Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 77 of 141
Found at i:25185134 original size:29 final size:29
Alignment explanation
Indices: 25185033--25185141 Score: 91
Period size: 30 Copynumber: 3.7 Consensus size: 29
25185023 TTGGGAAATT
25185033 TTAGGGTCAAAATATAA-TTC-TAGAAAAG
1 TTAGGGTCAAAATATAATTTCATA-AAAAG
** *
25185061 TTCAATAGTTAAAATATAATTTCA-AAAAAG
1 TT--AGGGTCAAAATATAATTTCATAAAAAG
*
25185091 TTTAGGGATTAAAATATAATTTCATAAAAA-
1 -TTAGGG-TCAAAATATAATTTCATAAAAAG
*
25185121 TTAGGAGTCAAAATACAATTT
1 TTAGG-GTCAAAATATAATTT
25185142 TTTTAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
28 2 0.03
29 19 0.29
30 34 0.52
31 11 0.17
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (29 bp):
TTAGGGTCAAAATATAATTTCATAAAAAG
Found at i:25185396 original size:23 final size:23
Alignment explanation
Indices: 25185366--25185411 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
25185356 GACTTGGAAA
25185366 TTCTCAACTTTGCTTTTTTCCAT
1 TTCTCAACTTTGCTTTTTTCCAT
25185389 TTCTCAACTTTGCTTTTTTCCAT
1 TTCTCAACTTTGCTTTTTTCCAT
25185412 GCCTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.26, G:0.04, T:0.57
Consensus pattern (23 bp):
TTCTCAACTTTGCTTTTTTCCAT
Found at i:25196372 original size:29 final size:29
Alignment explanation
Indices: 25196317--25196373 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
25196307 TTCAAAAAAT
* *
25196317 TTAAAAATTCTAATTAAGCCTTTAATTTG
1 TTAAAAATTCTAATTAAACCTTAAATTTG
*
25196346 TTAAAAATTTTAATTAAAACC-TAAATTT
1 TTAAAAATTCTAATT-AAACCTTAAATTT
25196374 TTTTTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (29 bp):
TTAAAAATTCTAATTAAACCTTAAATTTG
Found at i:25202970 original size:29 final size:27
Alignment explanation
Indices: 25202906--25202970 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 27
25202896 TTTTTATATG
*
25202906 TATAATTATACTAAATTAAAATTCATG
1 TATAATTATACTAAATTAAAATTCATA
*
25202933 TATTAAATTATACATTAAATTAAAGTTCATA
1 TA-T-AATTATAC--TAAATTAAAATTCATA
25202964 TATAATT
1 TATAATT
25202971 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 1 0.03
29 12 0.38
30 1 0.03
31 16 0.50
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (27 bp):
TATAATTATACTAAATTAAAATTCATA
Found at i:25205425 original size:15 final size:15
Alignment explanation
Indices: 25205405--25205433 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25205395 CAAATAAACT
25205405 GTAAAATATGAAATA
1 GTAAAATATGAAATA
25205420 GTAAAATATGAAAT
1 GTAAAATATGAAAT
25205434 TCGGTCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (15 bp):
GTAAAATATGAAATA
Found at i:25213807 original size:2 final size:2
Alignment explanation
Indices: 25213800--25213831 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
25213790 AACATGCATA
25213800 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25213832 CAGTTTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25215027 original size:31 final size:32
Alignment explanation
Indices: 25214985--25215046 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
25214975 GGCCCATTTT
*
25214985 TATTTTAAAAAT-TTTAAAAATTTAAAAAAAG
1 TATTTTAAAAATATTTAAAAATTAAAAAAAAG
* *
25215016 TATTTTTAAAATATTTGAAAATTAAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAAA
25215047 TTAAAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (32 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAAG
Found at i:25215031 original size:42 final size:42
Alignment explanation
Indices: 25214985--25215118 Score: 166
Period size: 41 Copynumber: 3.2 Consensus size: 42
25214975 GGCCCATTTT
* *
25214985 TATTTTAAAAATTTTAAAAATTTAAAAAAAGTATTTTTAAAA
1 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
* **
25215027 TA-TTTGAAAATTAAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
25215068 TATTTT-GAAATTTTAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTAAAAATTTT-AAAAAATTAAAAAAAGTATTTTAAAAA
25215109 TATTTTAAAA
1 TATTTTAAAA
25215119 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
41 63 0.81
42 15 0.19
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.37
Consensus pattern (42 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:25215045 original size:41 final size:41
Alignment explanation
Indices: 25215000--25215128 Score: 172
Period size: 41 Copynumber: 3.1 Consensus size: 41
25214990 TAAAAATTTT
*
25215000 AAAAATTTAAAAAAAGTATTTTTAAAATATTTGAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTGAAAATTAA
* *
25215041 AAAAAATTAAAAAAAGTATTTTAAAAATATTTTGAAATTTTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATA-TTTGAAA-ATTAA
* * *
25215084 AAAAA-TT-AAAAAAGTATGTAAAAAATATTTTAAAATTAA
1 AAAAATTTAAAAAAAGTATTTTAAAAATATTTGAAAATTAA
25215123 AAAAAT
1 AAAAAT
25215129 AAATATATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
39 9 0.12
40 6 0.08
41 45 0.58
42 9 0.12
43 9 0.12
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (41 bp):
AAAAATTTAAAAAAAGTATTTTAAAAATATTTGAAAATTAA
Found at i:25221519 original size:307 final size:306
