Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 85 of 187
Found at i:25189884 original size:41 final size:41
Alignment explanation
Indices: 25189839--25189938 Score: 182
Period size: 41 Copynumber: 2.4 Consensus size: 41
25189829 TAGAGTGTTA
* *
25189839 CATGATATGAATATTTACTTAAGCTTTGCCTTCAAGGCGAG
1 CATGATATGGATATTTACTTAAGCTTTACCTTCAAGGCGAG
25189880 CATGATATGGATATTTACTTAAGCTTTACCTTCAAGGCGAG
1 CATGATATGGATATTTACTTAAGCTTTACCTTCAAGGCGAG
25189921 CATGATATGGATATTTAC
1 CATGATATGGATATTTAC
25189939 ATAGATTTCA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (41 bp):
CATGATATGGATATTTACTTAAGCTTTACCTTCAAGGCGAG
Found at i:25190375 original size:21 final size:21
Alignment explanation
Indices: 25190327--25190376 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25190317 TCCAAAATCT
25190327 TATAAATATATATTCAAAAAA
1 TATAAATATATATTCAAAAAA
* *
25190348 TAAAAATATATATT-AAATATA
1 TATAAATATATATTCAAA-AAA
25190369 TATAAATA
1 TATAAATA
25190377 ATAAATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAAATATATATTCAAAAAA
Found at i:25191274 original size:73 final size:74
Alignment explanation
Indices: 25191187--25191332 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 74
25191177 TTTTCATTAA
* *
25191187 ATTTGGTACA-TTTTTAGTTTGATTTGATAAACTAATATAAATTAGTATCCAAATATTAATTTGG
1 ATTTGGTACATTTTTTAGTTTAATTTGATAAACTAATATAAAGTAGTATCCAAATATTAATTTGG
25191251 TAAAAAAAC
66 TAAAAAAAC
* * *
25191260 ATTTGGTA-ATTTTTTTAGTTTAATTTGGTAAACTAATATAAAGTAGTATCTATATATTAATTTG
1 ATTTGGTACA-TTTTTTAGTTTAATTTGATAAACTAATATAAAGTAGTATCCAAATATTAATTTG
*
25191324 GTAAGAAAA
65 GTAAAAAAA
25191333 TAATGTTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 1 0.02
73 8 0.12
74 56 0.86
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (74 bp):
ATTTGGTACATTTTTTAGTTTAATTTGATAAACTAATATAAAGTAGTATCCAAATATTAATTTGG
TAAAAAAAC
Found at i:25191320 original size:37 final size:37
Alignment explanation
Indices: 25191208--25191327 Score: 98
Period size: 37 Copynumber: 3.2 Consensus size: 37
25191198 TTTTAGTTTG
* * * *
25191208 ATTTGATAAACTAATATAAATTAGTATCCAAATATTA
1 ATTTGGTAAACTAATATAAAGTAGTATCTATATATTA
** * *** * * * *
25191245 ATTTGGTAAAAAAACATTTGGTAATTTTTTTAGT-TTA
1 ATTTGGTAAACTAATATAAAGTAGTATCTATA-TATTA
25191282 ATTTGGTAAACTAATATAAAGTAGTATCTATATATTA
1 ATTTGGTAAACTAATATAAAGTAGTATCTATATATTA
25191319 ATTTGGTAA
1 ATTTGGTAA
25191328 GAAAATAATG
Statistics
Matches: 57, Mismatches: 24, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
36 1 0.02
37 55 0.96
38 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (37 bp):
ATTTGGTAAACTAATATAAAGTAGTATCTATATATTA
Found at i:25191418 original size:62 final size:64
Alignment explanation
Indices: 25191294--25191419 Score: 159
Period size: 63 Copynumber: 2.0 Consensus size: 64
25191284 TTGGTAAACT
* * **
25191294 AATATAAAGTAGTATCTATATATTAATTTGGTAAGAAAATAATGTTAAATAATTGTCGTATCTA
1 AATATAAAGTAGTATCTAAATATTAATTTGATAAGAAAATAAACTTAAATAATTGTCGTATCTA
* * *
25191358 AATA-AAAGTAGTATTTAAATATTAATTTGATTA-AAGATAAACTTAAATAATTG-CGATATCTA
1 AATATAAAGTAGTATCTAAATATTAATTTGATAAGAAAATAAACTTAAATAATTGTCG-TATCTA
25191420 CTACAAATTG
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
61 2 0.04
62 23 0.43
63 25 0.46
64 4 0.07
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (64 bp):
AATATAAAGTAGTATCTAAATATTAATTTGATAAGAAAATAAACTTAAATAATTGTCGTATCTA
Found at i:25194943 original size:3 final size:3
Alignment explanation
Indices: 25194935--25194959 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
25194925 AAAGACATAA
25194935 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
25194960 TTAAGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:25198460 original size:12 final size:12
Alignment explanation
Indices: 25198420--25198462 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
25198410 CTAAGTCTAG
*
25198420 TTCTAAAACTAG
1 TTCTAAAACTAA
*
25198432 TTCTAGAGACTAA
1 TTCTA-AAACTAA
*
25198445 TTCTAAAACCAA
1 TTCTAAAACTAA
25198457 TTCTAA
1 TTCTAA
25198463 GCTTATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.33
Consensus pattern (12 bp):
TTCTAAAACTAA
Found at i:25199249 original size:200 final size:202
Alignment explanation
Indices: 25198899--25199314 Score: 741
Period size: 200 Copynumber: 2.1 Consensus size: 202
25198889 TAATTCGAAT
*
25198899 AAACCGAATACAAATTATAATATTTTACATTTTTACCCCAAACCCCCAAACCTTTTTACTTTTCT
1 AAACCGAATTCAAATTATAATATTTTACATTTTTACCCCAAACCCCCAAACCTTTTTACTTTTCT
*
25198964 CCCAAAACTTTTACTCCCCTTCGATCCCACCCCCGTCTACCCCAAACTCATTTTCCCGCCAATTT
66 CCCAAAACTTTTACTCCCCTCCGATCCCACCCCCGTCTACCCCAAACTCATTTTCCCGCCAATTT
25199029 TTTTGAATATTCCTCCCCCCCAAAAAAAA-TTAAGAAATTAAAAAATATACATCTTTAAGTAGGG
131 TTTTGAATATTCCTCCCCCCCAAAAAAAATTTAAGAAATTAAAAAATATACATCTTTAAGTAGGG
25199093 ATGAGCA
196 ATGAGCA
25199100 AAACCGAATTCAAATTATAATATTTTACATTTTTA-CCCAAACCCCCAAACCTTTTTACTTTTCT
1 AAACCGAATTCAAATTATAATATTTTACATTTTTACCCCAAACCCCCAAACCTTTTTACTTTTCT
*
25199164 CCCAAAACTTTTACTCCCCTCCGATCCCACCCCTGTCTACCCCAAACTCATTTTCCCGCCAATTT
66 CCCAAAACTTTTACTCCCCTCCGATCCCACCCCCGTCTACCCCAAACTCATTTTCCCGCCAA-TT
*
25199229 TTTTTGAATATTCC-CCCCCCCAAAAAAAATTTTAAGAAATTAAAAAATATATATCTTTAAGTAG
130 TTTTTGAATATTCCTCCCCCCCAAAAAAAA-TTTAAGAAATTAAAAAATATACATCTTTAAGTAG
25199293 GGATGAGCA
194 GGATGAGCA
25199302 AAACTCG-ATTCAA
1 AAAC-CGAATTCAA
25199315 CTCAAAAAAA
Statistics
Matches: 207, Mismatches: 4, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
200 104 0.50
201 50 0.24
202 51 0.25
203 2 0.01
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (202 bp):
AAACCGAATTCAAATTATAATATTTTACATTTTTACCCCAAACCCCCAAACCTTTTTACTTTTCT
CCCAAAACTTTTACTCCCCTCCGATCCCACCCCCGTCTACCCCAAACTCATTTTCCCGCCAATTT
TTTTGAATATTCCTCCCCCCCAAAAAAAATTTAAGAAATTAAAAAATATACATCTTTAAGTAGGG
ATGAGCA
Found at i:25202331 original size:63 final size:63
Alignment explanation
Indices: 25202210--25202333 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
25202200 ATGTGGCAAG
* * * * *
25202210 CCATGTAACTCACTGTTTTAGCATTAAAGGCCCACGGGCTAGAGACACGGGCAGGTGTCCAAA
1 CCATGTAACTCACTGTTTTAGAATTAAAGACACACGGGCCAGAGACACGAGCAGGTGTCCAAA
* * *
25202273 CCATGTAACTCACTGTTTTGGAATTAGAGACACACGGGCCAGAGACATGAGC-GTGTGTCCA
1 CCATGTAACTCACTGTTTTAGAATTAAAGACACACGGGCCAGAGACACGAGCAG-GTGTCCA
25202334 TGCCGTGTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
62 1 0.02
63 51 0.98
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (63 bp):
CCATGTAACTCACTGTTTTAGAATTAAAGACACACGGGCCAGAGACACGAGCAGGTGTCCAAA
Found at i:25203539 original size:18 final size:17
Alignment explanation
Indices: 25203516--25203551 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
25203506 GTTGTGTTAT
25203516 ATGATAAATTGATGATTG
1 ATGATAAATTGA-GATTG
25203534 ATGATAAATTGAGATTG
1 ATGATAAATTGAGATTG
25203551 A
1 A
25203552 AAGAATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (17 bp):
ATGATAAATTGAGATTG
Found at i:25204144 original size:20 final size:20
Alignment explanation
Indices: 25204121--25204161 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
25204111 TAGCTTGTTC
25204121 CATAAAGTGTTAGGTTAAGT
1 CATAAAGTGTTAGGTTAAGT
25204141 CATAAAGTGTTAGGTTAAGT
1 CATAAAGTGTTAGGTTAAGT
25204161 C
1 C
25204162 CTCCAATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (20 bp):
CATAAAGTGTTAGGTTAAGT
Found at i:25213338 original size:23 final size:22
Alignment explanation
Indices: 25213310--25213361 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
25213300 ATTAATAACC
**
25213310 ATAAAATTTATAAAAATAATTT
1 ATAAAATCCATAAAAATAATTT
* *
25213332 ATTAAAAACCATAAAAATTATTT
1 A-TAAAATCCATAAAAATAATTT
25213355 ATAAAAT
1 ATAAAAT
25213362 AATAATTAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAATCCATAAAAATAATTT
Found at i:25213473 original size:60 final size:61
Alignment explanation
Indices: 25213393--25213545 Score: 190
Period size: 61 Copynumber: 2.6 Consensus size: 61
25213383 TAGTAGTCAC
* * *
25213393 CTATGTTT-TTTTTTCTTTTTTGGTCACCCAATTATGAAAAGTTACAAA-ATGCTCACCCAA
1 CTATGTTTAATTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTA-AAATATGCTCAACCAA
* * *
25213453 CTATGTTTACTTTTTCTTTTTTGGTCACTCAACTATGAAAAGTTAAAATATGGTCAACCAA
1 CTATGTTTAATTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAATATGCTCAACCAA
*
25213514 CTA--TTTAATTTTGTCTTTCTTGGTCA-CCAACT
1 CTATGTTTAATTTT-TCTTTTTTGGTCACCCAACT
25213546 GACTAACGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
59 13 0.16
60 23 0.28
61 46 0.56
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.43
Consensus pattern (61 bp):
CTATGTTTAATTTTTCTTTTTTGGTCACCCAACTATGAAAAGTTAAAATATGCTCAACCAA
Found at i:25223384 original size:6 final size:6
Alignment explanation
Indices: 25223373--25223401 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
25223363 GCAAATAGAT
25223373 CATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTT
25223402 TTCAAAGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
CATTTC
Found at i:25223741 original size:28 final size:28
Alignment explanation
Indices: 25223701--25223758 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
25223691 ATGCCATTAC
* *
25223701 GAAAGCAACTACTCAGTGCTCGTCCAAT
1 GAAAGCAACTACTCAGTGATCATCCAAT
25223729 GAAAGCAACTACTCAGTGATCATCCAAT
1 GAAAGCAACTACTCAGTGATCATCCAAT
25223757 GA
1 GA
25223759 TATTGTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (28 bp):
GAAAGCAACTACTCAGTGATCATCCAAT
Found at i:25224910 original size:17 final size:18
Alignment explanation
