Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 111 of 126
Found at i:33225759 original size:28 final size:26
Alignment explanation
Indices: 33225728--33225782 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 26
33225718 ATATTTAATG
33225728 TCAAAA-AATAATTCAAAAATATAATAAA
1 TCAAAACAA-AATT-AAAAATAT-ATAAA
33225756 TCAAAATCAAAATTAAAAATATATAAA
1 TCAAAA-CAAAATTAAAAATATATAAA
33225783 AAAAAGTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.20
28 14 0.56
29 4 0.16
30 2 0.08
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (26 bp):
TCAAAACAAAATTAAAAATATATAAA
Found at i:33226440 original size:21 final size:21
Alignment explanation
Indices: 33226414--33226476 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
33226404 AATAAAAAAT
* *
33226414 ATAAAATTATTAAATATTAAA
1 ATAAAATTATAAAAAATTAAA
* *
33226435 ATAAAATAATAAAAAATTTAA
1 ATAAAATTATAAAAAATTAAA
33226456 A-AAAATTA-AAAATAATATAAA
1 ATAAAATTATAAAA-AAT-TAAA
33226477 CATACCTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 4 0.12
20 9 0.26
21 21 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAATTATAAAAAATTAAA
Found at i:33229923 original size:25 final size:25
Alignment explanation
Indices: 33229891--33229939 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
33229881 ATGTTTGAAA
33229891 TATTTTAATATAATTTAAAATAAAT
1 TATTTTAATATAATTTAAAATAAAT
33229916 TATTTTAATATAATTTAAAATAAA
1 TATTTTAATATAATTTAAAATAAA
33229940 AATAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTTTAATATAATTTAAAATAAAT
Found at i:33229979 original size:16 final size:16
Alignment explanation
Indices: 33229958--33229989 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33229948 TATTAAAAAC
*
33229958 ATTATTATATTATATT
1 ATTATTAAATTATATT
33229974 ATTATTAAATTATATT
1 ATTATTAAATTATATT
33229990 TAATAATAAT
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTAAATTATATT
Found at i:33230158 original size:44 final size:43
Alignment explanation
Indices: 33230103--33230211 Score: 146
Period size: 44 Copynumber: 2.5 Consensus size: 43
33230093 TATTATAACA
*
33230103 TCTATTATATTCAACCAAACACAATAATAATATTACAAATCTAT
1 TCTATT-TATTCAACCAAACACAAAAATAATATTACAAATCTAT
* * *
33230147 TCTATTCTATTCAACCAAACATAAAAATATTATTATAAATCTAT
1 TCTATT-TATTCAACCAAACACAAAAATAATATTACAAATCTAT
*
33230191 TTTATTTCATTCAACCAAACA
1 TCTATTT-ATTCAACCAAACA
33230212 ATTGAGTTAC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (43 bp):
TCTATTTATTCAACCAAACACAAAAATAATATTACAAATCTAT
Found at i:33232031 original size:27 final size:29
Alignment explanation
Indices: 33232001--33232060 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
33231991 GGACTTAAGA
* * *
33232001 TTTGGATTATAATTAATTTA-T-TTTGAG
1 TTTGGATAATAATAAATATATTATTTGAG
33232028 TTTGGATAATAATAAATATATTATTTGAG
1 TTTGGATAATAATAAATATATTATTTGAG
33232057 TTTG
1 TTTG
33232061 AGCTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 17 0.61
28 1 0.04
29 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (29 bp):
TTTGGATAATAATAAATATATTATTTGAG
Found at i:33232171 original size:7 final size:7
Alignment explanation
Indices: 33232149--33232184 Score: 63
Period size: 7 Copynumber: 5.0 Consensus size: 7
33232139 TCAATTGTTA
33232149 ATATAAT
1 ATATAAT
33232156 ATAATAAT
1 AT-ATAAT
33232164 ATATAAT
1 ATATAAT
33232171 ATATAAT
1 ATATAAT
33232178 ATATAAT
1 ATATAAT
33232185 GTACTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
ATATAAT
Found at i:33232457 original size:241 final size:236
Alignment explanation
Indices: 33232156--33232665 Score: 538
Period size: 241 Copynumber: 2.2 Consensus size: 236
33232146 TTAATATAAT
* * * *
33232156 ATAA-TAATATATAATATATAATATATAATGTACTATTATTATATTGTAGAATATAATAAAAGAT
1 ATAATTAATATATAATATATAATATATAATGTACTATTATTAAACTATAGAATATAATAAAAGAA
*** * * * * * *
33232220 ATGGTATTACATGATATTATAACATTTAATCATTTATGTATATATATCAACTATTAATATATTAT
66 ACAATACTACATGATATTATAACATTTAATCATTGATGCACATATATAAACTATTAATATATTAC
* * * * *
33232285 ATGCTATATGATTTGACATAACATTATATAATATAGTAGGAAGG-CTAAGTGTTAAATGTATGAA
131 AT--TATATG---TCACATAACATTATATAATATAGTA-GAAGGACTAACTCTTAAATATACGAA
33232349 AAATATAAAGACTCAGAGCATATTTCA-A-TATAATAATAAACAATA
190 AAATATAAAGACTCAGAGCATATTTCACACTATAATAATAAACAATA
* *
33232394 ATAATTAATATATAATGTACTACTAT-TATATGTAACTATTATTAAACTATA-AATTATAATAAA
1 ATAATTAATATATAATATA-TAATATATA-ATGT-ACTATTATTAAACTATAGAA-TATAATAAA
* **
33232457 AGAAACAATACTACATGATATTGTAATGTTTAATCATTGATGCACATATATAAACTATTAATATA
62 AGAAACAATACTACATGATATTATAACATTTAATCATTGATGCACATATATAAACTATTAATATA
* * * *
33232522 TTACATTATATGTCATATAACATTATATAATGTAGTAGAAGGATTATCTCTTAAATATACGAAAA
127 TTACATTATATGTCACATAACATTATATAATATAGTAGAAGGACTAACTCTTAAATATACGAAAA
* * *
33232587 TTATAAGGACTTAGAGCATATTTCAGCCACTATAATAAT--A-AATA
192 ATATAAAGACTCAGAGCATATTTCA--CACTATAATAATAAACAATA
* *
33232631 ATAA-TACAT-TATAATAAATAATATATTATGTACTA
1 ATAATTA-ATATATAATATATAATATATAATGTACTA
33232666 CTCTACTATT
Statistics
Matches: 226, Mismatches: 34, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
234 4 0.02
235 14 0.06
236 70 0.31
237 10 0.04
238 5 0.02
239 22 0.10
240 20 0.09
241 81 0.36
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (236 bp):
ATAATTAATATATAATATATAATATATAATGTACTATTATTAAACTATAGAATATAATAAAAGAA
ACAATACTACATGATATTATAACATTTAATCATTGATGCACATATATAAACTATTAATATATTAC
ATTATATGTCACATAACATTATATAATATAGTAGAAGGACTAACTCTTAAATATACGAAAAATAT
AAAGACTCAGAGCATATTTCACACTATAATAATAAACAATA
Found at i:33232633 original size:10 final size:10
Alignment explanation
Indices: 33232618--33232653 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
33232608 TTCAGCCACT
33232618 ATAATAATAA
1 ATAATAATAA
*
33232628 ATAATAATAC
1 ATAATAATAA
*
33232638 ATTATAATAA
1 ATAATAATAA
33232648 ATAATA
1 ATAATA
33232654 TATTATGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAATAATAA
Found at i:33236342 original size:29 final size:31
Alignment explanation
Indices: 33236280--33236348 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
33236270 TTTATTCAAC
* * *
33236280 ATATATTTGGATTACAATTAGAATTTCATGT
1 ATATAATTGGATTACAATTAAAATTTAATGT
*
33236311 ATATAATTGTATTA-AATTAAAATTTAAT-T
1 ATATAATTGGATTACAATTAAAATTTAATGT
*
33236340 ATACAATTG
1 ATATAATTG
33236349 CACATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 12 0.36
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (31 bp):
ATATAATTGGATTACAATTAAAATTTAATGT
Found at i:33243418 original size:18 final size:19
Alignment explanation
Indices: 33243395--33243448 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
33243385 ATTTTCGTTA
33243395 AAATCGAATTAA-TCGATT
1 AAATCGAATTAATTCGATT
*
33243413 AAATCGATTTAATTCGATT
1 AAATCGAATTAATTCGATT
* *
33243432 -AATTGATTTAATTCGAT
1 AAATCGAATTAATTCGAT
33243449 CAGAGATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 27 0.82
19 6 0.18
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (19 bp):
AAATCGAATTAATTCGATT
Found at i:33245297 original size:63 final size:61
Alignment explanation
Indices: 33245196--33245367 Score: 208
Period size: 67 Copynumber: 2.7 Consensus size: 61
33245186 TTTTGCTTTG
* *
33245196 TTATTTATTTATTTATTT-ATTTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCA-TAAAAATAATAAATAAATAATAAAACAAAATTAATATTATT
*
33245257 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCAT-AAA-AAT-AATAAATAAATAATAAAACAAAATTAATATTA
33245322 TT
60 TT
33245324 TTA--TATTTATTTATGTTCATAAAAATAAT-AATAAATAAATAAAA
1 TTATTTATTTATTTAT-TTCATAAAAATAATAAATAAAT-AATAAAA
33245368 ATAATAAGAA
Statistics
Matches: 99, Mismatches: 4, Indels: 17
0.82 0.03 0.14
Matches are distributed among these distances:
59 7 0.07
60 10 0.10
61 5 0.05
62 3 0.03
63 30 0.30
64 3 0.03
65 3 0.03
66 3 0.03
67 35 0.35
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (61 bp):
TTATTTATTTATTTATTTCATAAAAATAATAAATAAATAATAAAACAAAATTAATATTATT
Found at i:33245304 original size:67 final size:63
Alignment explanation
Indices: 33245196--33245365 Score: 231
Period size: 63 Copynumber: 2.7 Consensus size: 63
33245186 TTTTGCTTTG
**
33245196 TTATTTATTTATTTATTT-AT-TTATAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
*
33245257 TTACATTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTA
1 TT--ATTTATTTATTTAT-TTCATAAAATAAT-AATAAATAAATAATAAAACAAAATTAATATTA
33245322 TT
62 TT
33245324 TTA--TATTTATTTATGTTCATAAAAATAATAATAAATAAATAA
1 TTATTTATTTATTTAT-TTCAT-AAAATAATAATAAATAAATAA
33245366 AAATAATAAG
Statistics
Matches: 98, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
61 2 0.02
63 43 0.44
64 10 0.10
65 3 0.03
66 5 0.05
67 35 0.36
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (63 bp):
TTATTTATTTATTTATTTCATAAAATAATAATAAATAAATAATAAAACAAAATTAATATTATT
Found at i:33245366 original size:67 final size:65
Alignment explanation
Indices: 33245218--33245371 Score: 215
Period size: 67 Copynumber: 2.3 Consensus size: 65
33245208 TTATTTATTT
*
33245218 ATAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCATA
1 ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATA-T-AAA
33245282 AA
64 AA
* *
33245284 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTATATTTATTTATGTTCATA-AAA
1 ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTAT-TT-ATATAAA
33245348 ATA
64 A-A
33245351 ATAATAAATAAATAAA-AATAA
1 ATAATAAATAAATAAATAATAA
33245372 TAAGAAAAAT
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
66 13 0.16
67 63 0.78
68 2 0.02
69 3 0.04
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (65 bp):
ATAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATAAAAA
Found at i:33246091 original size:80 final size:80
Alignment explanation
Indices: 33245899--33246472 Score: 938
Period size: 80 Copynumber: 7.2 Consensus size: 80
33245889 ATAACTTTAG
* * * * *