Alignment explanation
Indices: 25220910--25221641 Score: 731
Period size: 307 Copynumber: 2.4 Consensus size: 306
25220900 TTATGCGCAT
* *
25220910 TTTAATCTTTTTTTTTTATTTTAACACCATACATATTTCATGTGTTATTATTAATTAGTTTCAAA
1 TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTC-AA
* * *
25220975 CCATACA-TTTCATTATTTATTGTATGTTACTTTTAAACACAAATTTACATTCTAAATACATGGT
65 CCATA-AGTTTCATTATTTATTGTATTTTA-TTTTTAACACATATTTACATTCTAAATACATGGT
* * ** * * * * *
25221039 TTTCATATGCGTACGCATGTTATAGAGTTTCTAGTATTAATAATATTGTTAATTGAATTGGTATC
128 TTCCACACACATACACATGTGATAGAGTTTCTA-TATAAATAATATTATTAATTGAATTGGTATC
* * * * * * *
25221104 ATGAATTAACTCGACACCAAATCATGGTTGATGACAACACATTGATCAATAATTGTATTCATTTA
192 ATAAATTAACTCGAAAACAAATCAAGGTTGATGACAACACATTGATAAACAATTATATTCATTTA
* * * * ** *
25221169 ATATTTTTAATTTGATTTATTTATGTGCTTAAAATTCGTTTTACTCACAA
257 ATATTCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
* *
25221219 TTTAATCTTTTTTTTTTCATTTTAGCAACATACATATTTCATGTGCTATTATTAATTAGTTTTAG
1 TTTAATCTTTTTTTTTT-ATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCA-
*** **
25221284 ACCATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTGTGTTCTAAATATGTGGTT
64 ACCATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTACATTCTAAATACATGGTT
* * * *
25221349 TCCACACATATACACAAT-TGATAGA-TATTCT-TATAAATAATATTATTGATTGAGTTGGTGTC
129 TCCACACACATACAC-ATGTGATAGAGT-TTCTATATAAATAATATTATTAATTGAATTGGTATC
* *
25221411 GTAAATTAACT-TAAAACAAA-CTAAGGATTGATGACAACACCA-TGATAAACAATTATATTCA-
192 ATAAATTAACTCGAAAACAAATC-AAGG-TTGATGACAACA-CATTGATAAACAATTATATTCAT
** * *
25221472 TTAAGTATTCTAAATCTAACGTATTTATATTTTTAAATTTTGTTTTACTCACAA
254 TTAA-TATTCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
* * * *
25221526 TTTAA------TATTTTATTTTAGTAACGTACATATTTCATGTGTTATTGTTAATTA-TTTCAAC
1 TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCAAC
* * * * *
25221584 TAATATGTTTTATTATTTATTATATTTTATTTTTAA-ACATATTTCTATATTCTAAATA
66 -CATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATA-TT-TACATTCTAAATA
25221642 TATAATTTCT
Statistics
Matches: 354, Mismatches: 57, Indels: 33
0.80 0.13 0.07
Matches are distributed among these distances:
298 7 0.02
299 37 0.10
300 47 0.13
301 5 0.01
305 1 0.00
306 13 0.04
307 106 0.30
308 3 0.01
309 65 0.18
310 70 0.20
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (306 bp):
TTTAATCTTTTTTTTTTATTTTAGCAACATACATATTTCATGTGTTATTATTAATTAGTTTCAAC
CATAAGTTTCATTATTTATTGTATTTTATTTTTAACACATATTTACATTCTAAATACATGGTTTC
CACACACATACACATGTGATAGAGTTTCTATATAAATAATATTATTAATTGAATTGGTATCATAA
ATTAACTCGAAAACAAATCAAGGTTGATGACAACACATTGATAAACAATTATATTCATTTAATAT
TCTAAATCTAACGTATTTATATGCTTAAAATTCGTTTTACTCACAA
Found at i:25224479 original size:17 final size:17
Alignment explanation
Indices: 25224457--25224509 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
25224447 ATATGGAATC
*
25224457 TAATCTTCTAAGATATG
1 TAATCTTATAAGATATG
*
25224474 TAATCTTAGATATGATATG
1 TAATCTT--ATAAGATATG
*
25224493 TAATCTTAGAAGATATG
1 TAATCTTATAAGATATG
25224510 ATTCCTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 15 0.50
19 15 0.50
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.40
Consensus pattern (17 bp):
TAATCTTATAAGATATG
Found at i:25231679 original size:3 final size:3
Alignment explanation
Indices: 25231673--25231792 Score: 68
Period size: 3 Copynumber: 40.0 Consensus size: 3
25231663 ACTAATAAAC
* * **
25231673 TAA TAA TAA GAA TAA TAA -AA TACA GTAA -AA TAA TAG TAA TCC TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA
* * * ** * *
25231718 -AA -AA TAC TAA GAA TAC TAA TGT TAA TAA TAA AAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
25231764 CAA TAA TAA TAAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA T-AA TAA TAA TAA
25231793 AAGCAAAAAC
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
2 8 0.09
3 68 0.79
4 8 0.09
5 2 0.02
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:25242728 original size:30 final size:30
Alignment explanation
Indices: 25242692--25242756 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
25242682 GAGATACTGT
*
25242692 TTGAGACAT-ATATAGAAGGTGAATCTAGAA
1 TTGAGAC-TCATATAGAAGGTGAATCCAGAA
* *
25242722 TTGAGACTCATATAGAAGGTGTATCCAGTA
1 TTGAGACTCATATAGAAGGTGAATCCAGAA
25242752 TTGAG
1 TTGAG
25242757 GATCTAGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (30 bp):
TTGAGACTCATATAGAAGGTGAATCCAGAA
Found at i:25245570 original size:21 final size:21
Alignment explanation
Indices: 25245539--25245593 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
25245529 TTCCAAAGTG
25245539 TGTCATGACATCGAACCCCGA
1 TGTCATGACATCGAACCCCGA
* * *
25245560 TGT-AGTGACATAGAACCTCTA
1 TGTCA-TGACATCGAACCCCGA
25245581 TGTCATGACATCG
1 TGTCATGACATCG
25245594 CTGCAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TGTCATGACATCGAACCCCGA
Found at i:25258150 original size:23 final size:23
Alignment explanation
Indices: 25258120--25258166 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