Indices: 25224888--25224927 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
25224878 AAAGCCAATC
25224888 TGGGCGTGTGGG-CCACA
1 TGGGCGTGTGGGTCCACA
25224905 TGGGCGTGTGGGTCCACA
1 TGGGCGTGTGGGTCCACA
*
25224923 AGGGC
1 TGGGC
25224928 AAGCCATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.17
Consensus pattern (18 bp):
TGGGCGTGTGGGTCCACA
Found at i:25234869 original size:19 final size:19
Alignment explanation
Indices: 25234842--25234898 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
25234832 TCCTTACAAG
*
25234842 ATTACTGAATCTCTTAAAA
1 ATTATTGAATCTCTTAAAA
* * *
25234861 ATTATTGAATTTCTTAGAC
1 ATTATTGAATCTCTTAAAA
* *
25234880 TTTATCGAATCTCTTAAAA
1 ATTATTGAATCTCTTAAAA
25234899 CATCATAGAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTATTGAATCTCTTAAAA
Found at i:25236555 original size:20 final size:20
Alignment explanation
Indices: 25236527--25236666 Score: 69
Period size: 20 Copynumber: 7.0 Consensus size: 20
25236517 CTCTTATAAA
25236527 TTCTAAATTTCTTACAAAAG
1 TTCTAAATTTCTTACAAAAG
* **
25236547 TTCTTAATTTCTTACAAACC
1 TTCTAAATTTCTTACAAAAG
* * * *
25236567 TACTAAATCTCTTAGACAA-
1 TTCTAAATTTCTTACAAAAG
* *
25236586 TTAC-ACAATCTCTTA-AACA-
1 TT-CTA-AATTTCTTACAAAAG
25236605 TTACGT-AATTTCTTACAAAAG
1 TT-C-TAAATTTCTTACAAAAG
* *
25236626 TACTAAATTTCTTA-AACTA-
1 TTCTAAATTTCTTACAA-AAG
*
25236645 TTATCAAATTTCTTACAAAAG
1 TTCT-AAATTTCTTACAAAAG
25236666 T
1 T
25236667 ACTTAAAATA
Statistics
Matches: 90, Mismatches: 19, Indels: 21
0.69 0.15 0.16
Matches are distributed among these distances:
19 21 0.23
20 65 0.72
21 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (20 bp):
TTCTAAATTTCTTACAAAAG
Found at i:25236586 original size:78 final size:79
Alignment explanation
Indices: 25236492--25236639 Score: 194
Period size: 78 Copynumber: 1.9 Consensus size: 79
25236482 ATTATTGAAT
* *** * *
25236492 TAAATCTTTTACACAATTATTGAATCTCTTATAA-ATT-C-TAAATTTCTTACAAAAGTTCTTAA
1 TAAATCTCTTACACAATTACACAATCTCTTA-AACATTACGT-AATTTCTTACAAAAGTACTAAA
25236554 TTTCTTACAAACCTAC
64 TTTCTTACAAACCTAC
*
25236570 TAAATCTCTTAGACAATTACACAATCTCTTAAACATTACGTAATTTCTTACAAAAGTACTAAATT
1 TAAATCTCTTACACAATTACACAATCTCTTAAACATTACGTAATTTCTTACAAAAGTACTAAATT
25236635 TCTTA
66 TCTTA
25236640 AACTATTATC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
77 2 0.03
78 29 0.48
79 28 0.47
80 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.03, T:0.40
Consensus pattern (79 bp):
TAAATCTCTTACACAATTACACAATCTCTTAAACATTACGTAATTTCTTACAAAAGTACTAAATT
TCTTACAAACCTAC
Found at i:25236836 original size:35 final size:37
Alignment explanation
Indices: 25236797--25236886 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 37
25236787 TTACTAAATA
*
25236797 TCTTACAAGATTATTAAATTTAAG-A-TTATTGAATC
1 TCTTACAAGATTACTAAATTTAAGAATTTATTGAATC
** * *
25236832 TCTTACAA-ATTACTATTTTTTAGAATTTTTTGAATC
1 TCTTACAAGATTACTAAATTTAAGAATTTATTGAATC
* *
25236868 TCTTAAAAGATTACCAAAT
1 TCTTACAAGATTACTAAAT
25236887 ATCTCTTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
34 11 0.26
35 9 0.21
36 16 0.37
37 7 0.16
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (37 bp):
TCTTACAAGATTACTAAATTTAAGAATTTATTGAATC
Found at i:25250189 original size:25 final size:25
Alignment explanation
Indices: 25250161--25250209 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
25250151 GCTTTAAAAC
*
25250161 ATACAAATTTTTCATCTTTTCGGAT
1 ATACAAATTTCTCATCTTTTCGGAT
25250186 ATACAAATTTCTCATCTTTTCGGA
1 ATACAAATTTCTCATCTTTTCGGA
25250210 GAAGTAGAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (25 bp):
ATACAAATTTCTCATCTTTTCGGAT
Found at i:25252992 original size:37 final size:37
Alignment explanation
Indices: 25252946--25253314 Score: 128
Period size: 37 Copynumber: 10.0 Consensus size: 37
25252936 ATTATGCAAT
* * *
25252946 TTATGATAGTCTGCTAGACTTGTCGTTATGTTTCAAG
1 TTATAATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
* * *
25252983 TTATAATAGTTTGCTGGACTTTTCCTCATGTTTCAAG
1 TTATAATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
* * * * *
25253020 TTATGACAGCCCGCT-GAACTTGTCCT-ATCGTATCAAG
1 TTATAATAGTCTGCTAG-ACTTGTCCTCAT-GTTTCAAG
* * * * * *
25253057 TTATGACATTCCGCT-GAACTTTTCCTCACGTTTCAAG
1 TTATAATAGTCTGCTAG-ACTTGTCCTCATGTTTCAAG
* * * *
25253094 TTATGACAT-TTC-GTTGGACTTGTCCTCACGTTTCAAG
1 TTAT-A-ATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
** * * * * *
25253131 TTATGGCT-GTCCGCTGGACTTATCGTCATGCTTCAAG
1 TTAT-AATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
* * * * * *
25253168 TTATGACAATCCGCTAGACTTTTCCTCACGTTTCAAG
1 TTATAATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
* * * * * *
25253205 TTATGACAT-TTC-GTTGGACTTATTCTCACGTTTCAAG
1 TTAT-A-ATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
*** * * * * *
25253242 TTATGGCAGTCCGCTGGACTTATCGTCATGCTTCAAG
1 TTATAATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
* *
25253279 TTATGACA-ATTC-GCTGGACTTGTCCTCATGTTTCAA
1 TTAT-A-ATAGTCTGCTAGACTTGTCCTCATGTTTCAA
25253315 TATATGATAG
Statistics
Matches: 258, Mismatches: 60, Indels: 28
0.75 0.17 0.08
Matches are distributed among these distances:
36 9 0.03
37 237 0.92
38 10 0.04
39 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (37 bp):
TTATAATAGTCTGCTAGACTTGTCCTCATGTTTCAAG
Found at i:25253145 original size:111 final size:111
Alignment explanation
Indices: 25252975--25253314 Score: 447
Period size: 111 Copynumber: 3.1 Consensus size: 111
25252965 TTGTCGTTAT
* * * * * * * *
25252975 GTTTCAAGTTATAATAGTTT-GCTGGACTTTTCCTCATGTTTCAAGTTATGACAGCCCGCTGAAC
1 GTTTCAAGTTATGACA-TTTCGTTGGACTTATCCTCACGTTTCAAGTTATGGCAGTCCGCTGGAC
* *
25253039 TTGTCCT-AT-CGTATCAAGTTATGACATTCCGCTGAACTTTTCCTCAC
65 TTATCGTCATGC-T-TCAAGTTATGACATTCCGCTGAACTTTTCCTCAC
* *
25253086 GTTTCAAGTTATGACATTTCGTTGGACTTGTCCTCACGTTTCAAGTTATGGCTGTCCGCTGGACT
1 GTTTCAAGTTATGACATTTCGTTGGACTTATCCTCACGTTTCAAGTTATGGCAGTCCGCTGGACT
*
25253151 TATCGTCATGCTTCAAGTTATGACAATCCGCT-AGACTTTTCCTCAC
66 TATCGTCATGCTTCAAGTTATGACATTCCGCTGA-ACTTTTCCTCAC
*
25253197 GTTTCAAGTTATGACATTTCGTTGGACTTATTCTCACGTTTCAAGTTATGGCAGTCCGCTGGACT
1 GTTTCAAGTTATGACATTTCGTTGGACTTATCCTCACGTTTCAAGTTATGGCAGTCCGCTGGACT
* * *
25253262 TATCGTCATGCTTCAAGTTATGACAATT-CGCTGGACTTGTCCTCAT
66 TATCGTCATGCTTCAAGTTATGAC-ATTCCGCTGAACTTTTCCTCAC
25253308 GTTTCAA
1 GTTTCAA
25253315 TATATGATAG
Statistics
Matches: 204, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
110 4 0.02
111 194 0.95
112 5 0.02
113 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (111 bp):
GTTTCAAGTTATGACATTTCGTTGGACTTATCCTCACGTTTCAAGTTATGGCAGTCCGCTGGACT
TATCGTCATGCTTCAAGTTATGACATTCCGCTGAACTTTTCCTCAC
Found at i:25253321 original size:37 final size:37
Alignment explanation
Indices: 25252995--25253314 Score: 318
Period size: 37 Copynumber: 8.6 Consensus size: 37
25252985 ATAATAGTTT
* **
25252995 GCTGGACTTTTCCTCATGTTTCAAGTTATGACAGCCC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* * * *
25253032 GCTGAACTTGTCCT-ATCGTATCAAGTTATGACATTCC
1 GCTGGACTTATCCTCAT-GTTTCAAGTTATGACAATCC
* * * * *
25253069 GCTGAACTTTTCCTCACGTTTCAAGTTATGACATTTC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* * * * **
25253106 GTTGGACTTGTCCTCACGTTTCAAGTTATGGCTGTCC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* *
25253143 GCTGGACTTATCGTCATGCTTCAAGTTATGACAATCC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* * * * *
25253180 GCTAGACTTTTCCTCACGTTTCAAGTTATGACATTTC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* * * * *
25253217 GTTGGACTTATTCTCACGTTTCAAGTTATGGCAGTCC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
* * *
25253254 GCTGGACTTATCGTCATGCTTCAAGTTATGACAATTC
1 GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
*
25253291 GCTGGACTTGTCCTCATGTTTCAA
1 GCTGGACTTATCCTCATGTTTCAA
25253315 TATATGATAG
Statistics
Matches: 232, Mismatches: 49, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
36 2 0.01
37 229 0.99
38 1 0.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (37 bp):
GCTGGACTTATCCTCATGTTTCAAGTTATGACAATCC
Found at i:25253540 original size:21 final size:22
Alignment explanation
Indices: 25253495--25253555 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
25253485 GGAAATTTTG
* *
25253495 AAATTTTAGTGTGGAAAGTTAA
1 AAATTTAAGTGTTGAAAGTTAA
25253517 AAATTTAAGTGTTGAAAGTT-A
1 AAATTTAAGTGTTGAAAGTTAA
25253538 AAATTGTAAGTGTTGAAA
1 AAATT-TAAGTGTTGAAA
25253556 TGCAGAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (22 bp):
AAATTTAAGTGTTGAAAGTTAA
Found at i:25262317 original size:49 final size:49
Alignment explanation
Indices: 25262240--25262359 Score: 186
Period size: 49 Copynumber: 2.4 Consensus size: 49
25262230 CTCAGCCAAA
* * *
25262240 GTAGAATATGAAAATAGTAAAAAACATCATTGTCGGGCCACCTGGGATG
1 GTAGAATATGAAAATAGTGAAAAACATCATTGTCGAGCCACCTGAGATG
* *
25262289 GTAGAATATGCAAATAGTGAAAACCATCATTGTCGAGCCACCTGAGATG
1 GTAGAATATGAAAATAGTGAAAAACATCATTGTCGAGCCACCTGAGATG
*
25262338 GTAGAATATGTAAATAGTGAAA
1 GTAGAATATGAAAATAGTGAAA
25262360 GTCATCGTTA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (49 bp):
GTAGAATATGAAAATAGTGAAAAACATCATTGTCGAGCCACCTGAGATG
Found at i:25262385 original size:49 final size:49
Alignment explanation
Indices: 25262240--25262395 Score: 152
Period size: 49 Copynumber: 3.2 Consensus size: 49
25262230 CTCAGCCAAA
* * * ** * *
25262240 GTAGAATATGAAAATAGTAAAAAACATCATTGTCGGGCCACCTGGGATG
1 GTAGAATATGCAAATAGTGAAAACCATCATTACCGAGCCACCTGAGATG
**
25262289 GTAGAATATGCAAATAGTGAAAACCATCATTGTCGAGCCACCTGAGATG