33245899 GGGTAAAAGATTAGATTGT-TTCAA-CTTGCCCCATGGTCGAGGTAAGAGATCTGATGGTCTTCA
1 GGGTAAAAGATTGGATT-TCTTCAATC-TGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCA
* *
33245962 ATC-TGCTCTTTGGTTA
64 ATCTTGCCCTCTGGTTA
*
33245978 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
33246043 CTTGCCCTCTAGTTC
66 CTTGCCCTCTGGTTA
* *
33246058 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
33246123 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
33246138 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGAGGTAGAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
33246203 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
33246218 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTATTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
33246283 CTTACCCTCTAGTTA
66 CTTGCCCTCTGGTTA
*
33246298 GGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
33246363 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
33246378 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
33246443 CTTGCCCTCTGGTGA
66 CTTGCCCTCTGGTTA
33246458 GGGTAAAAGATTGGA
1 GGGTAAAAGATTGGA
33246473 GGTTGTAATT
Statistics
Matches: 463, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
78 1 0.00
79 57 0.12
80 405 0.87
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:33246612 original size:50 final size:50
Alignment explanation
Indices: 33246558--33246703 Score: 168
Period size: 50 Copynumber: 2.9 Consensus size: 50
33246548 TTTAAATGAC
* * * * *
33246558 TGAGATTTGCCATTACAGCTTCATTTTAC-CCCTCTACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTACACCTTC-ACAGCTTTAGGTGTA
* * *
33246608 TGAGATTTGACATTGCGGTTTCAATCTGCACCTTCACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTACACCTTCACAGCTTTAGGTGTA
* * * *
33246658 TGAGATTTACCATTGCAGTTTCAATCTGCACCTCCACCGCTTTAGG
1 TGAGATTTGCCATTGCAGTTTCAATCTACACCTTCACAGCTTTAGG
33246704 GGTAAAAGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 78 0.95
51 4 0.05
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (50 bp):
TGAGATTTGCCATTGCAGTTTCAATCTACACCTTCACAGCTTTAGGTGTA
Found at i:33246715 original size:50 final size:50
Alignment explanation
Indices: 33246588--33246703 Score: 180
Period size: 50 Copynumber: 2.3 Consensus size: 50
33246578 TCATTTTACC
* *
33246588 CCTCTACAGCTTTAGGTGTATGAGATTTGACATTGCGGTTTCAATCTGCA
1 CCTCCACAGCTTTAGGTGTATGAGATTTGACATTGCAGTTTCAATCTGCA
*
33246638 CCTTCACAGCTTTAGGTGTATGAGATTT-ACCATTGCAGTTTCAATCTGCA
1 CCTCCACAGCTTTAGGTGTATGAGATTTGA-CATTGCAGTTTCAATCTGCA
*
33246688 CCTCCACCGCTTTAGG
1 CCTCCACAGCTTTAGG
33246704 GGTAAAAGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
CCTCCACAGCTTTAGGTGTATGAGATTTGACATTGCAGTTTCAATCTGCA
Found at i:33247637 original size:6 final size:6
Alignment explanation
Indices: 33247628--33247686 Score: 55
Period size: 6 Copynumber: 9.0 Consensus size: 6
33247618 TCGACCTCCC
* *
33247628 CTTTTT CTTTTT CTTTTCTT CTTTTT CCTTTT CTTTGTCT TTTTTT CTTTTTT
1 CTTTTT CTTTTT C-TTT-TT CTTTTT CTTTTT CTTT-T-T CTTTTT C-TTTTT
33247681 CTTTTT
1 CTTTTT
33247687 TTAATTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
6 23 0.52
7 14 0.32
8 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:33247651 original size:8 final size:7
Alignment explanation
Indices: 33247629--33247687 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
33247619 CGACCTCCCC
33247629 TTTTTC-
1 TTTTTCT
33247635 TTTTTCT
1 TTTTTCT
33247642 TTTCTTC-
1 TTT-TTCT
33247649 TTTTTC-
1 TTTTTCT
*
33247655 CTTTTC-
1 TTTTTCT
*
33247661 TTTGTCTT
1 TTTTTC-T
33247669 TTTTTCT
1 TTTTTCT
33247676 TTTTTCT
1 TTTTTCT
33247683 TTTTT
1 TTTTT
33247688 TAATTTTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
6 18 0.40
7 19 0.42
8 8 0.18
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:33247651 original size:20 final size:20
Alignment explanation
Indices: 33247628--33247685 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
33247618 TCGACCTCCC
33247628 CTTTTTCTTTTTCTTTTCTT
1 CTTTTTCTTTTTCTTTTCTT
*
33247648 CTTTTTCCTTTTCTTTGTCTT
1 CTTTTTCTTTTTCTTT-TCTT
33247669 -TTTTTCTTTTTTCTTTT
1 CTTTTTC-TTTTTCTTTT
33247686 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (20 bp):
CTTTTTCTTTTTCTTTTCTT
Found at i:33247659 original size:26 final size:26
Alignment explanation
Indices: 33247630--33247685 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
33247620 GACCTCCCCT
*
33247630 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
* *
33247656 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTTGTCTTTTCTTCTTTTTCC
33247682 TTTT
1 TTTT
33247686 TTTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTGTCTTTTCTTCTTTTTCC
Found at i:33247686 original size:15 final size:14
Alignment explanation
Indices: 33247629--33247688 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
33247619 CGACCTCCCC
33247629 TTTTTCTTTTTCTT
1 TTTTTCTTTTTCTT
*
33247643 TTCTTCTTTTTC--
1 TTTTTCTTTTTCTT
* *
33247655 CTTTTCTTTGTCTT
1 TTTTTCTTTTTCTT
33247669 TTTTTCTTTTTTCTT
1 TTTTTC-TTTTTCTT
33247684 TTTTT
1 TTTTT
33247689 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 9 0.24
14 16 0.43
15 12 0.32
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:33247688 original size:8 final size:8
Alignment explanation
Indices: 33247635--33247706 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
33247625 CCCCTTTTTC
33247635 TTTTTCTT
1 TTTTTCTT
*
33247643 TTCTTCTT
1 TTTTTCTT
33247651 TTTCCTT-TT
1 TTT--TTCTT
*
33247660 CTTTGTCTT
1 -TTTTTCTT
33247669 TTTTTC-T
1 TTTTTCTT
33247676 TTTTTCTT
1 TTTTTCTT
*
33247684 TTTTTAATT
1 TTTTT-CTT
33247693 TTTTATCTT
1 TTTT-TCTT
33247702 TTTTT
1 TTTTT
33247707 TTTGAAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.14
8 22 0.43
9 16 0.31
10 6 0.12
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:33247696 original size:26 final size:25
Alignment explanation
Indices: 33247630--33247709 Score: 74
Period size: 26 Copynumber: 3.2 Consensus size: 25
33247620 GACCTCCCCT
* * *
33247630 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTC-TTTACTTTTTTTCTTTTTTC
*
33247656 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTT-ACTTTTTTTCTTTTTTC
*
33247682 TTTT-TTTAATTTTTTATCTTTTTT-
1 TTTTCTTTACTTTTTT-TCTTTTTTC
33247706 TTTT
1 TTTT
33247710 GAAATTTCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.21
25 14 0.29
26 24 0.50
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (25 bp):
TTTTCTTTACTTTTTTTCTTTTTTC
Found at i:33247702 original size:33 final size:33
Alignment explanation
Indices: 33247635--33247706 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
33247625 CCCCTTTTTC
*
33247635 TTTTTCTTTTCTTCTTTTTCCTTTTCTTTGTCTT
1 TTTTTCTTTTCTTCTTTTT-CTTTTCTTTATCTT
*
33247669 TTTTTCTTTT-TTCTTTTT-TTAATTTTTTATCTT
1 TTTTTCTTTTCTTCTTTTTCTT--TTCTTTATCTT
33247702 TTTTT
1 TTTTT
33247707 TTTGAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 2 0.06
33 22 0.65
34 10 0.29
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (33 bp):
TTTTTCTTTTCTTCTTTTTCTTTTCTTTATCTT
Found at i:33247709 original size:15 final size:14
Alignment explanation
Indices: 33247629--33247709 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 14
33247619 CGACCTCCCC
*
33247629 TTTTTCTTTTTCTT
1 TTTTTCTTTTTTTT
*
33247643 TTCTTCTTTTTCCTTT
1 TTTTTCTTTTT--TTT
33247659 TCTTTGTCTTTTTTTCT
1 T-TTT-TCTTTTTTT-T
33247676 TTTTTCTTTTTTTAAT
1 TTTTTCTTTTTTT--T
*
33247692 TTTTTATCTTTTTTT
1 TTTTTCT-TTTTTTT
33247707 TTT
1 TTT
33247710 GAAATTTCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
14 10 0.18
15 13 0.24
16 15 0.27
17 10 0.18
18 7 0.13
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:33252762 original size:63 final size:60
Alignment explanation
Indices: 33252678--33252846 Score: 197
Period size: 67 Copynumber: 2.8 Consensus size: 60
33252668 TTTTGGTTTG
*
33252678 TTATTTATTTATTT-AT---AATAATAAATAAATAATAAAACAAAATTAATATTATTTTACA
1 TTATTTATTTATTTCATAAAAATAATAAATAAATAATAAAAAAAAATTAATATTATTTT--A
*
33252736 TTTATTTATTTATATTCATAAAATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTA
1 -TTATTTATTTAT-TTCAT-AAA-AAT-AATAAATAAATAATAAAAAAAAATTAATATTATTTTA
33252801 -TATTTATTTATGTTCATAAAAATAAT-AATAAATAAATAAAAAAAAA
1 TTATTTATTTAT-TTCATAAAAATAATAAATAAAT-AATAAAAAAAAA
33252847 AAAAAATTGG
Statistics
Matches: 98, Mismatches: 3, Indels: 17
0.83 0.03 0.14
Matches are distributed among these distances:
59 19 0.19
60 16 0.16
61 5 0.05
62 3 0.03
63 16 0.16
65 1 0.01
66 3 0.03
67 35 0.36
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (60 bp):
TTATTTATTTATTTCATAAAAATAATAAATAAATAATAAAAAAAAATTAATATTATTTTA
Found at i:33252788 original size:67 final size:63
Alignment explanation
Indices: 33252692--33252849 Score: 228
Period size: 63 Copynumber: 2.4 Consensus size: 63
33252682 TTATTTATTT
*
33252692 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-A
1 ATAATAATAAATAAATAATAAAAAAAAATTAATATTATTTT--A--TATTTATTTATATTCATAA
33252756 AA
62 AA
* *
33252758 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTATATTTATTTATGTTCATAAAA
1 ATAAT-AATAAATAAATAATAAAAAAAAATTAATATTATTTTATATTTATTTATATTCATAAAA
*
33252822 ATAATAATAAATAAATAAAAAAAAAAAA
1 ATAATAATAAATAAATAATAAAAAAAAA
33252850 AAATTGGAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
63 37 0.43
64 8 0.09
65 1 0.01
66 5 0.06
67 35 0.41
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (63 bp):
ATAATAATAAATAAATAATAAAAAAAAATTAATATTATTTTATATTTATTTATATTCATAAAA
Found at i:33261828 original size:27 final size:27
Alignment explanation
Indices: 33261795--33261874 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
33261785 TTTGAGGTTT
* *
33261795 CGAACTCTAAAAGAATAACCTTTGTGA
1 CGAACTCTAGAAGAATAGCCTTTGTGA
* * * *
33261822 TGAACTCCAGAAGAATAGCTTTTGTGG