25258110 TTAGCACATG
*
25258120 TTAGACACATCTTTCATATTGTA
1 TTAGACACATCCTTCATATTGTA
25258143 TTAGACACATCCTTCATATTGTA
1 TTAGACACATCCTTCATATTGTA
25258166 T
1 T
25258167 GATTTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.43
Consensus pattern (23 bp):
TTAGACACATCCTTCATATTGTA
Found at i:25259207 original size:30 final size:29
Alignment explanation
Indices: 25259171--25259227 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
25259161 ACAATCTTTA
25259171 ATTTTTTAAAGGGCAACACCTATATACTCT
1 ATTTTTTAAAGGGCAACACCTAT-TACTCT
25259201 ATTTTTTAAAGGGCAACACCTATTACT
1 ATTTTTTAAAGGGCAACACCTATTACT
25259228 ATAACCTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (29 bp):
ATTTTTTAAAGGGCAACACCTATTACTCT
Found at i:25265171 original size:23 final size:24
Alignment explanation
Indices: 25265121--25265171 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
25265111 AACACCGCTG
*
25265121 AAGCGGATAAACTGACCACCGTCA
1 AAGCGGATAAACTGACCACCGCCA
* * *
25265145 AAGCGGAT-AGCTGAGCACCGCCC
1 AAGCGGATAAACTGACCACCGCCA
25265168 AAGC
1 AAGC
25265172 AAATAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.33, C:0.31, G:0.25, T:0.10
Consensus pattern (24 bp):
AAGCGGATAAACTGACCACCGCCA
Found at i:25269238 original size:129 final size:134
Alignment explanation
Indices: 25268981--25269251 Score: 444
Period size: 138 Copynumber: 2.0 Consensus size: 134
25268971 AGTAGAAAGG
25268981 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
* *
25269046 TATAACTGTTTATAATAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATAATAATAAATTCGGT-AAATATAT--AA-TAATATTTTATATAAATCAAATT
*
25269111 TATATATT
127 CATATATT
25269119 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
25269184 TATAACTGTTTATAATAATAAATTCGGT-AA-A-AT-A-AATATTTTATATAAATCAAATTCATA
66 TATAACTGTTTATAATAATAAATTCGGTAAATATATAATAATATTTTATATAAATCAAATTCATA
25269244 TATT
131 TATT
25269248 AATT
1 AATT
25269252 TTATCTATAT
Statistics
Matches: 130, Mismatches: 3, Indels: 9
0.92 0.02 0.06
Matches are distributed among these distances:
129 31 0.24
131 1 0.01
134 2 0.02
135 1 0.01
136 2 0.02
138 93 0.72
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (134 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAACTGTTTATAATAATAAATTCGGTAAATATATAATAATATTTTATATAAATCAAATTCATA
TATT
Found at i:25271890 original size:13 final size:13
Alignment explanation
Indices: 25271872--25271900 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
25271862 ATGGCCAAAA
25271872 TGATTGCATCCTT
1 TGATTGCATCCTT
25271885 TGATTGCATCCTT
1 TGATTGCATCCTT
25271898 TGA
1 TGA
25271901 GTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (13 bp):
TGATTGCATCCTT
Found at i:25275743 original size:24 final size:25
Alignment explanation
Indices: 25275689--25275743 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
25275679 ATTTTCAATC
*
25275689 TTATTATTAAATTCACAGTTTAAAA
1 TTATTAATAAATTCACAGTTTAAAA
**
25275714 GAATTAATAATATTCA-A-TTTAAAA
1 TTATTAATAA-ATTCACAGTTTAAAA
25275738 TTATTA
1 TTATTA
25275744 GTTAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
24 11 0.46
25 8 0.33
26 5 0.21
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (25 bp):
TTATTAATAAATTCACAGTTTAAAA
Found at i:25277223 original size:29 final size:29
Alignment explanation
Indices: 25277183--25277253 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
25277173 CACAATAACG
* * *
25277183 TAAGTGACTAAAGCGCAATATTTCAAACA
1 TAAGTGACTAAAACGAAACATTTCAAACA
*
25277212 TCAGTGACTAAAACGAAACATTTCAAACA
1 TAAGTGACTAAAACGAAACATTTCAAACA
*
25277241 TAAGTGAGTAAAA
1 TAAGTGACTAAAA
25277254 TGTAACCTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (29 bp):
TAAGTGACTAAAACGAAACATTTCAAACA
Found at i:25287448 original size:20 final size:21
Alignment explanation
Indices: 25287409--25287448 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25287399 AAATTATGAC
*
25287409 TATAATTATTTCTGTAAAATT
1 TATAATTATTTCTCTAAAATT
25287430 TATAATTATTT-TCTAAAAT
1 TATAATTATTTCTCTAAAAT
25287449 CAGAACAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TATAATTATTTCTCTAAAATT
Found at i:25288236 original size:23 final size:23
Alignment explanation
Indices: 25288211--25288301 Score: 155
Period size: 23 Copynumber: 4.0 Consensus size: 23
25288201 CCACATTGAT
**
25288211 ATGTAGCCGAAGCTACCACTGTT
1 ATGTAGCCGAAGCTACCACTGAA
25288234 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
25288257 ATGTAGCCGAAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGAA
*
25288280 ATGTAGTCGAAGCTACCACTGA
1 ATGTAGCCGAAGCTACCACTGA
25288302 TCAATAACAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (23 bp):
ATGTAGCCGAAGCTACCACTGAA
Found at i:25293500 original size:65 final size:65
Alignment explanation
Indices: 25293396--25293525 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
25293386 CCAAAACTAT
*
25293396 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTCGTCTAG
1 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