1 GTAGAATATGCAAATAGTGAAAACCATCATTACCGAGCCACCTGAGATG
* ** * * *
25262338 GTAGAATATGTAAATAGTGAAAGTCATCGTTACCGGGTCA-CTCGAGATG
1 GTAGAATATGCAAATAGTGAAAACCATCATTACCGAGCCACCT-GAGATG
*
25262387 GTGGAATAT
1 GTAGAATAT
25262396 TCATATTATA
Statistics
Matches: 92, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 2 0.02
49 90 0.98
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (49 bp):
GTAGAATATGCAAATAGTGAAAACCATCATTACCGAGCCACCTGAGATG
Found at i:25264975 original size:17 final size:16
Alignment explanation
Indices: 25264951--25264982 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
25264941 ATATTATTTT
25264951 AATTAATTTAATATTA
1 AATTAATTTAATATTA
25264967 AATTAAATTTAATATT
1 AATT-AATTTAATATT
25264983 TATCTAGATA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTAATTTAATATTA
Found at i:25265151 original size:13 final size:14
Alignment explanation
Indices: 25265117--25265152 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
25265107 AAAATTTGTA
25265117 AAAAAAATTCTCTG
1 AAAAAAATTCTCTG
25265131 AAAAAAATTCTCT-
1 AAAAAAATTCTCTG
*
25265144 AAAGAAATT
1 AAAAAAATT
25265153 ATTTTAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (14 bp):
AAAAAAATTCTCTG
Found at i:25269953 original size:2 final size:2
Alignment explanation
Indices: 25269948--25269978 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25269938 TTGATAACTT
25269948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25269979 GAGAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25270986 original size:35 final size:35
Alignment explanation
Indices: 25270940--25271007 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
25270930 GGTACTTGGG
* *
25270940 TGTATGAGTACACTAATATGGGAACTCGTACATTT
1 TGTATGAGTACACTAACATGGGAACTCGAACATTT
* *
25270975 TGTATGAGTACACTAGCATGGGTACTCGAACAT
1 TGTATGAGTACACTAACATGGGAACTCGAACAT
25271008 ATGCCTCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (35 bp):
TGTATGAGTACACTAACATGGGAACTCGAACATTT
Found at i:25303256 original size:21 final size:21
Alignment explanation
Indices: 25303215--25303340 Score: 153
Period size: 21 Copynumber: 5.9 Consensus size: 21
25303205 AAAACAACCA
25303215 TTTCTCCCTTCGTTTTTGCTGG
1 TTTCTCCC-TCGTTTTTGCTGG
* *
25303237 TTTCTCCCTCATTCTTGCTGG
1 TTTCTCCCTCGTTTTTGCTGG
*
25303258 TTTCTCCGTCGTTTTTGCTGG
1 TTTCTCCCTCGTTTTTGCTGG
* *
25303279 TTTCTCCCTCGTTCTTGCTTG
1 TTTCTCCCTCGTTTTTGCTGG
* * *
25303300 TTTCTCCCTCATTTTTACTAG
1 TTTCTCCCTCGTTTTTGCTGG
*
25303321 TTTCTCCCCTCTTTTTTGCT
1 TTTCT-CCCTCGTTTTTGCT
25303341 TTGTTCTTGG
Statistics
Matches: 89, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
21 69 0.78
22 20 0.22
ACGTcount: A:0.03, C:0.30, G:0.13, T:0.53
Consensus pattern (21 bp):
TTTCTCCCTCGTTTTTGCTGG
Found at i:25303336 original size:63 final size:64
Alignment explanation
Indices: 25303215--25303340 Score: 173
Period size: 63 Copynumber: 2.0 Consensus size: 64
25303205 AAAACAACCA
* * * *
25303215 TTTCTCCCTTCGTTTTTGCTGGTTTCTCCCTCATTCTTGCTGGTTTCTCCGTCGTTTTTGCTGG
1 TTTCTCCCTTCGTTCTTGCTGGTTTCTCCCTCATTCTTACTAGTTTCTCCCTCGTTTTTGCTGG
* * *
25303279 TTTCTCCC-TCGTTCTTGCTTGTTTCTCCCTCATTTTTACTAGTTTCTCCCCTCTTTTTTGCT
1 TTTCTCCCTTCGTTCTTGCTGGTTTCTCCCTCATTCTTACTAGTTTCT-CCCTCGTTTTTGCT
25303341 TTGTTCTTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 34 0.63
64 20 0.37
ACGTcount: A:0.03, C:0.30, G:0.13, T:0.53
Consensus pattern (64 bp):
TTTCTCCCTTCGTTCTTGCTGGTTTCTCCCTCATTCTTACTAGTTTCTCCCTCGTTTTTGCTGG
Found at i:25308432 original size:21 final size:21
Alignment explanation
Indices: 25308385--25308435 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
25308375 ACCATTGTTT
* *
25308385 CTAATCTCACTGCTACAATAT
1 CTAATCTCACCGCTACAATAA
* *
25308406 CCAATCTCACCGCTACAGTAA
1 CTAATCTCACCGCTACAATAA
25308427 CTAATCTCA
1 CTAATCTCA
25308436 TCGCCACCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.33, G:0.06, T:0.27
Consensus pattern (21 bp):
CTAATCTCACCGCTACAATAA
Found at i:25312268 original size:2 final size:2
Alignment explanation
Indices: 25312261--25312297 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25312251 AGCTTATGCC
25312261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25312298 ATCTCAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25316426 original size:21 final size:22
Alignment explanation
Indices: 25316402--25316443 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
25316392 ATTGTTTTAT
*
25316402 TATTG-TTTGCTGCCATTTTGA
1 TATTGTTTTGCTACCATTTTGA
25316423 TATTGTTTTGCTACCATTTTG
1 TATTGTTTTGCTACCATTTTG
25316444 CAATTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.55
Consensus pattern (22 bp):
TATTGTTTTGCTACCATTTTGA
Found at i:25318811 original size:2 final size:2
Alignment explanation
Indices: 25318804--25318832 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25318794 CTCTAAATTA
25318804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25318833 ATCTTGAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25319418 original size:50 final size:50
Alignment explanation
Indices: 25319324--25319444 Score: 118
Period size: 50 Copynumber: 2.3 Consensus size: 50
25319314 ATTTTTGGGT
* * *
25319324 TGTTGGGACACTAATGGCTAGCACCCTTGTACTAGATTAAAAAAAATTGG
1 TGTTGGGACACTAATGGCTAGCACCCTTATACCAAATTAAAAAAAATTGG
* *
25319374 TGTTGGGACACTAATGG-TCGTTACCCTTATACCAAATTTTAAAAAAAAATTTGG
1 TGTTGGGACACTAATGGCTAG-CACCCTTATACCAAA--TT-AAAAAAAA-TTGG
* **
25319428 TGCTAAGACACTAATGG
1 TGTTGGGACACTAATGG
25319445 TTGACACCCT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 2 0.03
50 28 0.48
52 2 0.03
53 8 0.14
54 18 0.31
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (50 bp):
TGTTGGGACACTAATGGCTAGCACCCTTATACCAAATTAAAAAAAATTGG
Found at i:25321281 original size:54 final size:53
Alignment explanation
Indices: 25321223--25321355 Score: 180
Period size: 52 Copynumber: 2.5 Consensus size: 53
25321213 TTGGTACTGA
* *
25321223 GGTGCCAGCCATCAGTGTCCCAACACCCCAAATTTTTTTTAAGTCTGGTACAAG
1 GGTGCCAGCCATCAGTGTCCCAGCACCCCAAAATTTTTTTAA-TCTGGTACAAG
* * * *
25321277 GGTGCCAGCCATCAATGTCCCAGCA-CTCAAAATTTTTTTAATTTGGTACAAT
1 GGTGCCAGCCATCAGTGTCCCAGCACCCCAAAATTTTTTTAATCTGGTACAAG
25321329 GGTGCC-GACCATCAGTGTCCCAGCACC
1 GGTGCCAG-CCATCAGTGTCCCAGCACC
25321356 TAAATAACTA
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
51 1 0.01
52 31 0.44
53 15 0.21
54 23 0.33
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (53 bp):
GGTGCCAGCCATCAGTGTCCCAGCACCCCAAAATTTTTTTAATCTGGTACAAG
Found at i:25323916 original size:22 final size:22
Alignment explanation
Indices: 25323891--25323933 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
25323881 TTAAACTCTT
25323891 TAATTGTAGTGTTTGGTGAATC
1 TAATTGTAGTGTTTGGTGAATC
25323913 TAATTGTAGTGTTTGGTGAAT
1 TAATTGTAGTGTTTGGTGAAT
25323934 AGAGGTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (22 bp):
TAATTGTAGTGTTTGGTGAATC
Found at i:25327333 original size:16 final size:16
Alignment explanation
Indices: 25327312--25327376 Score: 87
Period size: 16 Copynumber: 4.1 Consensus size: 16
25327302 TTCGTTGTAT
*
25327312 TGGAATAGAGGCATAA
1 TGGAATAGAGGCGTAA
*
25327328 TGGAATAGA-GCTGTAT
1 TGGAATAGAGGC-GTAA
*
25327344 TGGAATAGAGACGTAA
1 TGGAATAGAGGCGTAA
25327360 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
25327376 T
1 T
25327377 AGCAAATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 2 0.05
16 39 0.93
17 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.23
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:25327348 original size:32 final size:32
Alignment explanation
Indices: 25327307--25327369 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
25327297 TTTGGTTCGT
*
25327307 TGTATTGGAATAGAGGCATAATGGAATAGAGC
1 TGTATTGGAATAGAGACATAATGGAATAGAGC
*
25327339 TGTATTGGAATAGAGACGTAATGGAATAGAG
1 TGTATTGGAATAGAGACATAATGGAATAGAG
25327370 GCGTAATAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.05, G:0.32, T:0.25
Consensus pattern (32 bp):
TGTATTGGAATAGAGACATAATGGAATAGAGC
Found at i:25327639 original size:14 final size:15
Alignment explanation
Indices: 25327584--25327641 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
25327574 AAATAATTTA
* *
25327584 ATTATATTTAAACAT
1 ATTATAATTAAATAT
*
25327599 AATTATTATTAAATAT
1 -ATTATAATTAAATAT
25327615 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
25327629 A-TATAATTTAATA
1 ATTATAATTAAATA
25327642 AAATACTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
15 11 0.31
16 12 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:25327738 original size:15 final size:16
Alignment explanation
Indices: 25327706--25327752 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
25327696 TACTATAAAA
*
25327706 TATAATTTAAC-ATAAT
1 TATAATTAAACTAT-AT
*
25327722 TATTATTAAA-TATAT
1 TATAATTAAACTATAT
25327737 TATAATTAAACTATAT
1 TATAATTAAACTATAT
25327753 AATTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAATTAAACTATAT
Found at i:25327873 original size:18 final size:17
Alignment explanation
Indices: 25327852--25327886 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25327842 TTATTATTAA
*
25327852 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
25327870 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
25327887 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:25328006 original size:59 final size:58
Alignment explanation
Indices: 25327687--25327996 Score: 206
Period size: 66 Copynumber: 5.2 Consensus size: 58
25327677 CTCAAACCAT