1 CGAACTCTAGAAGAATAGCCTTTGTGA
* *
33261849 CGAACTCTGGGAGAATAGCCTTTGTG
1 CGAACTCTAGAAGAATAGCCTTTGTG
33261875 GAGAATTATG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (27 bp):
CGAACTCTAGAAGAATAGCCTTTGTGA
Found at i:33262874 original size:20 final size:24
Alignment explanation
Indices: 33262825--33262875 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 24
33262815 TTTTAGTTCG
33262825 AAATTTTGTAATTAAGTAAGATGT
1 AAATTTTGTAATTAAGTAAGATGT
33262849 -AA-TTTGT-A-TAAGT-AGAT-T
1 AAATTTTGTAATTAAGTAAGATGT
33262867 AAATTTTGT
1 AAATTTTGT
33262876 CTGTATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
18 1 0.04
19 6 0.24
20 10 0.40
21 1 0.04
22 5 0.20
23 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (24 bp):
AAATTTTGTAATTAAGTAAGATGT
Found at i:33267861 original size:33 final size:32
Alignment explanation
Indices: 33267818--33267898 Score: 126
Period size: 33 Copynumber: 2.5 Consensus size: 32
33267808 TCATAACGGC
*
33267818 CCCCACCCCCAACGGTCATAAACCCAACGACT
1 CCCCACCCCCAACGATCATAAACCCAACGACT
*
33267850 CGCCCACCCCCAACAATCATAAACCCAACGACT
1 C-CCCACCCCCAACGATCATAAACCCAACGACT
33267883 CCCCAACCCCCAACGA
1 CCCC-ACCCCCAACGA
33267899 CTATTTCATA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 4 0.09
33 40 0.91
ACGTcount: A:0.33, C:0.52, G:0.07, T:0.07
Consensus pattern (32 bp):
CCCCACCCCCAACGATCATAAACCCAACGACT
Found at i:33270949 original size:16 final size:17
Alignment explanation
Indices: 33270912--33270958 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
33270902 AAAAACCCAA
*
33270912 ACAAAAT-AGAAAAACT
1 ACAAAATAAAAAAAACT
*
33270928 AAAAAATAAAAAAAAC-
1 ACAAAATAAAAAAAACT
33270944 ACAAAATTAAAAAAA
1 ACAAAA-TAAAAAAA
33270959 TCCATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.79, C:0.09, G:0.02, T:0.11
Consensus pattern (17 bp):
ACAAAATAAAAAAAACT
Found at i:33272592 original size:30 final size:27
Alignment explanation
Indices: 33272556--33272621 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
33272546 TATTATTATC
***
33272556 AATCCTTTTATTTTGTTTTCTTAAAAATT
1 AATCCTTTTATTCCCTTTT-TT-AAAATT
33272585 AAATCCTTTTATTCCCTTTTTTAAAATT
1 -AATCCTTTTATTCCCTTTTTTAAAATT
33272613 AATCCTTTT
1 AATCCTTTT
33272622 GTTATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.27
28 6 0.18
29 2 0.06
30 16 0.48
ACGTcount: A:0.27, C:0.15, G:0.02, T:0.56
Consensus pattern (27 bp):
AATCCTTTTATTCCCTTTTTTAAAATT
Found at i:33272631 original size:27 final size:28
Alignment explanation
Indices: 33272556--33272636 Score: 83
Period size: 27 Copynumber: 2.9 Consensus size: 28
33272546 TATTATTATC
* *
33272556 AATCCTTTTATTTTGTTTTCTTAAAAATTA
1 AATCCTTTTATTATATTTT-TT-AAAATTA
***
33272586 AATCCTTTTATTCCCTTTTTTAAAATT-
1 AATCCTTTTATTATATTTTTTAAAATTA
*
33272613 AATCCTTTTGTTATATTTTTTAAA
1 AATCCTTTTATTATATTTTTTAAA
33272637 TCCTTTAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
27 20 0.45
28 6 0.14
29 2 0.05
30 16 0.36
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.57
Consensus pattern (28 bp):
AATCCTTTTATTATATTTTTTAAAATTA
Found at i:33276147 original size:15 final size:15
Alignment explanation
Indices: 33276129--33276178 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
33276119 TATTAAAACC
33276129 AAAAA-AAGAAAAAGA
1 AAAAAGAAG-AAAAGA
33276144 AAAAAGAAGAAAAGA
1 AAAAAGAAGAAAAGA
*
33276159 AAAATGAATG-AAAGA
1 AAAAAGAA-GAAAAGA
33276174 AAAAA
1 AAAAA
33276179 ACTCAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 27 0.87
16 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAAGAAGAAAAGA
Found at i:33276147 original size:21 final size:21
Alignment explanation
Indices: 33276123--33276162 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
33276113 AGGGCATATT
*
33276123 AAAACCAAAAAAAGAAAAAGA
1 AAAAACAAAAAAAGAAAAAGA
* *
33276144 AAAAAGAAGAAAAGAAAAA
1 AAAAACAAAAAAAGAAAAA
33276163 TGAATGAAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAAAGAAAAAGA
Found at i:33276857 original size:23 final size:25
Alignment explanation
Indices: 33276831--33276876 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
33276821 CCAATTAAGA
33276831 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
33276854 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
33276877 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:33277961 original size:20 final size:18
Alignment explanation
Indices: 33277938--33277992 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 18
33277928 TAATTTAGCC
*
33277938 ATTTTTATTTTTATTTTCA
1 ATTTTTATTTTTAATTT-A
*
33277957 TATTTTTGTTTTTAATTTA
1 -ATTTTTATTTTTAATTTA
**
33277976 ATTTTTACATTTAATTT
1 ATTTTTATTTTTAATTT
33277993 TTTTATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 14 0.47
19 1 0.03
20 15 0.50
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
ATTTTTATTTTTAATTTA
Found at i:33277981 original size:13 final size:13
Alignment explanation
Indices: 33277965--33278006 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
33277955 CATATTTTTG
33277965 TTTTTAATTTAA-
1 TTTTTAATTTAAT
33277977 TTTTTACATTTAAT
1 TTTTTA-ATTTAAT
* *
33277991 TTTTTTATTTTAT
1 TTTTTAATTTAAT
33278004 TTT
1 TTT
33278007 ATAGGTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 6 0.23
13 15 0.58
14 5 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTAATTTAAT
Found at i:33277982 original size:12 final size:13
Alignment explanation
Indices: 33277965--33277994 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33277955 CATATTTTTG
33277965 TTTTTA-ATTTAA
1 TTTTTACATTTAA
33277977 TTTTTACATTTAA
1 TTTTTACATTTAA
33277990 TTTTT
1 TTTTT
33277995 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTACATTTAA
Found at i:33279506 original size:42 final size:42
Alignment explanation
Indices: 33279409--33279793 Score: 371
Period size: 42 Copynumber: 9.4 Consensus size: 42
33279399 GTTACGTCAT
* * * *
33279409 CCATCTAATCTCTTACTCCGGTCATGGGGTAGATTGAAG---
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* *
33279448 CCAT-CAATCTCTTACCCCGATCATAGGGTAGATTGAAGACA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
*
33279489 CCATCCAATCTCTTACCCCGATTATGGGGCAGATTG-A-AC-
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* *
33279528 CCATCCAATCTCTTACCCCGATCATAGGACAGATTGAAGA-A
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* * * * *
33279569 GCCATCCAATTTCTTACCCCGATCATGAGACAAATTAAAGACA
1 -CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
** * * * *
33279612 CCATTTAATCTCTTACCTCGATCATGAGGTAGATTG-AG--G
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* * * * *
33279651 TCATCCAATCTCTTACCTCGATCATGGGGAAAATTGAAGATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* * * * *
33279693 CCATACAATCTTTTACCCTGATTATGGGGCAGATTGAAGATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
* * *
33279735 TCA-CTCAATCTCTTACCCCGACCATGGGGCAGATTGAAAACA
1 CCATC-CAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
33279777 CCATCCAATCTCTTACC
1 CCATCCAATCTCTTACC
33279794 ATGACCATGA
Statistics
Matches: 284, Mismatches: 48, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
38 30 0.11
39 67 0.24
40 5 0.02
41 8 0.03
42 172 0.61
43 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (42 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACA
Found at i:33279574 original size:81 final size:81
Alignment explanation
Indices: 33279409--33279793 Score: 334
Period size: 81 Copynumber: 4.7 Consensus size: 81
33279399 GTTACGTCAT
* * * * *
33279409 CCATCTAATCTCTTACTCCGGTCATGGGGTAGATTGAAGCCAT-CAATCTCTTACCCCGATCATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATA
*
33279473 GGGTAGATTGAAGACA
66 GGGCAGATTGAAGACA
*
33279489 CCATCCAATCTCTTACCCCGATTATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATA
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATA
*
33279554 GGACAGATTGAAGA-A
66 GGGCAGATTGAAGACA
* * * * * ** *
33279569 GCCATCCAATTTCTTACCCCGATCATGAGACAAATTAAAGACACCATTTAATCTCTTACCTCGAT
1 -CCATCCAATCTCTTACCCCGATCATGGGGCAGATT-GA-AC-CCATCCAATCTCTTACCCCGAT
* *
33279634 CAT-GAGGTAGATTG-AG--G
62 CATAG-GGCAGATTGAAGACA
* * * * * * * * *
33279651 TCATCCAATCTCTTACCTCGATCATGGGGAAAATTGAAGATACCATACAATCTTTTACCCTGATT
1 CCATCCAATCTCTTACCCCGATCATGGGGCAGATTG-A-A-CCCATCCAATCTCTTACCCCGATC
* *
33279716 ATGGGGCAGATTGAAGATA
63 ATAGGGCAGATTGAAGACA
* *
33279735 TCA-CTCAATCTCTTACCCCGACCATGGGGCAGATTGAAAACACCATCCAATCTCTTACC
1 CCATC-CAATCTCTTACCCCGATCATGGGGCAGATTG--AAC-CCATCCAATCTCTTACC
33279794 ATGACCATGA
Statistics
Matches: 247, Mismatches: 43, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
80 38 0.15
81 122 0.49
82 4 0.02
83 6 0.02
84 75 0.30
85 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (81 bp):
CCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATA
GGGCAGATTGAAGACA
Found at i:33279624 original size:123 final size:122
Alignment explanation
Indices: 33279444--33279793 Score: 375
Period size: 123 Copynumber: 2.8 Consensus size: 122
33279434 GGGGTAGATT
* * *
33279444 GAAGCCATCAATCTCTTACCCCGATCAT-AGGGTAGATTGAAGACACCATCCAATCTCTTACCCC
1 GAAGCCATCAATTTCTTACCCCGATCATGA-GGCAGATTGAAGACACCATTCAATCTCTTACCCC
* *
33279508 GATTATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCAT-AGGACAGATTGAA
65 GATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATGAGGA-AAATTGAA
* * * * *
33279566 GAAGCCATCCAATTTCTTACCCCGATCATGAGACAAATTAAAGACACCATTTAATCTCTTACCTC
1 GAAGCCAT-CAATTTCTTACCCCGATCATGAGGCAGATTGAAGACACCATTCAATCTCTTACCCC
* * *** * *
33279631 GATCATGAGGTAGATTGAGGTCATCCAATCTCTTACCTCGATCATGGGGAAAATTGAA
65 GATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATGAGGAAAATTGAA
* * * * * *
33279689 GATA-CCATACAATCTT-TTACCCTGATTATGGGGCAGATTGAAGATATCACTCAATCTCTTACC