*
25293461 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTTGATTAGTCTAG
1 AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
25293526 GATGAACACG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (65 bp):
AACTTGGTTGTTATATCTAAAGTAATAAACACCTAATCAAAATTGTACCTTTTCGATTAGTCTAG
Found at i:25293922 original size:69 final size:68
Alignment explanation
Indices: 25293823--25293957 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
25293813 TGATTAAACT
* *
25293823 TAATCACTTTAATATTAAATTAATATAATACTTATCAAAATAAATATTAGATTAAATTTAATATT
1 TAATCACTTTAATATTAAATTAATAAAATAC-TATCAAAATAAATATTAAATTAAATTTAATATT
25293888 AAGA
65 AAGA
* * *
25293892 TAATCACTTTAATGTTAAATTAATAAAATACTATCAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATATTAAATTAATAAAATACTATCAAAATAAATATTAAATTAAATTTAATATTA
25293957 A
66 A
25293958 ATCTATTAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
68 32 0.52
69 29 0.48
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (68 bp):
TAATCACTTTAATATTAAATTAATAAAATACTATCAAAATAAATATTAAATTAAATTTAATATTA
AGA
Found at i:25297118 original size:15 final size:17
Alignment explanation
Indices: 25297098--25297131 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
25297088 CCCTACTTAG
25297098 AAAA-TTTCAT-CCTCT
1 AAAATTTTCATCCCTCT
25297113 AAAATTTTCATCCCTCT
1 AAAATTTTCATCCCTCT
25297130 AA
1 AA
25297132 TAGCCCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 6 0.35
17 7 0.41
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTTTCATCCCTCT
Found at i:25307674 original size:30 final size:31
Alignment explanation
Indices: 25307640--25307703 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
25307630 AATTAGTTTA
25307640 TTGTTAA-TTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
* * *
25307670 TTGTTAATTTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGACAT
25307701 TTG
1 TTG
25307704 CTTATTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.23
31 23 0.77
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGACAT
Found at i:25308078 original size:29 final size:30
Alignment explanation
Indices: 25308046--25308132 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 30
25308036 TTTAATGTAT
25308046 AATTATATACAT-AAACTTTAATTTGGTAC
1 AATTATATACATGAAACTTTAATTTGGTAC
* * * *
25308075 AATTATACACGTGAAACTCTAATTGTGGTTC
1 AATTATATACATGAAACTTTAATT-TGGTAC
* * *
25308106 AAATGTATACTTGAAACTTTAATTTGG
1 AATTATATACATGAAACTTTAATTTGG
25308133 ATTTAATCAT
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 10 0.21
30 13 0.28
31 24 0.51
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (30 bp):
AATTATATACATGAAACTTTAATTTGGTAC
Found at i:25308311 original size:31 final size:30
Alignment explanation
Indices: 25308273--25308332 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25308263 GAATTGGATC
* *
25308273 AAATCAAAATTTCATGTATA-AATTTACACAA
1 AAATC-AAAGTTCATATATATAA-TTACACAA
25308304 AAATCAAAGTTCATATATATAATTACACA
1 AAATCAAAGTTCATATATATAATTACACA
25308333 TTAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATATATATAATTACACAA
Found at i:25308330 original size:30 final size:31
Alignment explanation
Indices: 25308273--25308359 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 31
25308263 GAATTGGATC
* *
25308273 AAATCAAAATTTCATGTATAAATTTACACAA
1 AAATCAAAAGTTCATATATAAATTTACACAA
*
25308304 AAATC-AAAGTTCATATATATAA-TTACACATT
1 AAATCAAAAGTTCATATATA-AATTTACACA-A
*
25308335 AAA-CTAAAA-TTCATATATAATTTTA
1 AAATC-AAAAGTTCATATATAAATTTA
25308360 ATATTTATTC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
30 21 0.45
31 23 0.49
32 3 0.06
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (31 bp):
AAATCAAAAGTTCATATATAAATTTACACAA
Found at i:25312996 original size:186 final size:186
Alignment explanation
Indices: 25312682--25313056 Score: 732
Period size: 186 Copynumber: 2.0 Consensus size: 186
25312672 CTCCTTGGTC
*
25312682 TTGTGTTCAAATCTTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
1 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
25312747 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
66 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
25312812 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
131 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
25312868 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
1 TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
25312933 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
66 AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
*
25312998 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTTGATATTTAGTTCTTCGTT
131 TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
25313054 TTG
1 TTG
25313057 GTTTCTTCCT
Statistics
Matches: 187, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 187 1.00
ACGTcount: A:0.21, C:0.13, G:0.16, T:0.50
Consensus pattern (186 bp):
TTGTGTTCAAATCCTGGCGAAAGTAATAGGAAATATTTTATTTTGAATTTCATTGTATGGTAGTT