* *
25327687 AATATATGATACTATAAAATATAATTTAACATAATTATTATTAAATATATTATAATTAA
1 AATATATGATACTATAAAATATAATTTAA-ATAATTAATATTAAATATATTTTAATTAA
* * * * ** *
25327746 ACTATAT-A-A-TTTAAAA-AAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCA
1 AATATATGATACTATAAAATATAATT-TAAATAATTAATATT-AAATAT--ATTT--T--AATTA
*
25327807 T
58 A
* *
25327808 AATATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTTAA-ATAATTAATATTAAATATATTTTAATTAA
* * * * ** *
25327867 AATATAT-A-A-T-T-TAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCA
1 AATATATGATACTATAAAATATAATT-TAAATAATTAATATT-AAATAT--ATTT--T--AATTA
*
25327927 T
58 A
25327928 AATATATGATACTATAAAATATAATTTGAAATAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAATATAATTT-AAATAATTAATATTAAATATATTTTAATTAA
25327987 AATATATGAT
1 AATATATGAT
25327997 TTAATAAAAT
Statistics
Matches: 187, Mismatches: 37, Indels: 54
0.67 0.13 0.19
Matches are distributed among these distances:
54 17 0.09
55 23 0.12
56 13 0.07
57 6 0.03
58 5 0.03
59 32 0.17
60 1 0.01
61 13 0.07
62 11 0.06
63 10 0.05
64 2 0.01
65 18 0.10
66 36 0.19
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAATATAATTTAAATAATTAATATTAAATATATTTTAATTAA
Found at i:25328016 original size:120 final size:120
Alignment explanation
Indices: 25327589--25328007 Score: 705
Period size: 120 Copynumber: 3.5 Consensus size: 120
25327579 ATTTAATTAT
*
25327589 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATACTTAATA
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
25327654 ATCAATATTCTTATATGAATTTACTCAAACCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* *
25327710 ATTTAACATAATTATTATTAAATATATTATAATTAAACTATATAATTTAAAAAAAATTCTTAATA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTT-AATAAAATTCTTAATA
* *
25327775 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
*
25327831 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
25327896 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
* * *
25327951 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
25328008 TAAAATAATT
Statistics
Matches: 282, Mismatches: 14, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
120 163 0.58
121 119 0.42
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
Found at i:25328078 original size:26 final size:28
Alignment explanation
Indices: 25328048--25328392 Score: 97
Period size: 28 Copynumber: 11.6 Consensus size: 28
25328038 TATGAATTTG
*
25328048 TATAATTTAA-AATAAT-TATTATTTCA
1 TATAATTTAATAATAATATATAATTTCA
25328074 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTTCA
* * * *
25328102 TAAAATTCTTGATAATAA-AT-T-TTTTTA
1 TATAA-T-TTAATAATAATATATAATTTCA
*
25328129 TATGAATTTATATAATTTTAA-ATAATTAATATTAAA
1 TAT-AATTTA-ATAA---TAATAT-A-TAAT-TT-CA
*
25328165 TATAATTTAATAATGATATATAATTTCA
1 TATAATTTAATAATAATATATAATTTCA
* * *
25328193 TAAAATTCTTGATAATAAATTTTCTTATATGAA-TTTA
1 TATAA-T-TTAATAAT-AA------TATAT-AATTTCA
**
25328230 TATAATTTAA-AATAAT-TA-ATATTAAA
1 TATAATTTAATAATAATATATA-ATTTCA
*
25328256 TATAATTTAATAATGATATATAATTTCA
1 TATAATTTAATAATAATATATAATTTCA
* * *
25328284 TAAAATTCTTGATAATAAATTTTCTTATATGAA-TTTA
1 TATAA-T-TTAATAAT-AA------TATAT-AATTTCA
**
25328321 TATAATTTAA-AATAAT-TA-ATATTAAA
1 TATAATTTAATAATAATATATA-ATTTCA
*
25328347 TATAATTTAATAATGATATATAATTTCA
1 TATAATTTAATAATAATATATAATTTCA
*
25328375 TAAAATTCTTAATAATAA
1 TATAA-T-TTAATAATAA
25328393 AATGTTCTTA
Statistics
Matches: 236, Mismatches: 35, Indels: 92
0.65 0.10 0.25
Matches are distributed among these distances:
24 2 0.01
25 2 0.01
26 40 0.17
27 29 0.12
28 41 0.17
29 10 0.04
30 41 0.17
31 5 0.02
32 2 0.01
33 5 0.02
34 11 0.05
35 14 0.06
36 6 0.03
37 24 0.10
38 4 0.02
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTTCA
Found at i:25328096 original size:18 final size:18
Alignment explanation
Indices: 25328073--25328195 Score: 56
Period size: 18 Copynumber: 6.8 Consensus size: 18
25328063 TTATTATTTC
25328073 ATATAATTTAATAATAAT
1 ATATAATTTAATAATAAT
*
25328091 ATATAATTTCATAA-AATT
1 ATATAATTTAATAATAA-T
* * ** **
25328109 CTTGATAA-TAAATTTTTTT
1 -AT-ATAATTTAATAATAAT
**
25328128 ATATGAATTTATATAATTTT
1 ATAT-AATTTA-ATAATAAT
* *
25328148 AAATAA-TTAATATTAA-
1 ATATAATTTAATAATAAT
*
25328164 ATATAATTTAATAATGAT
1 ATATAATTTAATAATAAT
*
25328182 ATATAATTTCATAA
1 ATATAATTTAATAA
25328196 AATTCTTGAT
Statistics
Matches: 76, Mismatches: 20, Indels: 18
0.67 0.18 0.16
Matches are distributed among these distances:
16 5 0.07
17 16 0.21
18 33 0.43
19 9 0.12
20 13 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAATTTAATAATAAT
Found at i:25328118 original size:91 final size:91
Alignment explanation
Indices: 25328023--25328412 Score: 690
Period size: 91 Copynumber: 4.3 Consensus size: 91
25328013 TAATTATAAC
* * **
25328023 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTTCATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
25328088 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
* *
25328114 TAATAAATTTTTTTATATGAATTTATATAATTTTAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
25328179 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
25328205 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
25328270 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
25328296 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
25328361 GATATATAATTTCATAAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
*
25328387 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
25328413 CTAAACTCAT
Statistics
Matches: 287, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
91 267 0.93
92 20 0.07
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:25331573 original size:16 final size:16
Alignment explanation
Indices: 25331552--25331598 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
25331542 TACCAAATAC
25331552 TTGTTTTTTAATCAAG
1 TTGTTTTTTAATCAAG
25331568 TTGTTTTTTAATCAAG
1 TTGTTTTTTAATCAAG
25331584 TTGTTTTTTAATCAA
1 TTGTTTTTTAATCAA
25331599 TCATAATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (16 bp):
TTGTTTTTTAATCAAG
Found at i:25331723 original size:30 final size:30
Alignment explanation
Indices: 25331628--25331723 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
25331618 TTGTTTTTTA
25331628 ATCAAGTTGTTTACTTGATTATATCTAATG
1 ATCAAGTTGTTTACTTGATTATATCTAATG
* * * *
25331658 ATCCAA-TT-TTAATATATTGAATTTTTTTTAA--
1 AT-CAAGTTGTT--TA-CTTG-ATTATATCTAATG
25331689 ATCAAGTTGTTTACTTGATTATATCTAATG
1 ATCAAGTTGTTTACTTGATTATATCTAATG
25331719 ATCAA
1 ATCAA
25331724 ATTTTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 18
0.65 0.11 0.24
Matches are distributed among these distances:
28 8 0.16
29 5 0.10
30 14 0.29
31 9 0.18
32 5 0.10
33 8 0.16
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (30 bp):
ATCAAGTTGTTTACTTGATTATATCTAATG
Found at i:25331848 original size:24 final size:26
Alignment explanation
Indices: 25331796--25331845 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
25331786 TATATGTAAT
25331796 ATTATTAAAATAATATTTTTAATTTTA
1 ATTATTAAAATAATATTTTTAA-TTTA
*
25331823 ATTATTTAAA-AATATTTTTAATT
1 ATTATTAAAATAATATTTTTAATT
25331846 AATGCGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 11 0.50
27 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTATTAAAATAATATTTTTAATTTA
Found at i:25342271 original size:22 final size:23
Alignment explanation
Indices: 25342241--25342284 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
25342231 CAACCAATCC
*
25342241 ATTTCAACATATTTACAAGATAG
1 ATTTCAACATATTCACAAGATAG
*
25342264 ATTT-AACATATTCATAAGATA
1 ATTTCAACATATTCACAAGATA
25342285 ACCTCATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTTCAACATATTCACAAGATAG
Found at i:25349698 original size:29 final size:31
Alignment explanation
Indices: 25349631--25349700 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 31
25349621 TGTTAATGGT
25349631 TGACTGATTTGTCACTTTTCAATAACGTTAG
1 TGACTGATTTGTCACTTTTCAATAACGTTAG
* * *
25349662 TGATTGATTTGTTA-TTTTTAA-AA-GTTGAG
1 TGACTGATTTGTCACTTTTCAATAACGTT-AG
25349691 TGACTGATTT
1 TGACTGATTT
25349701 TAAAGTTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.09
29 13 0.38
30 6 0.18
31 12 0.35
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (31 bp):
TGACTGATTTGTCACTTTTCAATAACGTTAG
Found at i:25353051 original size:17 final size:18
Alignment explanation
Indices: 25353029--25353062 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
25353019 AAATATGTAA
*
25353029 CATATGTATATA-AGATG
1 CATATGCATATATAGATG
25353046 CATATGCATATATAGAT
1 CATATGCATATATAGAT
25353063 AAATATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (18 bp):
CATATGCATATATAGATG
Found at i:25354638 original size:23 final size:22
Alignment explanation
Indices: 25354608--25354652 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
25354598 TGAGTACAAT
25354608 AAAAATGATGAAATAAAATAATA
1 AAAAATGATGAAATAAAA-AATA
25354631 AAAAATGATGAAATAAAAAATA
1 AAAAATGATGAAATAAAAAATA
25354653 TTATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (22 bp):
AAAAATGATGAAATAAAAAATA
Found at i:25354894 original size:20 final size:22
Alignment explanation
Indices: 25354869--25354908 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
25354859 TACAGCAAGT
*
25354869 ACAT-GGACTTAATT-AAATGA
1 ACATGGGACTAAATTGAAATGA
25354889 ACATGGGACTAAATTGAAAT
1 ACATGGGACTAAATTGAAAT
25354909 TGTGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (22 bp):
ACATGGGACTAAATTGAAATGA