1 GA-AGCCAT-CAAT-TTCTTACCCCGATCATGAGGCAGATTGAAGACACCATTCAATCTCTTACC
*
33279752 CCGACCATGGGGCAGATTGAAAACACCATCCAATCTCTTACC
63 CCGATCATGGGGCAGATTG--AAC-CCATCCAATCTCTTACC
33279794 ATGACCATGA
Statistics
Matches: 185, Mismatches: 35, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
122 8 0.04
123 153 0.83
124 7 0.04
125 1 0.01
126 16 0.09
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (122 bp):
GAAGCCATCAATTTCTTACCCCGATCATGAGGCAGATTGAAGACACCATTCAATCTCTTACCCCG
ATCATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCATGAGGAAAATTGAA
Found at i:33279825 original size:123 final size:118
Alignment explanation
Indices: 33279439--33279832 Score: 346
Period size: 123 Copynumber: 3.2 Consensus size: 118
33279429 GTCATGGGGT
* * * *
33279439 AGATTGAAGCCAT-CAATCTCTTACCCCGATCATAGGGTAGATTGAAGACACCATCCAATCTCTT
1 AGATAGAAGCCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACACCAT-CAATCTCTT
* *
33279503 ACCCCGATTATGGGGCAGATTGAACCCATCCAATCTCTTACCCCGATCAT-AGGAC
65 ACCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTA-CCTGATCATGA-GAC
* * * * *
33279558 AGATTGAAGAAGCCATCCAAT-TTCTTACCCCGATCATGAGACAAATTAAAGACACCATTTAATC
1 AGA-T--AGAAGCCATCCAATCTT-TTACCCCGATCATGGGGCAGATTGAAGACACCA-TCAATC
* * * *** *
33279622 TCTTACCTCGATCATGAGGTAGATTGAGGTCATCCAATCTCTTACCTCGATCATGGGGA-
61 TCTTACCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTACCT-GATCAT-GAGAC
* * * * * * *
33279681 AAATTGAAGATACCATACAATCTTTTACCCTGATTATGGGGCAGATTGAAGATATCACTCAATCT
1 AGATAGAAG---CCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACACCA-TCAATCT
* *
33279746 CTTACCCCGACCATGGGGCAGATTGAAAACACCATCCAATCTCTTACCATGACCATGAGAC
62 CTTACCCCGATCATGGGGCAGATTG--AAC-CCATCCAATCTCTTACC-TGATCATGAGAC
*
33279807 AGATAGAAGTCATCCAATCTTTTACC
1 AGATAGAAGCCATCCAATCTTTTACC
33279833 ATAACCAGAG
Statistics
Matches: 213, Mismatches: 44, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
119 3 0.01
120 5 0.02
122 12 0.06
123 155 0.73
124 5 0.02
125 4 0.02
126 28 0.13
127 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (118 bp):
AGATAGAAGCCATCCAATCTTTTACCCCGATCATGGGGCAGATTGAAGACACCATCAATCTCTTA
CCCCGATCATGGGGCAGATTGAACCCATCCAATCTCTTACCTGATCATGAGAC
Found at i:33279832 original size:39 final size:40
Alignment explanation
Indices: 33279776--33279870 Score: 113
Period size: 39 Copynumber: 2.4 Consensus size: 40
33279766 GATTGAAAAC
* *
33279776 ACCATCCAATCTCTTACCATGACCATGA-GACAGATAGAAG
1 ACCATCCAATCTTTTACCATAACCA-GAGGACAGATAGAAG
* * *
33279816 -TCATCCAATCTTTTACCATAACCAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCATAACCAGAGGACAGATAGAAG
*
33279855 ACCATCCAATATTTTA
1 ACCATCCAATCTTTTA
33279871 TCCCTAATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.04
39 31 0.67
40 13 0.28
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCATAACCAGAGGACAGATAGAAG
Found at i:33279949 original size:45 final size:42
Alignment explanation
Indices: 33279761--33279949 Score: 129
Period size: 45 Copynumber: 4.5 Consensus size: 42
33279751 CCCGACCATG
* * * *
33279761 GGGCAGATTGAAAACACCATCCAATCTCTTACCATGA-CCATGA
1 GGGCAGATTG-AAGCACCATCCAATCTTTTACCCTAATCCA-GA
* * * *
33279804 -GACAGATAGAAG--TCATCCAATCTTTTACCATAA-CCAGA
1 GGGCAGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGA
* **
33279842 GGGCAGATTGAAG-ACCATCCAATATTTTATCCCTAATTAAGAA
1 GGGCAGATTGAAGCACCATCCAATCTTTTA-CCCTAATCCAG-A
* * * *
33279885 GGGTAGATTGAAACCACCATTCAATCTTTTACCCCCAATCCAGA
1 GGGCAGATTG-AAGCACCATCCAATCTTTTA-CCCTAATCCAGA
33279929 GGGGCAGATTGAAGCTACCAT
1 -GGGCAGATTGAAGC-ACCAT
33279950 ATCATAGAAG
Statistics
Matches: 114, Mismatches: 23, Indels: 16
0.75 0.15 0.10
Matches are distributed among these distances:
38 2 0.02
39 31 0.27
40 13 0.11
41 7 0.06
42 9 0.08
43 10 0.09
44 6 0.05
45 36 0.32
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (42 bp):
GGGCAGATTGAAGCACCATCCAATCTTTTACCCTAATCCAGA
Found at i:33282494 original size:109 final size:110
Alignment explanation
Indices: 33282297--33282497 Score: 289
Period size: 109 Copynumber: 1.8 Consensus size: 110
33282287 GGTAATGCTA
* ** *
33282297 TTTTATTTTAGGGAATTCAAGAAATTGTGCTCTAACGTGTTGGGTATGGTTTTTCCTTTGAACCT
1 TTTTATTTTAGGGAATTCAAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTCCTTTGAACCT
* *
33282362 AAATAATCGAGTATCTTTTTTAAAATCATTGAATGTTCAATGTTC
66 AAATAATCGAGTATCCTATTTAAAATCATTGAATGTTCAATGTTC
* *
33282407 TTTTA-TTTAGGGAATTCGAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTTCTTTGAACCT
1 TTTTATTTTAGGGAATTCAAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTCCTTTGAACCT
* *
33282471 AAGTAATTGA-TCATCCTATTTAAAATC
66 AAATAATCGAGT-ATCCTATTTAAAATC
33282498 GATAAATGTC
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
108 1 0.01
109 74 0.93
110 5 0.06
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (110 bp):
TTTTATTTTAGGGAATTCAAGAAATTGTGCTCAAACGTACTGGGTATGATTTTTCCTTTGAACCT
AAATAATCGAGTATCCTATTTAAAATCATTGAATGTTCAATGTTC
Found at i:33285161 original size:57 final size:57
Alignment explanation
Indices: 33285095--33285218 Score: 160
Period size: 57 Copynumber: 2.2 Consensus size: 57
33285085 ATTGTTTTCC
* * *
33285095 CAAATTTTCTCAAATTTTTTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTTT
1 CAAATTTTCTCAAACTTTCTCTCTTTCCAAACACACATTTTCTCTCATTATTTTTTT
* * * * * *
33285152 CAAATTTTCTCAGACTTTCTCTTTTTTCAAACATATATTTTCTCTCGTTATTTTTTT
1 CAAATTTTCTCAAACTTTCTCTCTTTCCAAACACACATTTTCTCTCATTATTTTTTT
33285209 -AAATTTTCTC
1 CAAATTTTCTC
33285219 TCATTATATT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
56 10 0.17
57 48 0.83
ACGTcount: A:0.23, C:0.22, G:0.02, T:0.54
Consensus pattern (57 bp):
CAAATTTTCTCAAACTTTCTCTCTTTCCAAACACACATTTTCTCTCATTATTTTTTT
Found at i:33290919 original size:23 final size:23
Alignment explanation
Indices: 33290889--33290938 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
33290879 CAGAATCCAT
33290889 CCATCGTTTTATAAGCTTCGAAA
1 CCATCGTTTTATAAGCTTCGAAA
33290912 CCATCGTTTTATAAGCTTCGAAA
1 CCATCGTTTTATAAGCTTCGAAA
33290935 CCAT
1 CCAT
33290939 ACAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (23 bp):
CCATCGTTTTATAAGCTTCGAAA
Found at i:33291836 original size:2 final size:2
Alignment explanation
Indices: 33291829--33291858 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33291819 AAACATGCAT
*
33291829 GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
33291859 AAGGGGTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33291859 original size:12 final size:12
Alignment explanation
Indices: 33291829--33291861 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33291819 AAACATGCAT
*
33291829 GAGAGAGAGAGA
1 GAGAGAAAGAGA
33291841 GAGAGAAAGAGA
1 GAGAGAAAGAGA
33291853 GAGAGAAAG
1 GAGAGAAAG
33291862 GGGTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
GAGAGAAAGAGA
Found at i:33293221 original size:16 final size:15
Alignment explanation
Indices: 33293181--33293213 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
33293171 AAATTTTAAA
33293181 AATCAAATTATCTCG
1 AATCAAATTATCTCG
33293196 AATCAAATTATCT-G
1 AATCAAATTATCTCG
33293210 AATC
1 AATC
33293214 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (15 bp):
AATCAAATTATCTCG
Found at i:33299805 original size:17 final size:17
Alignment explanation
Indices: 33299783--33299817 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33299773 TTTAGGTCGT
33299783 ATTAATTT-GAAGTTTGA
1 ATTAATTTCGAA-TTTGA
33299800 ATTAATTTCGAATTTGA
1 ATTAATTTCGAATTTGA
33299817 A
1 A
33299818 CCATTTCGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (17 bp):
ATTAATTTCGAATTTGA
Found at i:33300468 original size:32 final size:33
Alignment explanation
Indices: 33300420--33300486 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 33
33300410 TAAATAAAAT
*
33300420 TATGTATTTTTTTTATATTACTAGGTTTTGAAA
1 TATGTATTTTTTTTATATTACTAGATTTTGAAA
33300453 TATGTA-TTTTTTTATATTACTAGATTTTGAAA
1 TATGTATTTTTTTTATATTACTAGATTTTGAAA
33300485 TA
1 TA
33300487 CTCATAAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 27 0.82
33 6 0.18
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.57
Consensus pattern (33 bp):
TATGTATTTTTTTTATATTACTAGATTTTGAAA
Found at i:33301261 original size:15 final size:17
Alignment explanation
Indices: 33301231--33301263 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
33301221 ACTGCATTAA
33301231 ACATTTTATGAAAGTAC
1 ACATTTTATGAAAGTAC
33301248 ACATTTT-T-AAAGTAC
1 ACATTTTATGAAAGTAC
33301263 A
1 A
33301264 AGTATCACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.36
Consensus pattern (17 bp):
ACATTTTATGAAAGTAC
Found at i:33310789 original size:147 final size:149
Alignment explanation
Indices: 33310274--33310897 Score: 851
Period size: 147 Copynumber: 4.2 Consensus size: 149
33310264 AAATTTATCA
* * * * * *
33310274 AAGAAATCTATCTAATTTAGAAGAATATATTGC-AGGAAAGTAAGATGCACAAAGATTAGTTTCT
1 AAGAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTCT
* *
33310338 AGAAAAGAAATGCAATTGAACAAGAACGATGAAAACTCAATGAACAAAGATATATAAGAAGAAGA
66 AGAAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATA-A-GAGAA-AA-A
33310403 AAATGAACAAGACTCGATCAAAT
127 AAATGAACAAGACTCGATCAAAT
*
33310426 AAGAAATTTATCTGATTTGAGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTC
1 AAGAAATCTATCTGATTT-AGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTC
* * * *
33310491 TAGAAAAGAAAAGCAATTGAACAAGAACTATGAAAACACAATGAACAAAGGTAAGAGGAAAATAA
65 TAGAAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAGA-GAAAAAAA
*
33310556 ATGAACAAAACTCGATCAAAT
129 ATGAACAAGACTCGATCAAAT
* * * * *
33310577 AAGAACTCTATCTGATTCAGAAGAATATGCTACAAGAAAAGTAAAATTCACAAAGACTAATTTCT
1 AAGAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTCT
* * * * *
33310642 AGAAAAGAAATGCAATTCAACAAGAACAATGAAAACACAATGAATAAAGAT-A-AGAAAATATAT