AGTTTCGGTTGGTTACTTAAAACCTTTTAGAAACCTCTGGCAAGTTTTTCTTTTAACTTTTGTTC
TTTCCTTTTTTGTTATGTTTCTTCTATTAGTCGTTCTCGATATTTAGTTCTTCGTT
Found at i:25321101 original size:13 final size:13
Alignment explanation
Indices: 25321083--25321108 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25321073 TAAGTAAAAC
25321083 TATTATATTATTA
1 TATTATATTATTA
25321096 TATTATATTATTA
1 TATTATATTATTA
25321109 GAAAAAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATTATTA
Found at i:25322189 original size:23 final size:22
Alignment explanation
Indices: 25322162--25322242 Score: 105
Period size: 21 Copynumber: 3.8 Consensus size: 22
25322152 TTTCCGATCT
25322162 GGCACTTTATGTGTCGTATCTCA
1 GGCACTTTATGTGTCGTAT-TCA
*
25322185 GGCACTTTATGTGTCATA-TCA
1 GGCACTTTATGTGTCGTATTCA
* *
25322206 GGCACCTTGTGTGTCGT-TTCA
1 GGCACTTTATGTGTCGTATTCA
25322227 GGCAC-TTATGTGTCGT
1 GGCACTTTATGTGTCGT
25322243 TTATTGATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.19
21 25 0.48
23 17 0.33
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.38
Consensus pattern (22 bp):
GGCACTTTATGTGTCGTATTCA
Found at i:25323027 original size:18 final size:18
Alignment explanation
Indices: 25323004--25323039 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
25322994 ATGTCGAATG
25323004 ATGAT-AATGATTATGTTA
1 ATGATAAATG-TTATGTTA
25323022 ATGATAAATGTTATGTTA
1 ATGATAAATGTTATGTTA
25323040 TACTTGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.17, T:0.44
Consensus pattern (18 bp):
ATGATAAATGTTATGTTA
Found at i:25325797 original size:8 final size:9
Alignment explanation
Indices: 25325780--25325829 Score: 50
Period size: 8 Copynumber: 5.3 Consensus size: 9
25325770 TTTTTTTAAG
25325780 TATA-TTAT
1 TATATTTAT
25325788 TAT-TTTAT
1 TATATTTAT
25325796 TATATTGTAAAT
1 TATATT-T--AT
25325808 TATATTTAT
1 TATATTTAT
25325817 TATATTATAT
1 TATATT-TAT
25325827 TAT
1 TAT
25325830 TATATTTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
8 10 0.28
9 10 0.28
10 7 0.19
11 1 0.03
12 8 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (9 bp):
TATATTTAT
Found at i:25326857 original size:20 final size:20
Alignment explanation
Indices: 25326802--25326861 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
25326792 TTTCCGATCT
*
25326802 GGCACTTTATGTGTCGTATCA
1 GGCAC-TTATGTGTCGTTTCA
*
25326823 GGCACCTTGTGTGTCGTTTCA
1 GGCA-CTTATGTGTCGTTTCA
25326844 GGCACTTATGTGTCGTTT
1 GGCACTTATGTGTCGTTT
25326862 ATTGATCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 13 0.37
21 21 0.60
22 1 0.03
ACGTcount: A:0.13, C:0.20, G:0.27, T:0.40
Consensus pattern (20 bp):
GGCACTTATGTGTCGTTTCA
Found at i:25332428 original size:18 final size:18
Alignment explanation
Indices: 25332405--25332441 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25332395 TTAAAAATGA
25332405 AACTGTATTAACAACACC
1 AACTGTATTAACAACACC
25332423 AACTGTATTAACAACACC
1 AACTGTATTAACAACACC
25332441 A
1 A
25332442 TTTATGAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
AACTGTATTAACAACACC
Found at i:25335016 original size:22 final size:22
Alignment explanation
Indices: 25334991--25335051 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
25334981 AGGTGATTAA
25334991 TATGTGAACCCTTTATTTGTAC
1 TATGTGAACCCTTTATTTGTAC
*
25335013 TATGTGAACCATTTATTTGTAC
1 TATGTGAACCCTTTATTTGTAC
* *
25335035 TATGCGAACCCTATATT
1 TATGTGAACCCTTTATT
25335052 GCATAAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (22 bp):
TATGTGAACCCTTTATTTGTAC
Found at i:25335095 original size:23 final size:23
Alignment explanation
Indices: 25335069--25335132 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
25335059 AACCCTAAAC
*
25335069 ATTGTTACATACGAA-CTCTACAT
1 ATTGTTACATGCGAACCT-TACAT
* *
25335092 ATTGTTAGATGCGAACCTTTCAT
1 ATTGTTACATGCGAACCTTACAT
*
25335115 GTTGTTACATGCGAACCT
1 ATTGTTACATGCGAACCT
25335133 ATGTGTCTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (23 bp):
ATTGTTACATGCGAACCTTACAT
Found at i:25335260 original size:15 final size:15
Alignment explanation
Indices: 25335240--25335269 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25335230 TATGTGCGAA
25335240 CTACTTGCATGAACC
1 CTACTTGCATGAACC
*
25335255 CTACTTGTATGAACC
1 CTACTTGCATGAACC
25335270 TCTAGGTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (15 bp):
CTACTTGCATGAACC
Found at i:25355217 original size:54 final size:54
Alignment explanation
Indices: 25355150--25355261 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
25355140 GGATTGGTGG
25355150 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
1 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
25355204 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
1 ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
25355258 ACAC
1 ACAC
25355262 ACTTTTGTCT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (54 bp):
ACACCACTACTGAATTTTAGTTATCTCCCCTTCCCAAAATAAATAAATTTTCTT
Found at i:25359342 original size:14 final size:14
Alignment explanation