Found at i:25356726 original size:44 final size:44
Alignment explanation
Indices: 25356633--25356750 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 44
25356623 TTCAATCTAT
* * * * *
25356633 TCTACTGCAACTTCAGGGATATGAGATTTTTAGTTTCATTCGAA
1 TCTACTACAACTTCAGGGGTATAAGATTTGTAGCTTCATTCGAA
* * *
25356677 ACTACTACAACTTCAGGGGTATAAGATTTGTAGCTTCATCTTG-C
1 TCTACTACAACTTCAGGGGTATAAGATTTGTAGCTTCAT-TCGAA
*
25356721 TCTACTACAACTTCAAGGAG-ATAAGATTTG
1 TCTACTACAACTTC-AGGGGTATAAGATTTG
25356751 CTATGGTAGC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 56 0.90
45 6 0.10
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (44 bp):
TCTACTACAACTTCAGGGGTATAAGATTTGTAGCTTCATTCGAA
Found at i:25356821 original size:44 final size:44
Alignment explanation
Indices: 25356771--25356961 Score: 143
Period size: 44 Copynumber: 4.2 Consensus size: 44
25356761 TTCAATTCAA
25356771 TCCACTGCATCATCAGAGATATAGGATTTATAGCTTCATCTTGC
1 TCCACTGCATCATCAGAGATATAGGATTTATAGCTTCATCTTGC
* * * ** * * *
25356815 TTCACTGTATCTTCAAGGAGATCAGATTTGATATTATAACTTTGATC-TGA
1 TCCACTGCATCATC-A-GAGAT---ATAGGAT-TTATAGC-TTCATCTTGC
* * *
25356865 TCCACTGCAT-ATTTAGGGATGTAGGATTTATAGCTTCATCTTGC
1 TCCACTGCATCA-TCAGAGATATAGGATTTATAGCTTCATCTTGC
* * * * * *
25356909 TCTACTGCAACTTCAGAGATATAAGACTTGTAGCTTCATCTTGC
1 TCCACTGCATCATCAGAGATATAGGATTTATAGCTTCATCTTGC
25356953 TCCACTGCA
1 TCCACTGCA
25356962 GCCTCAGGGA
Statistics
Matches: 108, Mismatches: 29, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
43 5 0.05
44 61 0.56
45 5 0.05
46 5 0.05
48 4 0.04
49 6 0.06
50 17 0.16
51 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (44 bp):
TCCACTGCATCATCAGAGATATAGGATTTATAGCTTCATCTTGC
Found at i:25356901 original size:138 final size:138
Alignment explanation
Indices: 25356771--25357062 Score: 352
Period size: 138 Copynumber: 2.1 Consensus size: 138
25356761 TTCAATTCAA
* * * * * * *
25356771 TCCACTGCATCATCAGAGATATAGGATTTATAGCTTCATCTTGCTTCACTGTATCTTCAAGGAGA
1 TCCACTGCAACATCAGAGATATAAGACTTATAGCTTCATCTTGCTCCACTGCAGCCTCAAGGAGA
* * * * * * * *
25356836 TCAGATTTGA-TATTATAACTTTGATCTGATCCACTGCATATTTAGGGATGTAGGATTTATAGCT
66 TAAGA-TTCACCATTATAACTTTGATCTGATCCACTACATATTCAAGGATATAGAATTTATAGCT
*
25356900 TCATCTTGC
130 TCATATTGC
* * * *
25356909 TCTACTGCAACTTCAGAGATATAAGACTTGTAGCTTCATCTTGCTCCACTGCAGCCTCAGGGAGA
1 TCCACTGCAACATCAGAGATATAAGACTTATAGCTTCATCTTGCTCCACTGCAGCCTCAAGGAGA
*
25356974 TAAGATTCACCATTGTAACTTTGATCTGATCCACTACATATTCAAGGATATAGAATTTATAGCTT
66 TAAGATTCACCATTATAACTTTGATCTGATCCACTACATATTCAAGGATATAGAATTTATAGCTT
*
25357039 CATCTTGC
131 CATATTGC
* *
25357047 TCTACTGCAACTTCAG
1 TCCACTGCAACATCAG
25357063 GGGAGATAAG
Statistics
Matches: 133, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
137 3 0.02
138 130 0.98
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (138 bp):
TCCACTGCAACATCAGAGATATAAGACTTATAGCTTCATCTTGCTCCACTGCAGCCTCAAGGAGA
TAAGATTCACCATTATAACTTTGATCTGATCCACTACATATTCAAGGATATAGAATTTATAGCTT
CATATTGC
Found at i:25356923 original size:94 final size:94
Alignment explanation
Indices: 25356696--25356923 Score: 264
Period size: 94 Copynumber: 2.4 Consensus size: 94
25356686 ACTTCAGGGG
* * * * * *
25356696 TATAAGATTTGTAGCTTCATCTTGCTCTACTACAACTTCAAGGAGATAAGATTTGCTATGGTAGC
1 TATAGGATTTATAGCTTCATCTTGCTCTACTGCAACTTCAAGGAGATAAGATTTGATATGATAAC
25356761 TTCAATTCAATCCACTGCATCATCAGAGA
66 TTCAATTCAATCCACTGCATCATCAGAGA
* * * *
25356790 TATAGGATTTATAGCTTCATCTTGCT-TCACTGTATCTTCAAGGAGATCAGATTTGATATTATAA
1 TATAGGATTTATAGCTTCATCTTGCTCT-ACTGCAACTTCAAGGAGATAAGATTTGATATGATAA
** * * *
25356854 CTTTGA-TCTGATCCACTGCAT-ATTTAGGGA
65 CTTCAATTC-AATCCACTGCATCA-TCAGAGA
*
25356884 TGTAGGATTTATAGCTTCATCTTGCTCTACTGCAACTTCA
1 TATAGGATTTATAGCTTCATCTTGCTCTACTGCAACTTCA
25356924 GAGATATAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 4 0.04
94 107 0.96
95 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (94 bp):
TATAGGATTTATAGCTTCATCTTGCTCTACTGCAACTTCAAGGAGATAAGATTTGATATGATAAC
TTCAATTCAATCCACTGCATCATCAGAGA
Found at i:25356977 original size:44 final size:44
Alignment explanation
Indices: 25356895--25356978 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
25356885 GTAGGATTTA
* * *
25356895 TAGCTTCATCTTGCTCTACTGCAACTTCAGAGATATAAGACTTG
1 TAGCTTCATCTTGCTCCACTGCAACCTCAGAGAGATAAGACTTG
* *
25356939 TAGCTTCATCTTGCTCCACTGCAGCCTCAGGGAGATAAGA
1 TAGCTTCATCTTGCTCCACTGCAACCTCAGAGAGATAAGA
25356979 TTCACCATTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
TAGCTTCATCTTGCTCCACTGCAACCTCAGAGAGATAAGACTTG
Found at i:25357157 original size:44 final size:45
Alignment explanation
Indices: 25357087--25357196 Score: 161
Period size: 44 Copynumber: 2.5 Consensus size: 45
25357077 GATATTAATC
* * *
25357087 CACTGCATCTTTAGGGATA-AATGATTTATAGTTTCATCTTGCTA
1 CACTGCAACTTTAGGGAGATAATGATTTATAGTTTCATCTTACTA
*
25357131 CACTGCAACTTTAGGGAGATAA-GATTTATAGTTTCATCTTACTC
1 CACTGCAACTTTAGGGAGATAATGATTTATAGTTTCATCTTACTA
*
25357175 CACTACAACTTTAGGGAGATAA
1 CACTGCAACTTTAGGGAGATAA
25357197 AATTCGCCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 58 0.97
45 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (45 bp):
CACTGCAACTTTAGGGAGATAATGATTTATAGTTTCATCTTACTA
Found at i:25357227 original size:50 final size:50
Alignment explanation
Indices: 25357173--25357288 Score: 187
Period size: 50 Copynumber: 2.3 Consensus size: 50
25357163 TTCATCTTAC
*
25357173 TCCACTACAACTTTAGGGAGATAAAATTCGCCATTATAACTTTGATCCGA
1 TCCACTACAACTTCAGGGAGATAAAATTCGCCATTATAACTTTGATCCGA
* *
25357223 TCCACTGCATCTTCAGGGAGATAAAATTCGCCATTATAACTTTGATCCGA
1 TCCACTACAACTTCAGGGAGATAAAATTCGCCATTATAACTTTGATCCGA
* *
25357273 TCCACTGCATCTTCAG
1 TCCACTACAACTTCAG
25357289 CGATATGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (50 bp):
TCCACTACAACTTCAGGGAGATAAAATTCGCCATTATAACTTTGATCCGA
Found at i:25361953 original size:31 final size:31
Alignment explanation
Indices: 25361917--25361978 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
25361907 TTGGCACATC
*
25361917 CTCTGAATTTTGAATGATCAAACCCACGTCT
1 CTCTGAATTTTGAATAATCAAACCCACGTCT
25361948 CTCTGAATTTTGAATAATCAAACCCACGTCT
1 CTCTGAATTTTGAATAATCAAACCCACGTCT
25361979 ATCATTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (31 bp):
CTCTGAATTTTGAATAATCAAACCCACGTCT
Found at i:25366762 original size:23 final size:23
Alignment explanation
Indices: 25366732--25366775 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
25366722 TAATGAGTAC
25366732 AATAAAAAATGATGAAATAAATT
1 AATAAAAAATGATGAAATAAATT
25366755 AATAAAAAATGATGAAATAAA
1 AATAAAAAATGATGAAATAAA
25366776 AAAATTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (23 bp):
AATAAAAAATGATGAAATAAATT
Found at i:25369758 original size:12 final size:12
Alignment explanation
Indices: 25369741--25369765 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25369731 AGATAACCAG
25369741 TATTTTGTTAAA
1 TATTTTGTTAAA
25369753 TATTTTGTTAAA
1 TATTTTGTTAAA
25369765 T
1 T
25369766 TCATGTTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TATTTTGTTAAA
Found at i:25370047 original size:19 final size:19
Alignment explanation
Indices: 25370011--25370049 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
25370001 TATTATTAAT
**
25370011 ATATTTATAATTGTAATAA
1 ATATTTATAATTAAAATAA
*
25370030 ATATTTATCATTAAAATAA
1 ATATTTATAATTAAAATAA
25370049 A
1 A
25370050 ACTGAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:25370576 original size:14 final size:14
Alignment explanation
Indices: 25370553--25370597 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
25370543 TCGAATCATG
*
25370553 AATCCTAAACCCTA
1 AATCCAAAACCCTA
25370567 AATCCAAAA-CCTA
1 AATCCAAAACCCTA
* *
25370580 AAACCCAAACCCTA
1 AATCCAAAACCCTA
25370594 AATC
1 AATC
25370598 TTAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.16
Consensus pattern (14 bp):
AATCCAAAACCCTA
Found at i:25370637 original size:35 final size:35
Alignment explanation
Indices: 25370597--25370682 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
25370587 AACCCTAAAT
* *
25370597 CTTAAATCATAAACTTTAAATCTAGAATCTCAAAC
1 CTTAAACCATAAACTTTAAATCTAAAATCTCAAAC
* *
25370632 CTTAAACCCTAAACTTTAAATCTAAAATCTCGAAC
1 CTTAAACCATAAACTTTAAATCTAAAATCTCAAAC
*
25370667 CTTGAACCCA-AAACTT
1 CTT-AAACCATAAACTT
25370683 AGAAGCCCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
35 40 0.91
36 4 0.09
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.29
Consensus pattern (35 bp):
CTTAAACCATAAACTTTAAATCTAAAATCTCAAAC
Found at i:25370958 original size:27 final size:28
Alignment explanation
Indices: 25370903--25370959 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
25370893 AACCTTAAGA
* *
25370903 TTTGAGGTTTAAGGTTTAAGGGTTAGGG
1 TTTGAGGTTTAAGGTTCAAGAGTTAGGG
* *
25370931 TTTGA-GTTTAAGGTTCAAGATTTTGGG
1 TTTGAGGTTTAAGGTTCAAGAGTTAGGG
25370958 TT
1 TT
25370960 CAGGGTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.21, C:0.02, G:0.33, T:0.44
Consensus pattern (28 bp):
TTTGAGGTTTAAGGTTCAAGAGTTAGGG
Found at i:25371788 original size:17 final size:17
Alignment explanation
Indices: 25371766--25371799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25371756 CCAAAAAATA
*
25371766 TTGAAAATCATTTTATT
1 TTGAAAATCATGTTATT
*
25371783 TTGAAATTCATGTTATT
1 TTGAAAATCATGTTATT
25371800 ATATGTGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (17 bp):
TTGAAAATCATGTTATT
Found at i:25372987 original size:41 final size:41
Alignment explanation
Indices: 25372930--25373013 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