66 AGAAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAGAGAAAAAAAAT
*
33310705 GAGCAAGACTCGATCAAAT
131 GAACAAGACTCGATCAAAT
* * * *
33310724 TAGAAATCTATCTGATTTTGAAGAATATACTACAACAAAAATAAGATGCACAAAGACTAATTTCT
1 AAGAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTCT
* * * *
33310789 AGAAAAGAAATGAAATTGAGCAAGATCGATGAAAACACAATAAACAAAGATAAGAGAAAAAAAAT
66 AGAAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAGAGAAAAAAAAT
*
33310854 GAACAAGACTCGATCAAAC
131 GAACAAGACTCGATCAAAT
33310873 AA-ACAATCTATCTGATTTAGAAGAA
1 AAGA-AATCTATCTGATTTAGAAGAA
33310898 CTCTAAGCTT
Statistics
Matches: 416, Mismatches: 50, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
147 126 0.30
148 3 0.01
149 48 0.12
150 90 0.22
151 37 0.09
152 19 0.05
153 17 0.04
154 76 0.18
ACGTcount: A:0.53, C:0.12, G:0.15, T:0.20
Consensus pattern (149 bp):
AAGAAATCTATCTGATTTAGAAGAATATACTACAAGAAAAGTAAGATGCACAAAGACTAATTTCT
AGAAAAGAAATGCAATTGAACAAGAACGATGAAAACACAATGAACAAAGATAAGAGAAAAAAAAT
GAACAAGACTCGATCAAAT
Found at i:33311494 original size:31 final size:31
Alignment explanation
Indices: 33311459--33311523 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
33311449 TTAACATCCC
*
33311459 AATGACTTAAATAAAAACTTTCTAATAATTT
1 AATGACTTAAATAAAAACTTTCGAATAATTT
* *
33311490 AATGACTTAAATGAAAATTTTCGAATAATTT
1 AATGACTTAAATAAAAACTTTCGAATAATTT
33311521 AAT
1 AAT
33311524 AACCATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (31 bp):
AATGACTTAAATAAAAACTTTCGAATAATTT
Found at i:33313954 original size:20 final size:20
Alignment explanation
Indices: 33313931--33313968 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33313921 AAAAATTATA
33313931 TTTTTAA-AAAATTATAAAT
1 TTTTTAAGAAAATTATAAAT
*
33313950 TTTTTAAGAAAATTCTAAA
1 TTTTTAAGAAAATTATAAA
33313969 GAATATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTTTAAGAAAATTATAAAT
Found at i:33315286 original size:18 final size:18
Alignment explanation
Indices: 33315263--33315297 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33315253 CTTTAGAAAC
*
33315263 TTTTTAAAAAATTATAAT
1 TTTTTAAAAAAATATAAT
33315281 TTTTTAAAAAAATATAA
1 TTTTTAAAAAAATATAA
33315298 AATTTGACAT
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:0.00, T:0.46
Consensus pattern (18 bp):
TTTTTAAAAAAATATAAT
Found at i:33315408 original size:18 final size:18
Alignment explanation
Indices: 33315387--33315425 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
33315377 ATATCAATTT
* *
33315387 ATTATTTTAATTATTCAA
1 ATTATTTGAATAATTCAA
*
33315405 ATTATTTGAATAATTCGA
1 ATTATTTGAATAATTCAA
33315423 ATT
1 ATT
33315426 GTAAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTATTTGAATAATTCAA
Found at i:33329988 original size:28 final size:30
Alignment explanation
Indices: 33329928--33330008 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 30
33329918 ACTCGAGGAT
33329928 AAAATGATAATTTTAGGAAAATTTAGGGTTA
1 AAAATGATAATTTTA-GAAAATTTAGGGTTA
*
33329959 AAAATGAT-ATTTTA-AACATTTAAGGG-TA
1 AAAATGATAATTTTAGAAAATTT-AGGGTTA
33329987 AAACA--ATAATTTTTAGAAAATT
1 AAA-ATGATAA-TTTTAGAAAATT
33330009 CGAGATAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
27 2 0.05
28 12 0.28
29 10 0.23
30 11 0.26
31 8 0.19
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.36
Consensus pattern (30 bp):
AAAATGATAATTTTAGAAAATTTAGGGTTA
Found at i:33330088 original size:30 final size:29
Alignment explanation
Indices: 33330044--33330181 Score: 129
Period size: 29 Copynumber: 4.6 Consensus size: 29
33330034 ATCCGAGGGT
*
33330044 AAAATGGTAATTTTTGGATATTTT-AGGGTCA
1 AAAATGG-AATTTTTGGA-ATTTTGA-GGTAA
*
33330075 AAAATGGAATTTTTGGAAGTTTGAGGTAA
1 AAAATGGAATTTTTGGAATTTTGAGGTAA
* *
33330104 AAAATGGAATTTTTGGAAATTTGGGGATAA
1 AAAATGGAATTTTTGGAATTTTGAGG-TAA
* *
33330134 AAATAT--AATTTTTGGTAGTTTCGAGGTTAA
1 AAA-ATGGAATTTTTGG-AATTTTGAGG-TAA
*
33330164 AAAATTGAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
33330182 GTTCGGGGGG
Statistics
Matches: 91, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
29 43 0.47
30 30 0.33
31 18 0.20
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAATTTTGAGGTAA
Found at i:33330115 original size:59 final size:60
Alignment explanation
Indices: 33330044--33330181 Score: 174
Period size: 58 Copynumber: 2.3 Consensus size: 60
33330034 ATCCGAGGGT
* *
33330044 AAAATGGTAATTTTTGGATATTTTAGGG-TCAAAAATGGAATTTTTGGAAGTTT-GAGG-TAA
1 AAAATGG-AATTTTTGGA-AATTTAGGGAT-AAAAATAGAATTTTTGGAAGTTTCGAGGTTAA
* * *
33330104 AAAATGGAATTTTTGGAAATTTGGGGATAAAAATATAATTTTTGGTAGTTTCGAGGTTAA
1 AAAATGGAATTTTTGGAAATTTAGGGATAAAAATAGAATTTTTGGAAGTTTCGAGGTTAA
*
33330164 AAAATTGAATTTTTGGAA
1 AAAATGGAATTTTTGGAA
33330182 GTTCGGGGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
58 27 0.39
59 15 0.22
60 27 0.39
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.38
Consensus pattern (60 bp):
AAAATGGAATTTTTGGAAATTTAGGGATAAAAATAGAATTTTTGGAAGTTTCGAGGTTAA
Found at i:33330712 original size:26 final size:26
Alignment explanation
Indices: 33330682--33330733 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
33330672 GTTTTGGAGG
33330682 CTTATAAATAGCCTTCTTTTGATTTT
1 CTTATAAATAGCCTTCTTTTGATTTT
33330708 CTTATAAATAGCCTTCTTTTGATTTT
1 CTTATAAATAGCCTTCTTTTGATTTT
33330734 TTTCTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (26 bp):
CTTATAAATAGCCTTCTTTTGATTTT
Found at i:33331519 original size:6 final size:6
Alignment explanation
Indices: 33331499--33331574 Score: 54
Period size: 6 Copynumber: 13.0 Consensus size: 6
33331489 TTAAATTGGT
* *
33331499 TTTAAA TTT-AT TTTAAA TTTAAA TTTATCTAA -TTAAA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA
* *
33331547 TTTTAG TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
33331575 ACAATAATAA
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 35 0.62
8 3 0.05
9 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:33331536 original size:20 final size:17
Alignment explanation
Indices: 33331499--33331574 Score: 84
Period size: 17 Copynumber: 4.4 Consensus size: 17
33331489 TTAAATTGGT
33331499 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
33331516 TTTAAATTTATCTAATTAAA
1 TTTAAATTTAT-T--TTAAA
*
33331536 TTTAAATTTACTTTT-AG
1 TTTAAATTTA-TTTTAAA
*
33331553 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
33331569 TTTAAA
1 TTTAAA
33331575 ACAATAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
15 2 0.04
16 7 0.14
17 22 0.43
18 3 0.06
20 16 0.31
21 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:33331646 original size:20 final size:20
Alignment explanation
Indices: 33331612--33331650 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
33331602 AAACCCAATG
33331612 AATGTCCATATTACACAAACT
1 AATGTCCATATTACA-AAACT
33331633 AATGTCCA-ATTACAAAAC
1 AATGTCCATATTACAAAAC
33331651 AGACCTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (20 bp):
AATGTCCATATTACAAAACT
Found at i:33333615 original size:29 final size:30
Alignment explanation
Indices: 33333503--33333758 Score: 225
Period size: 30 Copynumber: 8.6 Consensus size: 30
33333493 AACTGTTCAG
* * * *
33333503 AAATTACGTTTTTAACCTCAAAACTTCTAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
* * **
33333533 AAATTATATTTTT-ACCCCTAGAACTTTTAA
1 AAATTACATTTTTGACCCC-AAAACTTCCAA
* *
33333563 AAATTACATTTTTGACCTCAAAACCTCCAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
*
33333593 AAATTACATTTTT-ACCCCTAAACTTCCAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
* * * * *
33333622 AAAAT-CAATTTTTGACCTCGAAATTTCCCA
1 AAATTAC-ATTTTTGACCCCAAAACTTCCAA
**
33333652 AAATTACATTTTT-ACCCCTGAACTTCCAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
* * *
33333681 AAATTTCATTTTTGACCCCAAAACCTCTAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
* ** *
33333711 AAATTACATTTTT-TCCCCCGAACTTTCAA
1 AAATTACATTTTTGACCCCAAAACTTCCAA
*
33333740 AAATTCCATTTTTGACCCC
1 AAATTACATTTTTGACCCC
33333759 GACACTTTTA
Statistics
Matches: 180, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
28 1 0.01
29 72 0.40
30 102 0.57
31 5 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTACATTTTTGACCCCAAAACTTCCAA
Found at i:33333758 original size:59 final size:59
Alignment explanation
Indices: 33333488--33333756 Score: 306
Period size: 59 Copynumber: 4.5 Consensus size: 59
33333478 CCCTGGAGGT
* * * * * * *
33333488 CCCTAAACTGTTCAGAAATTACGTTTTTAACCTCAAAACTTCTAAAAATTATATTTTTAC
1 CCCTGAACT-TTCAAAAATTACATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
*
33333548 CCCTAGAACTTTTAAAAATTACATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
1 CCCT-GAACTTTCAAAAATTACATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
* * * * ** *
33333608 CCCTAAACTTCCAAAAAAT-CAATTTTTGACCTCGAAATTTCCCAAAATTACATTTTTAC
1 CCCTGAACTTTCAAAAATTAC-ATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
* * * * *
33333667 CCCTGAACTTCCAAAAATTTCATTTTTGACCCCAAAACCTCTAAAAATTACATTTTTTC
1 CCCTGAACTTTCAAAAATTACATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
* *
33333726 CCCCGAACTTTCAAAAATTCCATTTTTGACC
1 CCCTGAACTTTCAAAAATTACATTTTTGACC
33333757 CCGACACTTT
Statistics
Matches: 178, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
58 1 0.01
59 121 0.68
60 52 0.29
61 4 0.02
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (59 bp):
CCCTGAACTTTCAAAAATTACATTTTTGACCTCAAAACCTCCAAAAATTACATTTTTAC
Found at i:33333771 original size:59 final size:59
Alignment explanation
Indices: 33333511--33333785 Score: 293
Period size: 59 Copynumber: 4.7 Consensus size: 59
33333501 AGAAATTACG
* * * ** *
33333511 TTTTTAACCTCAAAACTTCTAAAAATTATATTTTTACCCCTAGAACTTTTAAAAATTACA
1 TTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCT-GAACTTCCAAAAATTCCA
* * * * * *