Indices: 25359305--25359362 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
25359295 ATGAAAGTCC
25359305 ATTAGGTTAATTTAG
1 ATTA-GTTAATTTAG
*
25359320 GTTAGTTAATTTA-
1 ATTAGTTAATTTAG
*
25359333 ATTAGTTTAA-TTAA
1 ATTAG-TTAATTTAG
*
25359347 AATA-TTAATTTAG
1 ATTAGTTAATTTAG
25359360 ATT
1 ATT
25359363 CGCACTACTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.11
13 12 0.34
14 16 0.46
15 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (14 bp):
ATTAGTTAATTTAG
Found at i:25363029 original size:20 final size:21
Alignment explanation
Indices: 25362991--25363029 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25362981 TGCAACACGT
25362991 AGCCTTGTATTGAGCCACAAC
1 AGCCTTGTATTGAGCCACAAC
*
25363012 AGCCTTGTGTTG-GCCACA
1 AGCCTTGTATTGAGCCACA
25363030 TCAACCTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (21 bp):
AGCCTTGTATTGAGCCACAAC
Found at i:25364532 original size:73 final size:73
Alignment explanation
Indices: 25364440--25364598 Score: 300
Period size: 73 Copynumber: 2.2 Consensus size: 73
25364430 GACACAACCA
* *
25364440 TAGGATGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCATCAATGTCGCCAC
1 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
25364505 ACAGGCAC
66 ACAGGCAC
25364513 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
1 TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
25364578 ACAGGCAC
66 ACAGGCAC
25364586 TAGGGTGTCGCGA
1 TAGGGTGTCGCGA
25364599 CACCGACCCT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (73 bp):
TAGGGTGTCGCGAATCACCCTTGAAGCCATCCCTGAACCACAAATACTGCCACCAATGTCGCCAC
ACAGGCAC
Found at i:25366996 original size:24 final size:24
Alignment explanation
Indices: 25366960--25367005 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25366950 GTTTATTTCA
25366960 TTTCATTTTATTTATTA-ATATCT
1 TTTCATTTTATTTATTACATATCT
*
25366983 TTTCCTTTATATTTATTACATAT
1 TTTCATTT-TATTTATTACATAT
25367006 TTCATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 9 0.45
25 4 0.20
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTTATTTATTACATATCT
Found at i:25371679 original size:6 final size:6
Alignment explanation
Indices: 25371668--25371701 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
25371658 ATCCAAAAGC
25371668 TTTTAA TTTTAA TTTTAA TTTTGCAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTT--AA TTTTAA TT
25371702 GTCTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 20 0.77
8 6 0.23
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:25373539 original size:12 final size:12
Alignment explanation
Indices: 25373523--25373556 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
25373513 AAACAGAGTC
25373523 ATAAATATTTTT
1 ATAAATATTTTT
*
25373535 GTAAATATTTTT
1 ATAAATATTTTT
25373547 ATAAATATTT
1 ATAAATATTT
25373557 ATGGAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:25375133 original size:20 final size:19
Alignment explanation
Indices: 25375108--25375178 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 19
25375098 AAGCTTATTA
*
25375108 TAAGTAAATGGAATTGAAGG
1 TAAGTAAATGGAATGGAA-G
*
25375128 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGG-AAG
25375148 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGGAATGG-AAG
25375168 TAAG-AAATGGA
1 TAAGTAAATGGA
25375179 GTGGTTCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 7 0.15
20 37 0.80
21 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (19 bp):
TAAGTAAATGGAATGGAAG
Found at i:25375158 original size:15 final size:16
Alignment explanation
Indices: 25375138--25375170 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25375128 TAAGTAAATG
25375138 AAATGGAA-AGTAAGT
1 AAATGGAATAGTAAGT
*
25375153 AAATGGAATGGTAAGT
1 AAATGGAATAGTAAGT
25375169 AA
1 AA
25375171 GAAATGGAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (16 bp):
AAATGGAATAGTAAGT
Found at i:25375496 original size:92 final size:92
Alignment explanation
Indices: 25375339--25375526 Score: 376
Period size: 92 Copynumber: 2.0 Consensus size: 92
25375329 TAGGTTTATA
25375339 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
1 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
25375404 ATTCATTGCTTACGTAGTTATTTTCCT
66 ATTCATTGCTTACGTAGTTATTTTCCT
25375431 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
1 TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
25375496 ATTCATTGCTTACGTAGTTATTTTCCT
66 ATTCATTGCTTACGTAGTTATTTTCCT
25375523 TTAC
1 TTAC
25375527 TTTTCAGATT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 96 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.40
Consensus pattern (92 bp):
TTACCCTATAAAGTTCATTATTGAAATAGAAAGTTATGTTAAAAGTTTATACGAGCTTACTAAGC
ATTCATTGCTTACGTAGTTATTTTCCT
Found at i:25380534 original size:20 final size:20
Alignment explanation
Indices: 25380483--25380534 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
25380473 CTTATGCTAG
* *
25380483 GTAAATGGAATGGAAAGAAA
1 GTAAATAGAATGAAAAGAAA
* * *
25380503 GTAAATAAAATGAAAAGTAT