25372920 ACAATTAAAG
25372930 ATTTAACTAATCTAATTGATAAGGCAACTGATCGCAGCCGC
1 ATTTAACTAATCTAATTGATAAGGCAACTGATCGCAGCCGC
25372971 ATTTAACTAATCTAATTGATAAGGCAACTGATCGCAGCCGC
1 ATTTAACTAATCTAATTGATAAGGCAACTGATCGCAGCCGC
25373012 AT
1 AT
25373014 CTATCTCTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (41 bp):
ATTTAACTAATCTAATTGATAAGGCAACTGATCGCAGCCGC
Found at i:25373924 original size:6 final size:6
Alignment explanation
Indices: 25373917--25373957 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
25373907 CGAAAACTAA
* *
25373917 TAAAAA TAAAAC TAAAAC TAAAAC TAAAAC TAAAAA TAAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAA
25373958 TAATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAC
Found at i:25378984 original size:16 final size:16
Alignment explanation
Indices: 25378963--25378993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25378953 AAAACATTTA
*
25378963 TAATATATATGTATAT
1 TAATATATATATATAT
25378979 TAATATATATATATA
1 TAATATATATATATA
25378994 GGCGAACACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATATATATATATAT
Found at i:25390363 original size:4 final size:4
Alignment explanation
Indices: 25390354--25390384 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
25390344 CCATGTTCAG
25390354 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATT
25390385 CATACATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:25391646 original size:13 final size:15
Alignment explanation
Indices: 25391620--25391653 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25391610 AGAATATCAA
25391620 ATAAATGAACAAAAT
1 ATAAATGAACAAAAT
* *
25391635 ATAAATGAAAAAAAC
1 ATAAATGAACAAAAT
25391650 ATAA
1 ATAA
25391654 GTCAATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (15 bp):
ATAAATGAACAAAAT
Found at i:25391840 original size:3 final size:3
Alignment explanation
Indices: 25391832--25391867 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25391822 TACTAATATT
25391832 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
25391868 GTAAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:25393119 original size:26 final size:26
Alignment explanation
Indices: 25393076--25393125 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
25393066 CTTGCTGCAG
*
25393076 GTGAAGATCGGGGCTGCGGCGCGAAC
1 GTGAAGATCCGGGCTGCGGCGCGAAC
* * *
25393102 GTGAAGATCCTGGTTGCGGTGCGA
1 GTGAAGATCCGGGCTGCGGCGCGA
25393126 GGCTCCCCCT
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:0.18, C:0.20, G:0.44, T:0.18
Consensus pattern (26 bp):
GTGAAGATCCGGGCTGCGGCGCGAAC
Found at i:25393575 original size:44 final size:44
Alignment explanation
Indices: 25393523--25393633 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 44
25393513 AATTTGCTCT
* * * *
25393523 CTGCAACTTCAGAGAGATAAGATC-TGTGGTTTTAATCAGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCAT-CGGCTCTAATCAGCTCCA
* * *
25393567 CTGCAACTTTAGGGAGATAGGATCATCGGCTCTAATCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCATCGGCTCTAATCAGCTCCA
25393611 CTGCAACTTCAGGGAGATAAGAT
1 CTGCAACTTCAGGGAGATAAGAT
25393634 TCACCATCTT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 56 0.98
45 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (44 bp):
CTGCAACTTCAGGGAGATAAGATCATCGGCTCTAATCAGCTCCA
Found at i:25393719 original size:44 final size:45
Alignment explanation
Indices: 25393561--25394372 Score: 214
Period size: 44 Copynumber: 18.6 Consensus size: 45
25393551 GTTTTAATCA
* * * ** *
25393561 GCTCCACTGCAACTTTAGGGAGATAGGAT-CATCGGC-TCTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTC-AGTCT
*
25393605 GCTCCACTGCAACTTCAGGGAGATAAGATTCACCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
** * *
25393650 GC-CTCACTGCAACTTCA-GGAGGATAAGA-CCTGCTTACTT-AGTTT
1 GCTC-CACTGCAACTTCAGGGA-GATAAGATCCACCAT-CTTCAGTCT
* * ** *
25393694 GCTCCACTGAAACTTCAGGGAGATAA-A---ACTAGATGC-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAG-TCT
* ** ** * * *
25393735 GCT-CTCTGCAACTTCAAAGAGATAAGATCCAAGAT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
** * * * * ** * **
25393778 GCTCCACTAAAACTTTAGGGAGATAGGAT-TATCGGCTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* ***
25393822 GCTCCACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* * * *
25393867 GCCCCACTGCAACTTTA-GGAGGATAAGA-CTTA-CTTACTT-AGTCT
1 GCTCCACTGCAACTTCAGGGA-GATAAGATC-CACCAT-CTTCAGTCT
* * * *
25393911 GCTTCACTGCAACTTCAGGGAGATAAGA-CTA-GA--TGC-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAG-TCT
* * * * ** * * *
25393952 GCT-CTCTACAACTTCAGAGTGATAAGATCCAAGAT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* * * **** * **
25393995 GCTTCACTGCAACTTCAGGGAGATAGGAT-TATTGGCTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* * ***
25394039 GCTCCACTGCAACTTCAAGGAGATAAGGTTTGCCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* ** *
25394084 GC-CTCACTGCAACTTCA-GGAGGGTAAGA-CCTTCTTACTT-AGTCT
1 GCTC-CACTGCAACTTCAGGGA-GATAAGATCCACCAT-CTTCAGTCT
* * * *
25394128 GCTCCACTGTAACTTCAGGGAGATAAGA-CTA-GA--TGC-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAG-TCT
* * ** * ** * * *
25394169 GCT-CTCTACAACTTCAGAAAGATAAGATCTAAGAT-TTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
* * * * * * ** * **
25394212 GCTCCACTACAACTTTAAGGAGATAGGAT-TATCGGCTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
***
25394256 GCTCCACTGCAACTTCAGGGAGATAATG-TTTGCCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATCCACCATCTTCAGTCT
* ** * *
25394301 GCCCCACTGCAACTTCA-GGAGGATAAGA-CCTGCTTACTT-AGTTT
1 GCTCCACTGCAACTTCAGGGA-GATAAGATCCACCAT-CTTCAGTCT
25394345 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
25394373 CTAGATGCGA
Statistics
Matches: 563, Mismatches: 156, Indels: 98
0.69 0.19 0.12
Matches are distributed among these distances:
40 63 0.11
41 23 0.04
42 4 0.01
43 25 0.04
44 303 0.54
45 143 0.25
46 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCCACCATCTTCAGTCT
Found at i:25393860 original size:217 final size:217
Alignment explanation
Indices: 25393479--25394464 Score: 1576
Period size: 217 Copynumber: 4.5 Consensus size: 217
25393469 TTCGATCCAT
** * *
25393479 TCCACTGCAACACCAGGGAGATAAGACTAGATGCAATTTGCTCTCTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
*** * * * * * *
25393544 ATCTGTGGTTTTAATCAGCTCCACTGCAACTTTAGGGAGATAGGATCATCGGCTCTAATCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* ** *
25393609 CACTGCAACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
131 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
*
25393674 AAGACCTGCTTACTTAGTTTGC
196 AAGACCTGCTTACTTAGTCTGC
* * *
25393696 TCCACTGAAACTTCAGGGAGATAAAACTAGATGCGATCTGCTCTCTGCAACTTCAAAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
*
25393761 ATCCAAGATTTTAATCCGCTCCACTAAAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
*
25393826 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTTAGGAGGAT
131 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
* *
25393891 AAGACTTACTTACTTAGTCTGC
196 AAGACCTGCTTACTTAGTCTGC
* * *
25393913 TTCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAGTGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* * * *
25393978 ATCCAAGATTTTAATCCGCTTCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAACCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
* * *
25394043 CACTGCAACTTCAAGGAGATAAGGTTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGGT
131 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
*
25394108 AAGACCTTCTTACTTAGTCTGC
196 AAGACCTGCTTACTTAGTCTGC
* * *
25394130 TCCACTGTAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTACAACTTCAGAAAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
* *
25394195 ATCTAAGATTTTAATCCGCTCCACTACAACTTTAAGGAGATAGGATTATCGGCTTTAACCTGCTC
66 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
*
25394260 CACTGCAACTTCAGGGAGATAATGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
131 CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
*
25394325 AAGACCTGCTTACTTAGTTTGC
196 AAGACCTGCTTACTTAGTCTGC
25394347 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
*
25394412 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAAGGAGATAGGATTATCGGC
66 ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGC
25394465 CACCGATCCG
Statistics
Matches: 707, Mismatches: 62, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
217 707 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (217 bp):
TCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
ATCCAAGATTTTAATCCGCTCCACTACAACTTTAGGGAGATAGGATTATCGGCTTTAACCTGCTC
CACTGCAACTTCAGGGAGATAAGGTTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGAT
AAGACCTGCTTACTTAGTCTGC
Found at i:25406626 original size:3 final size:3
Alignment explanation
Indices: 25406618--25406674 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
25406608 ATATATATAT
25406618 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25406666 ATA A-A ATA A
1 ATA ATA ATA A
25406675 GTAAATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:25406787 original size:23 final size:23
Alignment explanation
Indices: 25406761--25406812 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
25406751 TTAAAAAAAC
25406761 AAAATAT-ATATACATATATAGAT
1 AAAATATAAT-TACATATATAGAT
* *
25406784 AAAAAATAATTACATATATATAT
1 AAAATATAATTACATATATAGAT
25406807 ATAAAT
1 A-AAAT
25406813 TACATTATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAATATAATTACATATATAGAT
Found at i:25408657 original size:26 final size:26
Alignment explanation
Indices: 25408628--25408677 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
25408618 GGCTGTTAAA
*
25408628 TCATCAGTTAATTCTCCAAAGATGCC
1 TCATCAATTAATTCTCCAAAGATGCC
* *
25408654 TCATCAATTAATTCTTCTAAGATG
1 TCATCAATTAATTCTCCAAAGATG
25408678 ATTACCAAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (26 bp):
TCATCAATTAATTCTCCAAAGATGCC
Found at i:25409800 original size:26 final size:24
Alignment explanation
Indices: 25409769--25409836 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 24
25409759 GCGTCCCGTT
*
25409769 ATATGGCTCTTTGTGAGCTTCCTG
1 ATATGGCTCTTTGTGAGCTTCCCG
*
25409793 ATTAATGGCTCTCTG-GAGCTTCCCG
1 A-T-ATGGCTCTTTGTGAGCTTCCCG
*
25409818 ATATGGCTCGTT-TGAGCTT
1 ATATGGCTCTTTGTGAGCTT
25409837 ATTGATATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 14 0.38
24 2 0.05
25 11 0.30
26 10 0.27
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (24 bp):
ATATGGCTCTTTGTGAGCTTCCCG
Found at i:25409834 original size:23 final size:22
Alignment explanation
Indices: 25409749--25409836 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 22
25409739 GCACACCGCA
*
25409749 GCTCTTATGAGCGTCCCGTTATATG
1 GCTCTT-TGAGCTTCCCG--ATATG
*
25409774 GCTCTTTGTGAGCTTCCTGATTAATG
1 GCTC-TT-TGAGCTTCCCGA-T-ATG
*
25409800 GCTCTCTGGAGCTTCCCGATATG
1 GCTCT-TTGAGCTTCCCGATATG
25409823 GCTCGTTTGAGCTT
1 GCTC-TTTGAGCTT
25409837 ATTGATATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 14 0.27
24 3 0.06
25 16 0.31
26 19 0.37
ACGTcount: A:0.14, C:0.24, G:0.25, T:0.38
Consensus pattern (22 bp):
GCTCTTTGAGCTTCCCGATATG
Found at i:25409873 original size:49 final size:50
Alignment explanation
Indices: 25409757--25409875 Score: 127
Period size: 48 Copynumber: 2.4 Consensus size: 50
25409747 CAGCTCTTAT
* * * * *
25409757 GAGCGTCCCGTTATATGGCTCTTTGTGAGCTTCCTGATTAATGGCTCTCTG
1 GAGCTTCCCGTTA-ATGGCTCGTTGTGAGCTTACTGATTAATGGCTATCCG
* *
25409808 GAGCTTCCCGAT-ATGGCTCGTT-TGAGCTTATTGA-TATATGGCTATCCG
1 GAGCTTCCCGTTAATGGCTCGTTGTGAGCTTACTGATTA-ATGGCTATCCG
*
25409856 GAGCTTCTCGTTAATGGCTC
1 GAGCTTCCCGTTAATGGCTC
25409876 TTCAGAGCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
47 2 0.04
48 29 0.51
49 16 0.28
51 10 0.18
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (50 bp):
GAGCTTCCCGTTAATGGCTCGTTGTGAGCTTACTGATTAATGGCTATCCG
Found at i:25409921 original size:24 final size:23
Alignment explanation
Indices: 25409894--25409941 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
25409884 TACCCGTTAT
25409894 TGGCTCTAATGAGCTTCCTAATTA
1 TGGCTCTAATGAGCTTCCT-ATTA
*
25409918 TGGCTCTTATGAGCTTCCTATTA
1 TGGCTCTAATGAGCTTCCTATTA
25409941 T
1 T
25409942 ACAACTCGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.42
Consensus pattern (23 bp):
TGGCTCTAATGAGCTTCCTATTA
Found at i:25418826 original size:36 final size:36
Alignment explanation
Indices: 25418746--25418827 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 36
25418736 CACAGTTTGG
* * *
25418746 CAAATTAAAATAGTTCGCCATATTAATACAAGTCAC
1 CAAATTAACACAGTTCGCCATAATAATACAAGTCAC
* * *
25418782 CAAATTAACACAGTTCGCCATAATAATATAATTCGC
1 CAAATTAACACAGTTCGCCATAATAATACAAGTCAC
*
25418818 CAAGTTAACA
1 CAAATTAACA
25418828 TGGTTCACAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (36 bp):
CAAATTAACACAGTTCGCCATAATAATACAAGTCAC
Found at i:25418845 original size:17 final size:18
Alignment explanation
Indices: 25418823--25418860 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
25418813 TTCGCCAAGT
* *
25418823 TAACATGGTTCAC-AATA
1 TAACATAGTACACAAATA
25418840 TAACATAGTACACAAATA
1 TAACATAGTACACAAATA
25418858 TAA
1 TAA
25418861 TTGACTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (18 bp):
TAACATAGTACACAAATA
Found at i:25419112 original size:29 final size:28
Alignment explanation
Indices: 25419079--25419179 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 28
25419069 ATATACGAAT
*
25419079 ATATATAATATATACAACAAAGCCCATGC
1 ATATATAATATATATAACAAAGCCCAT-C
25419108 ATATATAATATATATAACAAAGCCACA-C
1 ATATATAATATATATAACAAAGCC-CATC
* * *
25419136 CTATATTATATATATAACAAAACCCCTATAC
1 ATATATAATATATATAAC-AAAGCCC-AT-C
*
25419167 ATATATATTATAT
1 ATATATAATATAT
25419180 GAAACAATAC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
28 18 0.30
29 29 0.48
30 2 0.03
31 11 0.18
ACGTcount: A:0.49, C:0.18, G:0.03, T:0.31
Consensus pattern (28 bp):
ATATATAATATATATAACAAAGCCCATC
Found at i:25420741 original size:16 final size:16
Alignment explanation
Indices: 25420720--25420766 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
25420710 TATTAATACC
*
25420720 ATTATTATTTTATTTA
1 ATTATTATTTTATCTA
*
25420736 ATTATT-TTATTAACTA
1 ATTATTATT-TTATCTA
25420752 ATTAATTATTTTATC
1 ATT-ATTATTTTATC
25420767 CTATTTCAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 7 0.28
18 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATTATTTTATCTA
Found at i:25428333 original size:2 final size:2
Alignment explanation
Indices: 25428326--25428356 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25428316 AAATAGCAAT
25428326 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25428357 ATATCGGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25433503 original size:20 final size:21
Alignment explanation
Indices: 25433478--25433518 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
25433468 TTACGTATAC
*
25433478 GTAAATATTTTTTTA-TAAAA
1 GTAAATATTTTATTATTAAAA
*
25433498 GTAAATCTTTTATTATTAAAA
1 GTAAATATTTTATTATTAAAA
25433519 TATTCCAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
GTAAATATTTTATTATTAAAA
Found at i:25458918 original size:36 final size:36
Alignment explanation
Indices: 25458871--25458940 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
25458861 AGGACGATAT
25458871 GAGCCAAATTAATGGTTAATGCTAACAGTTTAACAC
1 GAGCCAAATTAATGGTTAATGCTAACAGTTTAACAC
25458907 GAGCCAAATTAATGGTTAATGCTAACAGTTTAAC
1 GAGCCAAATTAATGGTTAATGCTAACAGTTTAAC
25458941 TCGTTCATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (36 bp):
GAGCCAAATTAATGGTTAATGCTAACAGTTTAACAC
Found at i:25462947 original size:18 final size:19
Alignment explanation
Indices: 25462910--25462947 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
25462900 CGTTTGATTT
*
25462910 AATTTTGTAGGTCCATTGG
1 AATTTTGTACGTCCATTGG
*
25462929 AATTTTG-ACGTCGATTGG
1 AATTTTGTACGTCCATTGG
25462947 A
1 A
25462948 TCAGCTCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (19 bp):
AATTTTGTACGTCCATTGG
Found at i:25464090 original size:20 final size:20
Alignment explanation
Indices: 25464046--25464083 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
25464036 CCTTAAATTG
* *
25464046 TTTTATTTATAATATTATTC
1 TTTTACTTATAAAATTATTC
25464066 TTTTACTTATAAAATTAT
1 TTTTACTTATAAAATTAT
25464084 CATTTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTACTTATAAAATTATTC
Found at i:25464231 original size:19 final size:20
Alignment explanation
Indices: 25464207--25464255 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
25464197 AAAAATAAAA
25464207 TTTTAATATATTTTTT-ATT
1 TTTTAATATATTTTTTAATT
25464226 TTTTAA-A-AGTTTTTTAATT
1 TTTTAATATA-TTTTTTAATT
25464245 TTTTAAT-TATT
1 TTTTAATATATT
25464256 AAGAATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.04
18 7 0.27
19 17 0.65
20 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTAATATATTTTTTAATT
Found at i:25466434 original size:16 final size:16
Alignment explanation
Indices: 25466404--25466437 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25466394 ATTCAGCCTC
**
25466404 TCATTTCCTTTTCATT
1 TCATTTCCTCCTCATT
25466420 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
25466436 TC
1 TC
25466438 CTCTCTGTTT
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:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:25470405 original size:2 final size:2
Alignment explanation
Indices: 25470394--25470436 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
25470384 TTATCTCTTG
25470394 AT AT -T 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 AT AT
25470435 AT
1 AT
25470437 GTTCTTCGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:25473089 original size:20 final size:20
Alignment explanation
Indices: 25473064--25473101 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
25473054 AAACACCAGG
25473064 AAAGTAAATCATTTTCCAAA
1 AAAGTAAATCATTTTCCAAA
25473084 AAAGTAAATCATTTTCCA
1 AAAGTAAATCATTTTCCA
25473102 GAAATCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAGTAAATCATTTTCCAAA
Found at i:25473108 original size:14 final size:14
Alignment explanation
Indices: 25473089--25473167 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 14
25473079 CCAAAAAAGT
25473089 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
25473103 AAATCATTTTTC-G
1 AAATCATTTTCCAG
* *
25473116 AAAAACATTTTACTGACAC
1 -AAATCATTTT-C---CAG
*
25473135 ACAAACATTTTCCAG
1 A-AATCATTTTCCAG
25473150 AAATCATTTTCCAG
1 AAATCATTTTCCAG
25473164 AAAT
1 AAAT
25473168 GTAAATTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
13 1 0.02
14 36 0.69
15 3 0.06
18 3 0.06
19 9 0.17
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:25473125 original size:201 final size:205
Alignment explanation
Indices: 25472748--25473130 Score: 524
Period size: 210 Copynumber: 1.9 Consensus size: 205
25472738 TATAAAAATT
* * *
25472748 TATTAATATATATTAATATATGTAAAAATAAATTTTCCAGAAAATATTTTCAGGAAATCTGCCAA