33333571 TTTTTGACCTCAAAACCTCCAAAAATTACATTTTTACCCCTAAACTTCCAAAAAATCAA
1 TTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCA
* * * ** *
33333630 TTTTTGACCTCGAAATTTCCCAAAATTACATTTTTACCCCTGAACTTCCAAAAATTTCA
1 TTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCA
* * * *
33333689 TTTTTGACCCCAAAACCTCTAAAAATTACATTTTTTCCCCCGAACTTTCAAAAATTCCA
1 TTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCA
* * *
33333748 TTTTTGACCCCGACACTT-TTAAAATTACCA-TTTTACCC
1 TTTTTGACCCCAAAACTTCTAAAAATTA-CATTTTTACCC
33333786 TCGAATGTCT
Statistics
Matches: 181, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
58 15 0.08
59 129 0.71
60 37 0.20
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.36
Consensus pattern (59 bp):
TTTTTGACCCCAAAACTTCTAAAAATTACATTTTTACCCCTGAACTTCCAAAAATTCCA
Found at i:33333800 original size:29 final size:29
Alignment explanation
Indices: 33333768--33333846 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
33333758 CGACACTTTT
33333768 AAAATTACCATTTTACCCTCGAATGTCTG
1 AAAATTACCATTTTACCCTCGAATGTCTG
* * * *
33333797 AAAATT-TCATTTTTGATCCT-GATTTTCTG
1 AAAATTACCA-TTTT-ACCCTCGAATGTCTG
* *
33333826 AAAATTACCGTTTTACGCTCG
1 AAAATTACCATTTTACCCTCG
33333847 GATAGCTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
28 5 0.13
29 28 0.74
30 5 0.13
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAATGTCTG
Found at i:33333808 original size:58 final size:58
Alignment explanation
Indices: 33333629--33333897 Score: 164
Period size: 58 Copynumber: 4.6 Consensus size: 58
33333619 CAAAAAATCA
* * *
33333629 ATTTTTGACCTCGAAA-TTTCCCAAAATTA-CATTTTTACCC-CTGAACT-TCCAAAAATTTC
1 ATTTTTGACCCCGAAACTTT-TCAAAATTACCA-TTTTACCCTC-GAA-TGT-CTAAAATTTC
* * * * * * * * *
33333688 ATTTTTGACCCCAAAACCTCTAAAAATTA-CATTTTTTCCCCCGAACTTTCAAAAATTCC
1 ATTTTTGACCCCGAAACTTTTCAAAATTACCA-TTTTACCCTCGAA-TGTCTAAAATTTC
*
33333747 ATTTTTGACCCCGACACTTTT-AAAATTACCATTTTACCCTCGAATGTCTGAAAATTTC
1 ATTTTTGACCCCGAAACTTTTCAAAATTACCATTTTACCCTCGAATGTCT-AAAATTTC
* * * * * *
33333805 ATTTTTGATCCTG--A-TTTTCTGAAAATTACCGTTTTACGCTCGGATAG-CTAAAATGTC
1 ATTTTTGACCCCGAAACTTTTC--AAAATTACCATTTTACCCTCGAAT-GTCTAAAATTTC
* *
33333862 ATTTTTAACCCC-AAAATTTTCCAAAATTACCATTTT
1 ATTTTTGACCCCGAAACTTTT-CAAAATTACCATTTT
33333898 TGCCCCTCGA
Statistics
Matches: 170, Mismatches: 27, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
55 4 0.02
56 1 0.01
57 19 0.11
58 73 0.43
59 69 0.41
60 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (58 bp):
ATTTTTGACCCCGAAACTTTTCAAAATTACCATTTTACCCTCGAATGTCTAAAATTTC
Found at i:33335022 original size:3 final size:3
Alignment explanation
Indices: 33335014--33335052 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
33335004 GACAGCATTA
*
33335014 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT TTT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
33335053 ATGCCATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33335758 original size:6 final size:6
Alignment explanation
Indices: 33335747--33335801 Score: 60
Period size: 6 Copynumber: 9.5 Consensus size: 6
33335737 AAATAAAATA
* * * *
33335747 AAATTT AAATTT AAAATT -AATTT AAATTC AAATTT AAA-AT AAATCT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
33335793 AAATTT AAA
1 AAATTT AAA
33335802 AGGGGCCGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
5 8 0.20
6 32 0.80
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:33335783 original size:17 final size:17
Alignment explanation
Indices: 33335748--33335783 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
33335738 AATAAAATAA
*
33335748 AATTTAAATTTAAAATT
1 AATTTAAATTCAAAATT
*
33335765 AATTTAAATTCAAATTT
1 AATTTAAATTCAAAATT
33335782 AA
1 AA
33335784 AATAAATCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTAAATTCAAAATT
Found at i:33335795 original size:23 final size:22
Alignment explanation
Indices: 33335730--33335797 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 22
33335720 CTTTTTTTTT
* *
33335730 AATTTGAAAATAAAATAAAATTTA
1 AATTT-AAAAT-AAATTAAATTCA
*
33335754 AATTTAAAATTAATTTAAATTCA
1 AATTTAAAA-TAAATTAAATTCA
33335777 AATTTAAAATAAATCTAAATT
1 AATTTAAAATAAAT-TAAATT
33335798 TAAAAGGGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
22 4 0.11
23 28 0.74
24 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (22 bp):
AATTTAAAATAAATTAAATTCA
Found at i:33342725 original size:28 final size:29
Alignment explanation
Indices: 33342689--33342745 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
33342679 TTAGTTCAGA
*
33342689 ATTTCAAATTTTTTGT-TCATGTTTGTTT
1 ATTTCAAATTATTTGTGTCATGTTTGTTT
*
33342717 ATTTTAAATTATTTGTGTCATGTTTGTTT
1 ATTTCAAATTATTTGTGTCATGTTTGTTT
33342746 GTTTAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.63
Consensus pattern (29 bp):
ATTTCAAATTATTTGTGTCATGTTTGTTT
Found at i:33342750 original size:28 final size:28
Alignment explanation
Indices: 33342694--33342751 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
33342684 TCAGAATTTC
* *
33342694 AAATTTTTTGTTCATGTTTGTTTATTTT
1 AAATTATTTGTTCATGTTTGTTTAGTTT
33342722 AAATTATTTGTGTCATGTTTGTTT-GTTT
1 AAATTATTTGT-TCATGTTTGTTTAGTTT
33342750 AA
1 AA
33342752 TGTTCACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (28 bp):
AAATTATTTGTTCATGTTTGTTTAGTTT
Found at i:33343421 original size:14 final size:15
Alignment explanation
Indices: 33343402--33343430 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33343392 TGATGCGTTC
33343402 TCATTGTTC-ATTGT
1 TCATTGTTCAATTGT
33343416 TCATTGTTCAATTGT
1 TCATTGTTCAATTGT
33343431 CGAGTATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
TCATTGTTCAATTGT
Found at i:33347011 original size:1 final size:1
Alignment explanation
Indices: 33347000--33347035 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
33346990 AAAATTTAGG
*
33347000 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33347036 GTGCTTGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:33357589 original size:41 final size:41
Alignment explanation
Indices: 33357538--33357694 Score: 190
Period size: 41 Copynumber: 3.8 Consensus size: 41
33357528 AAAAGGTAAA
*
33357538 GCATTAGCGGCGCTTATGTAGAAGCGCCGCCAAAGATCGAG
1 GCATTAGCGGCGCTTATGTAGAAGCGCCGCTAAAGATCGAG
* * *
33357579 GCATTAGCGGCGCTTTTGAAGAAGCGCCACTAAAGATC-AGG
1 GCATTAGCGGCGCTTATGTAGAAGCGCCGCTAAAGATCGA-G
* * * * * *
33357620 GCATTAGCAGCGCTTATGGAGATGCGCTGCTAAAGATTGGG
1 GCATTAGCGGCGCTTATGTAGAAGCGCCGCTAAAGATCGAG
* *
33357661 GCATTAGCGGCGCGTATGTAAAAGCGCCGCTAAA
1 GCATTAGCGGCGCTTATGTAGAAGCGCCGCTAAA
33357695 AGTGGATTTT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 1 0.01
41 95 0.99
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTATGTAGAAGCGCCGCTAAAGATCGAG
Found at i:33361008 original size:43 final size:43
Alignment explanation
Indices: 33360947--33361047 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 43
33360937 TAAAGATTGT
* **
33360947 TAAAGATCATGTTTTTTAGCGGCGTTTGTAGG-AAAAGCGTTGC
1 TAAAGATCATGTTCTTTAGCGGCGTTTGT-GGAAAAAGCGCCGC
33360990 TAAAGATCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGC
1 TAAAGATCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGC
* *
33361033 TAAAGACCTTGTTCT
1 TAAAGATCATGTTCT
33361048 ATAGGAAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
42 2 0.04
43 50 0.96
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
TAAAGATCATGTTCTTTAGCGGCGTTTGTGGAAAAAGCGCCGC
Found at i:33373329 original size:16 final size:17
Alignment explanation
Indices: 33373308--33373340 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33373298 TGGGAATGAT
*
33373308 AAATAATAATT-TTTTA
1 AAATAACAATTCTTTTA
33373324 AAATAACAATTCTTTTA
1 AAATAACAATTCTTTTA
33373341 TCTATGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAACAATTCTTTTA
Found at i:33376872 original size:16 final size:16
Alignment explanation
Indices: 33376851--33376883 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33376841 TAAATTTAAG
33376851 AAAATAA-ATCAATTTA
1 AAAATAATAT-AATTTA
33376867 AAAATAATATAATTTA
1 AAAATAATATAATTTA
33376883 A
1 A
33376884 TAAGTGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATATAATTTA
Found at i:33377239 original size:22 final size:20
Alignment explanation
Indices: 33377200--33377239 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
33377190 TTTATTTGCT
33377200 ATGAATTTTAATTATTTTTA
1 ATGAATTTTAATTATTTTTA
*
33377220 ATGACATTATTAATTGTTTT
1 ATGA-ATT-TTAATTATTTT
33377240 CTAAGTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 3 0.18
22 10 0.59
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (20 bp):
ATGAATTTTAATTATTTTTA
Found at i:33378355 original size:23 final size:20
Alignment explanation
Indices: 33378313--33378392 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 20
33378303 ATTCTTTAGA
* *
33378313 TTTTAAAAAA-ATTATAATT
1 TTTTAAAAAATATTTTGATT
33378332 TTTTAAAAATATAATTTTGGATTT
1 TTTTAAAAA-AT-ATTTT-GA-TT
*
33378356 TTTTATAAAATATTTTGA-T
1 TTTTAAAAAATATTTTGATT
**
33378375 TTTTAAAATTTATTTTGA
1 TTTTAAAAAATATTTTGA
33378393 AATTTTGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
19 25 0.50
20 1 0.02
21 2 0.04
22 9 0.18
23 3 0.06
24 10 0.20
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTAAAAAATATTTTGATT
Found at i:33380008 original size:14 final size:14
Alignment explanation
Indices: 33379989--33380016 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33379979 TAATTTTAGC
33379989 ATTTTTACCCAAAT
1 ATTTTTACCCAAAT
33380003 ATTTTTACCCAAAT
1 ATTTTTACCCAAAT
33380017 TGAATTTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTTTTACCCAAAT
Found at i:33381162 original size:21 final size:21
Alignment explanation
Indices: 33381136--33381187 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
33381126 ATTGTATTAT