1 GTAAATAGAATGAAAAGAAA
*
25380523 GTAAATTGAATG
1 GTAAATAGAATG
25380535 GTAAGTAAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (20 bp):
GTAAATAGAATGAAAAGAAA
Found at i:25396544 original size:16 final size:18
Alignment explanation
Indices: 25396506--25396546 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
25396496 ATATGAACAC
25396506 TGATTTACGAGCTCCTCA
1 TGATTTACGAGCTCCTCA
*
25396524 TGATTTGCGAGCT-CT-A
1 TGATTTACGAGCTCCTCA
25396540 TGATTTA
1 TGATTTA
25396547 GTAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.39
Consensus pattern (18 bp):
TGATTTACGAGCTCCTCA
Found at i:25400563 original size:130 final size:130
Alignment explanation
Indices: 25400314--25400926 Score: 474
Period size: 130 Copynumber: 4.7 Consensus size: 130
25400304 ACAGTTCACC
* * * * * * *
25400314 GATTTAATATCCCAATTGATATTATTAAGGCT-AGCTAATTTACTATCACAGCCTAAGTTCATT-
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCA-CTGATTTACGATCATAGTCTAAGTTCATTG
** * * * *
25400377 -TCAGACTATCATGAATAATCTTCTCTACGATAACTGATTTACTATCGCTACTCCAAATA-CTTC
65 AT-TTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGC-TC
*
25400440 ACT
128 GCT
* * * * *
25400443 GATTTAAGATCACAGCTGGTATTATTAAAGCTCATTGATTTACGATCATAGTCTAAGTTGATT-A
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTGA
* * *
25400507 TTTTACTATCATGAACAATCTTCTCTAAGTTAGCAT-ACTTGCTAACGCTACTCCAAATAGCTCG
66 -TTTACTATCATGAACAATCTTCTCTAAGTTAGC-TGATTTACTATCGCTACTCCAAATAGCTCG
*
25400571 TT
129 CT
* * * * * * *
25400573 GATTTAATATCATAATTGGTATTATTAAGGTTCGCTGATTT-CTAATCATAATCTAAGTTTATTG
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTAC-GATCATAGTCTAAGTTCATTG
* * * * * * *
25400637 ATTTACTGTCATTAAAAATCTTCTTTGAGTTAGTTGATTTACTATCGCTACTCCAAACAGCTCGC
65 ATTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCGC
25400702 T
130 T
* * * * *
25400703 GATTTCATATCACAGTTGATATTATTATGGCTCACTGGTTTACGATCACAGGT-TAAGTTCATTG
1 GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATA-GTCTAAGTTCATTG
* * * * * * *** * *
25400767 ATTTACTATAATGAACAATCTTC-CATGAGTTAGCTGATTTTCCATAGCTATTTTGAACAACTCG
65 ATTTACTATCATGAACAATCTTCTC-TAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCG
*
25400831 AT
129 CT
* *** * * * *
25400833 GATTTAATATCACA-ATGGATATTATTAAGGCTTGTTGATTTATGATGATAGCCTAAGTTTATTG
1 GATTTAATATCACAGTTGG-TATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTG
* * * *
25400897 ATTTACGAACCTGAATAATCTTCT-TAAGTT
65 ATTTACTATCATGAACAATCTTCTCTAAGTT
25400927 GATTTATGAT
Statistics
Matches: 379, Mismatches: 91, Indels: 28
0.76 0.18 0.06
Matches are distributed among these distances:
129 59 0.16
130 314 0.83
131 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (130 bp):
GATTTAATATCACAGTTGGTATTATTAAGGCTCACTGATTTACGATCATAGTCTAAGTTCATTGA
TTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATTTACTATCGCTACTCCAAATAGCTCGCT
Found at i:25400838 original size:260 final size:260
Alignment explanation
Indices: 25400411--25400902 Score: 577
Period size: 260 Copynumber: 1.9 Consensus size: 260
25400401 CTACGATAAC
* *
25400411 TGATTTACTATCGCTACTCCAAATACTTCACTGATTTAAGATCACAGCTGGTATTATTAAAGCTC
1 TGATTTACTATCGCTACTCCAAACACTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCTC
* * * *
25400476 ATTGATTTACGATCATAGTCTAAGTTGATTATTTTACTATCATGAACAATCTTCTCTAAGTTAGC
66 ACTGATTTACGATCACAGTCTAAGTTCATTATTTTACTATAATGAACAATCTTCTCTAAGTTAGC
* * * * *
25400541 ATACTTGCTAACGCTACTCCAAATAGCTCGTTGATTTAATATCATAATTGG-TATTATTAAGG-T
131 ATACTTGCCAACGCTACTCCAAACAACTCGATGATTTAATATCACAA-TGGATATTATTAAGGCT
* *
25400604 TCGCTGATTTCTAATCATAATCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTA
195 T-GCTGATTTATAATCATAACCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTA
25400669 GT
259 GT
* * * * **
25400671 TGATTTACTATCGCTACTCCAAACAGC-TCGCTGATTTCATATCACAGTTGATATTATTATGGCT
1 TGATTTACTATCGCTACTCCAAACA-CTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCT
* *
25400735 CACTGGTTTACGATCACAGGT-TAAGTTCATTGA-TTTACTATAATGAACAATCTTC-CATGAGT
65 CACTGATTTACGATCACA-GTCTAAGTTCATT-ATTTTACTATAATGAACAATCTTCTC-TAAGT
* * * ***
25400797 TAGC-TGATTTTCCATA-GCTATTTTGAACAACTCGATGATTTAATATCACAATGGATATTATTA
127 TAGCAT-ACTTGCCA-ACGCTACTCCAAACAACTCGATGATTTAATATCACAATGGATATTATTA
* * * *
25400860 AGGCTTGTTGATTTATGATGATAGCCTAAGTTTATTGATTTAC
190 AGGCTTGCTGATTTATAATCATAACCTAAGTTTATTGATTTAC
25400903 GAACCTGAAT
Statistics
Matches: 193, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
259 5 0.03
260 181 0.94
261 7 0.04
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (260 bp):
TGATTTACTATCGCTACTCCAAACACTTCACTGATTTAAGATCACAGCTGATATTATTAAAGCTC
ACTGATTTACGATCACAGTCTAAGTTCATTATTTTACTATAATGAACAATCTTCTCTAAGTTAGC
ATACTTGCCAACGCTACTCCAAACAACTCGATGATTTAATATCACAATGGATATTATTAAGGCTT
GCTGATTTATAATCATAACCTAAGTTTATTGATTTACTGTCATTAAAAATCTTCTTTGAGTTAGT
Found at i:25415105 original size:19 final size:18
Alignment explanation
Indices: 25415078--25415114 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
