AAAAACAGAATTTTAAAAGAATAC
* * * * ** * *
3816384 CTCAGC--GTGACTCGAGGCTCAACTCACCTCTTGCAATATGAGGTGATTTTTGAAAAAC-AGAA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAG-A
* * * * *
3816446 ATTAAAAAAAATACCTCGGCGTGACCC-ATGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTT
65 ATT--GAAAAATACCTCGGCGTGACCCGA-GACTCAACTCACCTCTTGCAATATGAGTTGATTTT
* *
3816509 TTGAAAAAACAGAAATTTAAAAAAATAC
127 TTG-AAAAACAGAATTTTAAAAGAATAC
* * * *** * *
3816537 CTCAGC--GTGACTCGAGGCTCAACTCACCTTTCGTATTATGAGTTGATTTTTGAAAAACATA-A
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACA-AGA
* * * *
3816599 ATTTAAAAGAAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAATTGA-TTT
65 A-TT-GAA-AAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTT
* *
3816663 TTGAAAAACATAAATTTAAAAGAAATAC
127 TTGAAAAACAGAATTTTAAAAG-AATAC
* * * * * ** * *
3816691 CTCAGCATG-G-TCCAAGGGTCAACTCACCTCTTGCAATATGAGTTAATTTTTGAAAAA-ACAGA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACA-AG-
* * * * * *
3816753 AATTAAAAAAATACCTCGGCGTGACCCAAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT
64 AATT-GAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTT
* * *
3816817 TGAAAAAACAGAAATTTAAAAAAATGC
128 TG-AAAAACAGAATTTTAAAAGAATAC
* * * *
3816844 CTCAGCAT--GACCCGAGGCTCAACTCA-CCTATCGTATTATGAGTTGATTTTTGAAAAAC-AGA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCA-CGCAGTATGAGTTGATTTTTGAAAAACAAG-
* * * * *
3816905 AATTTAAAAGAAATACCTCGACGTGACCCGAGGCTCAACTCACCTCTTGTATTATGAGTTGA-TT
64 AA-TT-GAA-AAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTT
* *
3816969 TTTGAAAAAACAGAAATTAAAAAGAAATAC
126 TTTG-AAAAACAGAATTTTAAAAG-AATAC
* * * * * *
3816999 CTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTTTTG-AAAACA
1 CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGA----TTTTTGAAAAACA
* * * ** * * *
3817062 AAAATTTGAAAGAAATACCTTGGCATGGTCCGAGGCTCAACTCACCCCTCGCAATATGAGTTGA-
62 AGAA-TTG-AA-AAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGAT
3817126 TTTTTGAAAAACA
124 TTTTTGAAAAACA
3817139 AAAATTGAAA
Statistics
Matches: 3304, Mismatches: 152, Indels: 115
0.93 0.04 0.03
Matches are distributed among these distances:
150 1 0.00
151 65 0.02
152 42 0.01
153 2328 0.70
154 500 0.15
155 60 0.02
156 176 0.05
157 50 0.02
158 13 0.00
159 62 0.02
160 7 0.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (153 bp):
CTCGGCATGCGACCCGAGGCTCAACTCACCCCACGCAGTATGAGTTGATTTTTGAAAAACAAGAA
TTGAAAAATACCTCGGCGTGACCCGAGACTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGA
AAAACAGAATTTTAAAAGAATAC
Found at i:3818028 original size:7 final size:7
Alignment explanation
Indices: 3818005--3818056 Score: 81
Period size: 7 Copynumber: 7.6 Consensus size: 7
3817995 TCATCTTGAT
3818005 TTTTCT-
1 TTTTCTA
3818011 TTTT-TA
1 TTTTCTA
3818017 CTTTTCTA
1 -TTTTCTA
3818025 TTTTCTA
1 TTTTCTA
3818032 TTTTCTA
1 TTTTCTA
3818039 TTTTCTA
1 TTTTCTA
3818046 TTTTCTA
1 TTTTCTA
3818053 TTTT
1 TTTT
3818057 TTTGTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.02
6 4 0.09
7 36 0.84
8 2 0.05
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCTA
Found at i:3818076 original size:8 final size:8
Alignment explanation
Indices: 3818053--3818078 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
3818043 CTATTTTCTA
3818053 TTTTTTTG
1 TTTTTTTG
3818061 TTTTTTTG
1 TTTTTTTG
3818069 TTTTTTTG
1 TTTTTTTG
3818077 TT
1 TT
3818079 AGGCATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3825807 original size:19 final size:20
Alignment explanation
Indices: 3825785--3825838 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
3825775 AACATGAAAA
3825785 TTTTGAAACACGAGA-TTT-T
1 TTTTGAAACACGA-ATTTTCT
3825804 TTTTGAAAACACGAATTTTCT
1 TTTTG-AAACACGAATTTTCT
*
3825825 TTTTGAAACGCGAA
1 TTTTGAAACACGAA
3825839 AATTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 6 0.19
20 19 0.61
21 6 0.19
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (20 bp):
TTTTGAAACACGAATTTTCT
Done.