33381136 TAAATAATT-TATTA-AAATAA
1 TAAATAATTATATTATAAAT-A
33381156 TAAA-ATATTATATTATTAAATA
1 TAAATA-ATTATATTA-TAAATA
33381178 TAAATAATTA
1 TAAATAATTA
33381188 AACATGTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 7 0.26
21 5 0.19
22 9 0.33
23 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATAATTATATTATAAATA
Found at i:33381260 original size:23 final size:25
Alignment explanation
Indices: 33381229--33381289 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 25
33381219 AATATTTGGT
* *
33381229 ATTAGTATTTTAAAT-ATT-TTAAA
1 ATTAATATTATAAATGATTATTAAA
33381252 ATTAATATTATAAATGATTATTAATA
1 ATTAATATTATAAATGATTATTAA-A
*
33381278 TAATAATATTAT
1 -ATTAATATTAT
33381290 GTTTGATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 13 0.42
24 3 0.10
25 4 0.13
26 1 0.03
27 10 0.32
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
ATTAATATTATAAATGATTATTAAA
Found at i:33381481 original size:16 final size:16
Alignment explanation
Indices: 33381451--33381480 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33381441 ACACAAAAAA
33381451 GTAAATAATATTTTTC
1 GTAAATAATATTTTTC
33381467 GTAAATAAT-TTTTT
1 GTAAATAATATTTTT
33381481 TAATATACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (16 bp):
GTAAATAATATTTTTC
Found at i:33386204 original size:270 final size:270
Alignment explanation
Indices: 33385772--33386319 Score: 999
Period size: 276 Copynumber: 2.0 Consensus size: 270
33385762 ACAATTATTA
*
33385772 GAAAATAATTTTTAAAACAATCAATCCCTTTGCTAGTTCGTTGAAATAAAAAATGAATTTATATG
1 GAAAATAATTTTTAAAACAATCAATCCCTCTGCTAGTTCGTTGAAATAAAAAATGAATTTATATG
*
33385837 TTAATCAAAATGAACAGAAGGAATTGAAACGGAAAAATGGAAAACATTCAAGAAGCGATTATGAT
66 TTAATCAAAATGAACAGAAGGAATTGAAACAGAAAAATGGAAAACATTCAAGAAGCGATTATGAT
*
33385902 TTTCTCCAAAATGAATGTGATTCTTTTC-AAAATGAAAATGAGAAATTAACAAAGAATTCTCAAA
131 TTTCTCCAAAATGAATGTGATTCTTTTCAAAAATGAAAATGAGAAATGAACAAAGAATTCTCAAA
33385966 AATGATTACAAGATTCAGTTTATGTTTTTAAACTACTTTAAAGTTGAAAATGAAAATAAATCATA
196 AATGATTACAAGATTCAGTTTATGTTTTTAAACTACTTTAAAGTTGAAAATGAAAATAAATCATA
33386031 TGATCTTAAT
261 TGATCTTAAT
33386041 GAAAATAATTTTTAAAACAATCAATCCCTCTGCTAGTTCGTTGAAATAAAAAATGAATTTATATG
1 GAAAATAATTTTTAAAACAATCAATCCCTCTGCTAGTTCGTTGAAATAAAAAATGAATTTATATG
33386106 TTGAATCAAAATGAACAGAAGGAATTGAAACAGAAAAATGGAAAACATTCAAGAAGCGATTATGA
66 TT-AATCAAAATGAACAGAAGGAATTGAAACAGAAAAATGGAAAACATTCAAGAAGCGATTATGA
*
33386171 TTTTCTCCAAAATGGATGTGATTCTTTTCAAAATAAAAATGAAAATGAGAAATGAACAAAGAATT
130 TTTTCTCCAAAATGAATGTGATTCTTTTC-----AAAAATGAAAATGAGAAATGAACAAAGAATT
33386236 CTCAAAAATGATTACAAGATTCAGTTTATGTTTTTAAACTACTTTAAAGTTGAAAATGAAAATAA
190 CTCAAAAATGATTACAAGATTCAGTTTATGTTTTTAAACTACTTTAAAGTTGAAAATGAAAATAA
33386301 ATCATATGATCTTAAT
255 ATCATATGATCTTAAT
33386317 GAA
1 GAA
33386320 CAAGTTGAAT
Statistics
Matches: 268, Mismatches: 4, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
269 66 0.25
270 89 0.33
276 113 0.42
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (270 bp):
GAAAATAATTTTTAAAACAATCAATCCCTCTGCTAGTTCGTTGAAATAAAAAATGAATTTATATG
TTAATCAAAATGAACAGAAGGAATTGAAACAGAAAAATGGAAAACATTCAAGAAGCGATTATGAT
TTTCTCCAAAATGAATGTGATTCTTTTCAAAAATGAAAATGAGAAATGAACAAAGAATTCTCAAA
AATGATTACAAGATTCAGTTTATGTTTTTAAACTACTTTAAAGTTGAAAATGAAAATAAATCATA
TGATCTTAAT
Found at i:33386392 original size:42 final size:42
Alignment explanation
Indices: 33386345--33386428 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
33386335 AATATTAAAT
* **
33386345 TGTAACATCCGTGTTTTTGAA-CAGGAGTTGGAACAGTAATAG
1 TGTAACATCCGCGTGCTTGAATC-GGAGTTGGAACAGTAATAG
* *
33386387 TGTAACATCCGCGTGCTTGAATCGGATTTGGAACAGTGATAG
1 TGTAACATCCGCGTGCTTGAATCGGAGTTGGAACAGTAATAG
33386429 AGTACAATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (42 bp):
TGTAACATCCGCGTGCTTGAATCGGAGTTGGAACAGTAATAG
Found at i:33388139 original size:6 final size:6
Alignment explanation
Indices: 33388128--33388172 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
33388118 TGATCAAAAT
* * *
33388128 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
33388173 TAAGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:33389211 original size:25 final size:25
Alignment explanation
Indices: 33389183--33389234 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
33389173 ATTTTATTTT
*
33389183 TTGAGATAAAAATAT-AAATATTGGG
1 TTGA-ATAAAAATATAAAACATTGGG
* *
33389208 TTGAATCAAATTATAAAACATTGGG
1 TTGAATAAAAATATAAAACATTGGG
33389233 TT
1 TT
33389235 AAAAGCCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (25 bp):
TTGAATAAAAATATAAAACATTGGG
Found at i:33391166 original size:31 final size:33
Alignment explanation
Indices: 33391119--33391187 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 33
33391109 AAAAGTATTG
33391119 AAAAATAATAATTTTTT-ATACTTTT-AAAATTTT
1 AAAAATAATAATTTTTTGA-A-TTTTAAAAATTTT
33391152 AAAAAT-A-AATTTTTTGAATTTTAAAAATTTT
1 AAAAATAATAATTTTTTGAATTTTAAAAATTTT
33391183 AAAAA
1 AAAAA
33391188 ATATTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 4 0.12
31 22 0.65
32 2 0.06
33 6 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (33 bp):
AAAAATAATAATTTTTTGAATTTTAAAAATTTT
Found at i:33391824 original size:27 final size:28
Alignment explanation
Indices: 33391772--33391827 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
33391762 CGAATTTTAG
**
33391772 GGTTTTTGTCCTAAATAATACAAAAAAA
1 GGTTTTTAACCTAAATAATACAAAAAAA
33391800 GGTTTTTAACCTAAATAATACAAAAAAA
1 GGTTTTTAACCTAAATAATACAAAAAAA
33391828 AATTATACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (28 bp):
GGTTTTTAACCTAAATAATACAAAAAAA
Found at i:33391835 original size:15 final size:15
Alignment explanation
Indices: 33391812--33391856 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
33391802 TTTTTAACCT
33391812 AAATAATACAAAAAA
1 AAATAATACAAAAAA
* **
33391827 AAATTATACACCAAA
1 AAATAATACAAAAAA
*
33391842 ATATAATACAAAAAA
1 AAATAATACAAAAAA
33391857 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAATACAAAAAA
Found at i:33391843 original size:28 final size:29
Alignment explanation
Indices: 33391784--33391856 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
33391774 TTTTTGTCCT
** * *
33391784 AAATAATACAAAAAAAGGTTTTTAACC-T
1 AAATAATACAAAAAAAGAATTATAACCAA
33391812 AAATAATACAAAAAAA-AATTATACACCAA
1 AAATAATACAAAAAAAGAATTATA-ACCAA
33391841 AATATAATACAAAAAA
1 AA-ATAATACAAAAAA
33391857 TAAAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 19 0.50
29 2 0.05
30 13 0.34
ACGTcount: A:0.64, C:0.11, G:0.03, T:0.22
Consensus pattern (29 bp):
AAATAATACAAAAAAAGAATTATAACCAA
Found at i:33391878 original size:30 final size:27
Alignment explanation
Indices: 33391783--33391879 Score: 77
Period size: 28 Copynumber: 3.3 Consensus size: 27
33391773 GTTTTTGTCC
** * *
33391783 TAAATAATACAAAAAAAGGTTTTTAACC
1 TAAATAATACAAAAAAA-AATTATAACA
33391811 TAAATAATACAAAAAAAAATTATACACCA
1 TAAATAATACAAAAAAAAATTATA-A-CA
* *
33391840 AAATATAATACAAAAAATAAAATTAATAACT
1 TAA-ATAATAC-AAAAA-AAAATT-ATAACA
33391871 TAAATAATA
1 TAAATAATA
33391880 TAAATATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
27 4 0.07
28 18 0.32
29 3 0.05
30 13 0.23
31 8 0.14
32 7 0.12
33 3 0.05
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (27 bp):
TAAATAATACAAAAAAAAATTATAACA
Found at i:33392209 original size:27 final size:27
Alignment explanation
Indices: 33392163--33392229 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
33392153 TTAAAATTTG
*
33392163 ACAAATGGTGCCTTTAGGGTAGGA-GGC
1 ACAAATGGTGCCTCTAGGGTA-GACGGC
33392190 ACAAATGGTGCCTACT-GGGTAGACGGC
1 ACAAATGGTGCCT-CTAGGGTAGACGGC
* *
33392217 ACTAGTGGTGCCT
1 ACAAATGGTGCCT
33392230 TTGTCAAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 2 0.06
27 32 0.91
28 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (27 bp):
ACAAATGGTGCCTCTAGGGTAGACGGC
Found at i:33395210 original size:26 final size:26
Alignment explanation
Indices: 33395161--33395210 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
33395151 TCTGTTTAAA
**
33395161 TTTGAAATTATTTAATAATTTTTATG
1 TTTGAAATTATTTAATAAGGTTTATG
* *
33395187 TTTGAATTTATTTAATGAGGTTTA
1 TTTGAAATTATTTAATAAGGTTTA
33395211 GCATATGACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (26 bp):
TTTGAAATTATTTAATAAGGTTTATG
Found at i:33398094 original size:17 final size:17
Alignment explanation
Indices: 33398072--33398105 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
33398062 CTTACAATAA
*
33398072 TTAAATAATATTTAAAT
1 TTAAATAACATTTAAAT
33398089 TTAAATAACATTTAAAT
1 TTAAATAACATTTAAAT
33398106 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATAACATTTAAAT
Found at i:33401766 original size:41 final size:40
Alignment explanation
Indices: 33401716--33401924 Score: 247
Period size: 41 Copynumber: 5.1 Consensus size: 40
33401706 TAGAGCGTCA
* *
33401716 CTAAAGGTCAGAGCAATAGCGGCGCTTATGGTCAAGCGTCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTATGG-CAAGCGCCG
* *
33401757 CTAAAGGTCAGAGCAATAGCGACGCTTATGAGAAATCGCCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTATG-GCAAGCGCCG
*
33401798 CTAAAGGTCAGAGCAATAGCGACTCTTATGGGCAAGCGCCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTAT-GGCAAGCGCCG
* * * *
33401839 CTAAATGTCAGAGCAATAGTGACGCTTGTGAGCAACCGCCG
1 CTAAAGGTCAGAGCAATAGCGACGCTTATG-GCAAGCGCCG
* * ** *
33401880 CTAAAAGTCAGAGCAATAACGGGGCTTATGGGCAAGCGCCA
1 CTAAAGGTCAGAGCAATAGCGACGCTTAT-GGCAAGCGCCG
33401921 CTAA
1 CTAA
33401925 TTTATTTAAA
Statistics
Matches: 144, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
40 1 0.01
41 140 0.97
42 3 0.02
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (40 bp):
CTAAAGGTCAGAGCAATAGCGACGCTTATGGCAAGCGCCG
Found at i:33401782 original size:24 final size:24
Alignment explanation