1 TATTAATATATATTAATATATGTAAAAACAAATTTTCCAGAAAATATTTGCAGGAAAGCTGCCAA
*
25472813 ACAGCAGAAAATATTTTACACAGATTCAATCAAACACCAGAAAATATTTTTCAGTAAATCATTTT
66 ACAACAGAAAATATTTTACACAGATTCAATCAAACACCAG-AAATA----T-AGTAAATCATTTT
* *
25472878 ACAGAAAAGTAAAACATTTTCCAAAAATCATTTTACGGAAAACATTTTACTGGCAATCAAACGGA
125 ACAAAAAAGTAAAACATTTTCCAAAAATCATTTTACGAAAAACATTTTACTGGCAATCAAACGGA
25472943 CCCTTATTAATATGTA
190 CCCTTATTAATATGTA
* * *
25472959 TATTAA-ATTTATTAATATATGTAAAAACAATTTTTCCGGAAAATATTTGCAGGAAAGCTGCCAA
1 TATTAATATATATTAATATATGTAAAAACAAATTTTCCAGAAAATATTTGCAGGAAAGCTGCCAA
* * * *
25473023 ACAATAGAAAATATTTTACATAGATTC-ATCCAAACACCAG-GA-A-AGTAAATCATTTTCCAAA
66 ACAACAGAAAATATTTTACACAGATTCAAT-CAAACACCAGAAATATAGTAAATCATTTTACAAA
* * *
25473084 AAAGTAAATCATTTTCCAGAAATCATTTTTCGAAAAACATTTTACTG
130 AAAGTAAAACATTTTCCAAAAATCATTTTACGAAAAACATTTTACTG
25473131 ACACACAAAC
Statistics
Matches: 155, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
201 59 0.38
207 1 0.01
208 1 0.01
209 2 0.01
210 86 0.55
211 6 0.04
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (205 bp):
TATTAATATATATTAATATATGTAAAAACAAATTTTCCAGAAAATATTTGCAGGAAAGCTGCCAA
ACAACAGAAAATATTTTACACAGATTCAATCAAACACCAGAAATATAGTAAATCATTTTACAAAA
AAGTAAAACATTTTCCAAAAATCATTTTACGAAAAACATTTTACTGGCAATCAAACGGACCCTTA
TTAATATGTA
Found at i:25473246 original size:2 final size:2
Alignment explanation
Indices: 25473239--25473268 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25473229 GAAGATTTAT
25473239 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25473269 CATGGGAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25485687 original size:16 final size:16
Alignment explanation
Indices: 25485666--25485703 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
25485656 TTTGGTTTGC
25485666 TGTAATGGAATAGAGT
1 TGTAATGGAATAGAGT
*
25485682 TGTAATGTAATAGAGT
1 TGTAATGGAATAGAGT
25485698 TGTAAT
1 TGTAAT
25485704 CAGTAATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:25485869 original size:7 final size:7
Alignment explanation
Indices: 25485857--25485883 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25485847 AAAATAATTT
25485857 AATAATA
1 AATAATA
25485864 AATAATA
1 AATAATA
25485871 AATAATA
1 AATAATA
25485878 AATAAT
1 AATAAT
25485884 TTAGTCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATAATA
Found at i:25485962 original size:63 final size:65
Alignment explanation
Indices: 25485826--25485971 Score: 192
Period size: 66 Copynumber: 2.3 Consensus size: 65
25485816 TTATTATTAA
* * *
25485826 ATTTTAATAGAATTATTATTAAAAATAATTTAATAATAAATAATAAATAATAAATAATTTAGTCA
1 ATTTTAATATAATTATTATTAAAAATAATTTAATAATAAATAATAAATAAT-AATAATTTAATAA
25485891 T
65 T
* *
25485892 ATTTTAATATAATTATTATTAGATATAATTTAATAA-AAATGAA-AAAT-AT-ATAATTTAATAA
1 ATTTTAATATAATTATTATTAAAAATAATTTAATAATAAAT-AATAAATAATAATAATTTAATAA
25485953 T
65 T
25485954 ATTTTTAATATAATTATT
1 A-TTTTAATATAATTATT
25485972 TTTATAGTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
62 12 0.16
63 16 0.22
64 2 0.03
65 8 0.11
66 35 0.48
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.45
Consensus pattern (65 bp):
ATTTTAATATAATTATTATTAAAAATAATTTAATAATAAATAATAAATAATAATAATTTAATAAT
Found at i:25485992 original size:10 final size:10
Alignment explanation
Indices: 25485973--25486058 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
25485963 ATAATTATTT
*
25485973 TTATAGTAAA
1 TTATATTAAA
25485983 TTATATTAAA
1 TTATATTAAA
*
25485993 ATAT-TTAAA
1 TTATATTAAA
25486002 --ATATT---
1 TTATATTAAA
25486007 TTATATTAAA
1 TTATATTAAA
25486017 TTATATTTTGAAA
1 TTATA--TT-AAA
* **
25486030 TTA-AATATT
1 TTATATTAAA
25486039 TTATATTAAA
1 TTATATTAAA
25486049 TTATATTAAA
1 TTATATTAAA
25486059 ATATTTCAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
7 7 0.12
8 2 0.03
9 9 0.16
10 31 0.53
12 3 0.05
13 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (10 bp):
TTATATTAAA
Found at i:25485996 original size:32 final size:31
Alignment explanation
Indices: 25485960--25486062 Score: 102
Period size: 32 Copynumber: 3.2 Consensus size: 31
25485950 TAATATTTTT
*
25485960 AATATAATTATTTTTATAGTAAATTATATTAA
1 AATATAA-TATTTTTATATTAAATTATATTAA
* *
25485992 AATATTTAAAATATTTTATATTAAATTATATTTTGA
1 AATA--TAATAT-TTTTATATTAAATTATA--TTAA
25486028 AAT-TAA-ATATTTTATATTAAATTATATTAA
1 AATATAATAT-TTTTATATTAAATTATATTAA
25486058 AATAT
1 AATAT
25486063 TTCAAATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
30 6 0.10
31 1 0.02
32 24 0.39
33 5 0.08
34 19 0.31
36 6 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (31 bp):
AATATAATATTTTTATATTAAATTATATTAA
Found at i:25486010 original size:34 final size:33
Alignment explanation
Indices: 25485971--25486076 Score: 144
Period size: 34 Copynumber: 3.2 Consensus size: 33
25485961 ATATAATTAT
*
25485971 TTTTATAGTAAATTATATTAAAATATTTAAAATA
1 TTTTATATTAAATTATATTAAAATATTT-AAATA
**
25486005 TTTTATATTAAATTATATTTTGAA-A-TTAAATA
1 TTTTATATTAAATTATA-TTAAAATATTTAAATA
25486037 TTTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTTATATTAAATTATATTAAAATATTT-AAATA
25486071 TTTTAT
1 TTTTAT
25486077 TTTTATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
31 4 0.06
32 23 0.37
33 4 0.06
34 28 0.44
35 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (33 bp):
TTTTATATTAAATTATATTAAAATATTTAAATA
Found at i:25531095 original size:6 final size:6
Alignment explanation
Indices: 25531084--25531108 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
25531074 GATTTTCTTC
25531084 AAAATG AAAATG AAAATG AAAATG A
1 AAAATG AAAATG AAAATG AAAATG A
25531109 CTTGGAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:25532504 original size:16 final size:16
Alignment explanation
Indices: 25532480--25532531 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
25532470 TGAAATCATT
25532480 TTTTAAATTTTAAAAA
1 TTTTAAATTTTAAAAA
* **
25532496 TTTTCAATTTTATATTA
1 TTTTAAATTTTA-AAAA
* *
25532513 TTTTGAATTTTCAAAA
1 TTTTAAATTTTAAAAA
25532529 TTT
1 TTT
25532532 ATATTTATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTAAATTTTAAAAA
Found at i:25534289 original size:10 final size:10
Alignment explanation
Indices: 25534274--25534317 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
25534264 ATTAAATTTA
25534274 TAAAAAATAT
1 TAAAAAATAT
25534284 TAAAAAATA-
1 TAAAAAATAT
*
25534293 T-AAAAATAG
1 TAAAAAATAT
*
25534302 TAAACAATAT
1 TAAAAAATAT
25534312 TAAAAA
1 TAAAAA
25534318 TTGTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.24
9 2 0.07
10 20 0.69
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:25534297 original size:18 final size:19
Alignment explanation
Indices: 25534276--25534332 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
25534266 TAAATTTATA
25534276 AAAAATATTAAAAAATA-T
1 AAAAATATTAAAAAATATT
* *
25534294 AAAAATAGTAAACAATATT
1 AAAAATATTAAAAAATATT
*
25534313 AAAAAT-TGTAAAAAAAATT
1 AAAAATAT-TAAAAAATATT
25534332 A
1 A
25534333 TTTAAAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAAATATTAAAAAATATT
Found at i:25542558 original size:15 final size:16
Alignment explanation
Indices: 25542532--25542573 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
25542522 AAAATATGAT
25542532 GAAAAGAAAA-GGGGAA
1 GAAAA-AAAAGGGGGAA
25542548 GAAAAAAAAGGGGGAA
1 GAAAAAAAAGGGGGAA
25542564 GAAATAAAAA
1 GAAA-AAAAA
25542574 AAAAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (16 bp):
GAAAAAAAAGGGGGAA
Found at i:25554396 original size:155 final size:155
Alignment explanation
Indices: 25554125--25554403 Score: 452
Period size: 155 Copynumber: 1.8 Consensus size: 155
25554115 AAAATCTAAG
*
25554125 TTTTCTTAAAAACCAAAGCTTTATTTCGAAATAATTGAAAAAAGATCAAAACATTGTTTTAAAAA
1 TTTTCTTAAAAACCAAAGCTTTATTTCGAAATAATTGAAAAAAGATCAAAACATTATTTTAAAAA
* * *
25554190 TTTAAACTTTTCCTTTAAAATGACTAAAACAATATTATTATTTTTAAAAATCTAAACTTTCTCCT
66 TTTAAAATTTTCCTGTAAAATGACTAAAAAAATATTATTATTTTTAAAAATCTAAACTTTCTCCT
25554255 TTTTTTAATGATAAAAAATCACTAT
131 TTTTTTAATGATAAAAAATCACTAT
* ** * *
25554280 TTTTCTTAAAAATCAAAGCTTTATTTCGAAATGGTTG-AAAAATATCAAAACTTTATTTTAAAAA
1 TTTTCTTAAAAACCAAAGCTTTATTTCGAAATAATTGAAAAAAGATCAAAACATTATTTTAAAAA
*
25554344 TTTAAAATTTTCCTGTAAAATGACTAAAAAACATATTTTTATTTTTAAAAATCTAAACTT
66 TTTAAAATTTTCCTGTAAAATGACTAAAAAA-ATATTATTATTTTTAAAAATCTAAACTT
25554404 CCTTTGTTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
154 52 0.46
155 61 0.54
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (155 bp):
TTTTCTTAAAAACCAAAGCTTTATTTCGAAATAATTGAAAAAAGATCAAAACATTATTTTAAAAA
TTTAAAATTTTCCTGTAAAATGACTAAAAAAATATTATTATTTTTAAAAATCTAAACTTTCTCCT
TTTTTTAATGATAAAAAATCACTAT
Found at i:25560136 original size:28 final size:29
Alignment explanation
Indices: 25560090--25560144 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
25560080 CCATCACTGG
*
25560090 TACATAGTACCTAAAACTGTAA-CACCGA
1 TACAAAGTACCTAAAACTGTAATCACCGA
* *
25560118 TACAAAGTACCTGATACTGTAATCACC
1 TACAAAGTACCTAAAACTGTAATCACC
25560145 AACAACTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (29 bp):
TACAAAGTACCTAAAACTGTAATCACCGA
Found at i:25561121 original size:21 final size:21
Alignment explanation
Indices: 25561080--25561122 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
25561070 TTATTACAAT
* *
25561080 TAACATTATTTTAATATAAAA
1 TAACATTAATTTAATAGAAAA
25561101 TAACATATAATTTAA-AGAAAA
1 TAACAT-TAATTTAATAGAAAA
25561122 T
1 T
25561123 TCCCTCAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TAACATTAATTTAATAGAAAA
Done.