Indices: 33401750--33401820 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
33401740 CTTATGGTCA
*
33401750 AGCGTCGCTAAAGGTCAGAGCAAT
1 AGCGACGCTAAAGGTCAGAGCAAT
*
33401774 AGCGACGCT-TA--T--GAG-AA-
1 AGCGACGCTAAAGGTCAGAGCAAT
* *
33401791 ATCGCCGCTAAAGGTCAGAGCAAT
1 AGCGACGCTAAAGGTCAGAGCAAT
33401815 AGCGAC
1 AGCGAC
33401821 TCTTATGGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 14
0.61 0.13 0.26
Matches are distributed among these distances:
17 7 0.21
18 3 0.09
19 3 0.09
20 1 0.03
21 1 0.03
22 3 0.09
23 3 0.09
24 12 0.36
ACGTcount: A:0.34, C:0.23, G:0.28, T:0.15
Consensus pattern (24 bp):
AGCGACGCTAAAGGTCAGAGCAAT
Found at i:33401801 original size:108 final size:105
Alignment explanation
Indices: 33401604--33401816 Score: 279
Period size: 108 Copynumber: 2.0 Consensus size: 105
33401594 CTTATGAGAA
* * *
33401604 AGCGTCGCTAAAGGTCATAGCAATAGCAGTGCTTATGGGTGCCGCTAAAAGGTCAAAGCAATAGC
1 AGCGTCACTAAAGGTCAGAGCAATAGCAGCGCTTATGGGTGCCGCTAAAAGGTCAAAGCAATAGC
* *
33401669 GACGCTTTCTCATAAACGCCGCTAAAGGTCAGAGCAATAG
66 GACGCTTTATCAGAAACGCCGCTAAAGGTCAGAGCAATAG
* *
33401709 AGCGTCACTAAAGGTCAGAGCAATAGCGGCGCTTAT-GGTCAAGCGTCGCT-AAAGGTCAGAGCA
1 AGCGTCACTAAAGGTCAGAGCAATAGCAGCGCTTATGGGT---GC--CGCTAAAAGGTCAAAGCA
*
33401772 ATAGCGACGC-TTATGAGAAATCGCCGCTAAAGGTCAGAGCAATAG
61 ATAGCGACGCTTTATCAGAAA-CGCCGCTAAAGGTCAGAGCAATAG
33401817 CGACTCTTAT
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
104 3 0.03
105 32 0.34
107 9 0.10
108 46 0.49
109 4 0.04
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (105 bp):
AGCGTCACTAAAGGTCAGAGCAATAGCAGCGCTTATGGGTGCCGCTAAAAGGTCAAAGCAATAGC
GACGCTTTATCAGAAACGCCGCTAAAGGTCAGAGCAATAG
Found at i:33401853 original size:82 final size:82
Alignment explanation
Indices: 33401716--33401924 Score: 301
Period size: 82 Copynumber: 2.5 Consensus size: 82
33401706 TAGAGCGTCA
* *
33401716 CTAAAGGTCAGAGCAATAGCGGCGCTTATGGTCAAGCGTCGCTAAAGGTCAGAGCAATAGCGACG
1 CTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACG
*
33401781 CTTATGAGAAATCGCCG
66 CTTATGAGAAACCGCCG
* * * *
33401798 CTAAAGGTCAGAGCAATAGCGACTCTTATGGGCAAGCGCCGCTAAATGTCAGAGCAATAGTGACG
1 CTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACG
* *
33401863 CTTGTGAGCAACCGCCG
66 CTTATGAGAAACCGCCG
* * * *
33401880 CTAAAAGTCAGAGCAATAACGGGGCTTATGGGCAAGCGCCACTAA
1 CTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAA
33401925 TTTATTTAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 112 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (82 bp):
CTAAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTCAGAGCAATAGCGACG
CTTATGAGAAACCGCCG
Found at i:33406978 original size:43 final size:43
Alignment explanation
Indices: 33406923--33407142 Score: 251
Period size: 43 Copynumber: 5.1 Consensus size: 43
33406913 ATATTAGTGA
* * * *
33406923 CGTTTGTGGGAAAAATGCCACTAAAGATCATGTTCTTTAGCGA
1 CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
* * * * *
33406966 TGTTTGCTGGAAAAGTGCCGTTAAAGATCATGGTCTTTAGTGG
1 CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
* * * *
33407009 CGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAACGG
1 CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
* * * *
33407052 CGTTTGTTCGAAAAGTTCTGCTAAAGATCATGTTCTTTAACGG
1 CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
* * * *
33407095 CGTTTGTTCGAAAAGCGTCGCTAAAGATCATGTTCTATAGCGG
1 CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
33407138 CGTTT
1 CGTTT
33407143 TTTCATAAGC
Statistics
Matches: 147, Mismatches: 30, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
CGTTTGTTGGAAAAGTGCCGCTAAAGATCATGTTCTTTAGCGG
Found at i:33407065 original size:86 final size:86
Alignment explanation
Indices: 33406916--33407142 Score: 283
Period size: 86 Copynumber: 2.6 Consensus size: 86
33406906 TTTGTTAATA
* ** * * ** *
33406916 TTAGTGACGTTTGTGGGAAAAATGCCACTAAAGATCATGTTCTTTAGCGATGTTTGCTGGAAAAG
1 TTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCGTTTGCTCGAAAAG
*
33406981 TGCCGTTAAAGATCATGGTCT
66 TGCCGCTAAAGATCATGGTCT
* *
33407002 TTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAACGGCGTTTGTTCGAAAAG
1 TTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCGTTTGCTCGAAAAG
* * *
33407067 TTCTGCTAAAGATCATGTTCT
66 TGCCGCTAAAGATCATGGTCT
** ** *
33407088 TTAACGGCGTTTGTTCGAAAAGCGTCGCTAAAGATCATGTTCTATAGCGGCGTTT
1 TTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCGTTT
33407143 TTTCATAAGC
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 121 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (86 bp):
TTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGATCATGTTCTTTAGCGGCGTTTGCTCGAAAAG
TGCCGCTAAAGATCATGGTCT
Found at i:33407448 original size:21 final size:20
Alignment explanation
Indices: 33407410--33407448 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33407400 TTCAATTGGA
*
33407410 TTTTTATTAATTGTTGCAAT
1 TTTTTATTAATTCTTGCAAT
*
33407430 TTTTTTTTAATTCTATGCA
1 TTTTTATTAATTCT-TGCA
33407449 TATATATTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTATTAATTCTTGCAAT
Found at i:33408838 original size:2 final size:2
Alignment explanation
Indices: 33408831--33408868 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
33408821 AACATCAGTA
33408831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33408869 GCTACTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33418551 original size:26 final size:26
Alignment explanation
Indices: 33418499--33418562 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
33418489 AAGGGAAGGT
* ** * *
33418499 AAAAAAGGGAAAATCGAAATATGGTG
1 AAAAAAGGAAAAATAAAAAAATAGTG
33418525 AAAAAAGGAAAAATAAAAAAATAGTG
1 AAAAAAGGAAAAATAAAAAAATAGTG
33418551 AAAAGAA-GAAAA
1 AAAA-AAGGAAAA
33418563 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 30 0.94
27 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (26 bp):
AAAAAAGGAAAAATAAAAAAATAGTG
Found at i:33422356 original size:39 final size:39
Alignment explanation
Indices: 33422302--33422381 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
33422292 GACCATATAA
33422302 TATCATGATTTATAATATATAAATCACCTTAAAATGTCT
1 TATCATGATTTATAATATATAAATCACCTTAAAATGTCT
33422341 TATCATGATTTATAATATATAAATCACCTTAAAATGTCT
1 TATCATGATTTATAATATATAAATCACCTTAAAATGTCT
33422380 TA
1 TA
33422382 CTTTCAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.41
Consensus pattern (39 bp):
TATCATGATTTATAATATATAAATCACCTTAAAATGTCT
Found at i:33427607 original size:17 final size:17
Alignment explanation
Indices: 33427569--33427608 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
33427559 AATTATTTTG
*
33427569 AATTATTAATTATTCATC
1 AATT-TTAATTATTAATC
*
33427587 AATTTTAATTATTAATT
1 AATTTTAATTATTAATC
33427604 AATTT
1 AATTT
33427609 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTTTAATTATTAATC
Found at i:33429474 original size:18 final size:19
Alignment explanation
Indices: 33429423--33429465 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
33429413 ATTTCAGTTG
*
33429423 GAATCGAATTAA-TCGATT
1 GAATTGAATTAATTCGATT
33429441 GAATTGAATTAATTCGATT
1 GAATTGAATTAATTCGATT
33429460 -AATTGA
1 GAATTGA
33429466 TCTAGTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (19 bp):
GAATTGAATTAATTCGATT
Found at i:33437277 original size:19 final size:17
Alignment explanation
Indices: 33437258--33437289 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33437248 TTTAAAATAA
33437258 AAAATTTAAAATAAAGT
1 AAAATTTAAAATAAAGT
33437275 AAAATTTAAAA-AAAG
1 AAAATTTAAAATAAAG
33437290 AGAGAGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAATTTAAAATAAAGT
Found at i:33438216 original size:35 final size:34
Alignment explanation
Indices: 33438157--33438223 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 34
33438147 TGTAGTAGTA
33438157 GTAATTATTTAGTTTTTAATTTTA-TTGTTTAAT
1 GTAATTATTTAGTTTTTAATTTTATTTGTTTAAT
33438190 GTAATTGATTTA-TTATTATAATTTTATTTGTTTA
1 GTAATT-ATTTAGTT-TT-TAATTTTATTTGTTTA
33438224 GTAAGTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 8 0.27
34 7 0.23
35 8 0.27
36 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (34 bp):
GTAATTATTTAGTTTTTAATTTTATTTGTTTAAT
Found at i:33438354 original size:25 final size:24
Alignment explanation
Indices: 33438323--33438377 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
33438313 TTATTTTAAG
*
33438323 TTATTTGTTTTGTTTGATTTAA-TTT
1 TTATTTGATTTG-TT-ATTTAATTTT
33438348 TTATTTGATTTGTTATTTAATTTT
1 TTATTTGATTTGTTATTTAATTTT
33438372 TTATTT
1 TTATTT
33438378 AGTTGAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 6 0.21
24 11 0.39
25 11 0.39
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.73
Consensus pattern (24 bp):
TTATTTGATTTGTTATTTAATTTT
Found at i:33438365 original size:12 final size:12
Alignment explanation
Indices: 33438339--33438378 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
33438329 GTTTTGTTTG
33438339 ATTTAATTT-TT
1 ATTTAATTTGTT
*
33438350 ATTTGATTTGTT
1 ATTTAATTTGTT
*
33438362 ATTTAATTTTTT
1 ATTTAATTTGTT
33438374 ATTTA
1 ATTTA
33438379 GTTGAGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (12 bp):
ATTTAATTTGTT
Found at i:33438438 original size:5 final size:5
Alignment explanation
Indices: 33438423--33438452 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
33438413 GTTTGGTTAT
33438423 TTTTAA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
33438453 GTCAGTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:33438857 original size:3 final size:3
Alignment explanation
Indices: 33438849--33438887 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
33438839 TTTTAATTAA
33438849 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33438888 CAAAGATCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.