25415068 CTAGTTAGAA
*
25415078 TAATTTATTATTTGTAATT
1 TAATATATTATTT-TAATT
25415097 TAATATATTATTTTAATT
1 TAATATATTATTTTAATT
25415115 AGGGTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TAATATATTATTTTAATT
Found at i:25421099 original size:3 final size:3
Alignment explanation
Indices: 25421091--25421121 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
25421081 GCTATGGTAA
25421091 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG T
25421122 TTAGAGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TAG
Found at i:25425543 original size:90 final size:90
Alignment explanation
Indices: 25425421--25425704 Score: 464
Period size: 90 Copynumber: 3.2 Consensus size: 90
25425411 CTTAGGGAGG
*
25425421 TAAGATCT-GTAATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGTTTTCTTTCGA
1 TAAGATCTGGT-ATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGA
* *
25425485 TCTGCTTCACCACTAGTATGGGAAGA
65 TCTGCTTCGCCACCAGTATGGGAAGA
*
25425511 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTT-GAT
1 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
*
25425575 CTGCTTCGCCACCAGTATGGGAAGG
66 CTGCTTCGCCACCAGTATGGGAAGA
* * *
25425600 CAAGATCTGATATCTCTGATCTACTTCACGCCAGTTCATGAAGTCAAGATCTGCTTTCTTTCGAT
1 TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
25425665 CTGCTTCGCCACCAGTATGGGAAGA
66 CTGCTTCGCCACCAGTATGGGAAGA
*
25425690 TAAGATCTGTTATCT
1 TAAGATCTGGTATCT
25425705 TTTCAACCTG
Statistics
Matches: 180, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
89 82 0.46
90 96 0.53
91 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (90 bp):
TAAGATCTGGTATCTCTGATCTACTTCACGCCAGTACATGAAGTCAAGATCTGCTTTCTTTCGAT
CTGCTTCGCCACCAGTATGGGAAGA
Found at i:25441793 original size:15 final size:17
Alignment explanation
Indices: 25441768--25441801 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
25441758 AATAATTTAA
25441768 ATTTCTTTTT-AAAATT
1 ATTTCTTTTTAAAAATT
25441784 ATTT-TTTTTAAAAATT
1 ATTTCTTTTTAAAAATT
25441800 AT
1 AT
25441802 GAAAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTCTTTTTAAAAATT
Found at i:25441818 original size:21 final size:21
Alignment explanation
Indices: 25441792--25441834 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25441782 TTATTTTTTT
* * *
25441792 TAAAAATTATGAAAAAATATA
1 TAAAAATCATAAAAAAAAATA
25441813 TAAAAATCATAAAAAAAAATA
1 TAAAAATCATAAAAAAAAATA
25441834 T
1 T
25441835 TTTGTTACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAATCATAAAAAAAAATA
Found at i:25447230 original size:15 final size:14
Alignment explanation
Indices: 25447210--25447256 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
25447200 GCCATTTTTA
*
25447210 TTTTTATTTTAATAT
1 TTTTTAATTTAAT-T
25447225 TTTTTAATTTAATT
1 TTTTTAATTTAATT
*
25447239 TTTTAAATTCTAATT
1 TTTTTAATT-TAATT
25447254 TTT
1 TTT
25447257 CTTTTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 9 0.31
15 20 0.69
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTAATT
Found at i:25454051 original size:16 final size:16
Alignment explanation
Indices: 25454030--25454061 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
25454020 CTTAGTTAAT
25454030 TCTTAGTTATTAGATC
1 TCTTAGTTATTAGATC
25454046 TCTTAGTTATTAGATC
1 TCTTAGTTATTAGATC
25454062 ACCTATTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
TCTTAGTTATTAGATC
Found at i:25456633 original size:25 final size:25
Alignment explanation
Indices: 25456605--25456662 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
25456595 CATGTAAACT
*
25456605 GGAAGCTCTTATGAGCCATATAACA
1 GGAAGCTCGTATGAGCCATATAACA
* * *
25456630 GGAAGCTCGTGTGAGCTATATAACG
1 GGAAGCTCGTATGAGCCATATAACA
25456655 GGAAGCTC
1 GGAAGCTC
25456663 AATCAAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (25 bp):
GGAAGCTCGTATGAGCCATATAACA
Found at i:25456671 original size:25 final size:25
Alignment explanation
Indices: 25456643--25456709 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
25456633 AGCTCGTGTG
*
25456643 AGCTATATAACGGGAAGCTCAATCA
1 AGCTATATATCGGGAAGCTCAATCA
* * *
25456668 AGCTATATATCGAGAAACTTAATCA
1 AGCTATATATCGGGAAGCTCAATCA
25456693 AGCTATATATCGGGAAG
1 AGCTATATATCGGGAAG
25456710 TTCATGCGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.24
Consensus pattern (25 bp):
AGCTATATATCGGGAAGCTCAATCA
Found at i:25476533 original size:21 final size:22
Alignment explanation
Indices: 25476509--25476552 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25476499 ACTATATATT
25476509 AATTCAATC-ATAT-AACATTTC
1 AATTCAATCAAT-TCAACATTTC
*
25476530 AATTCACTCAATTCAACATTTC
1 AATTCAATCAATTCAACATTTC
25476552 A
1 A
25476553 TTCTCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.41, C:0.23, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTCAATCAATTCAACATTTC
Found at i:25476933 original size:18 final size:19
Alignment explanation
Indices: 25476893--25476939 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
25476883 GCTCCCAACT
25476893 CATTTCACAATTTCATATTC
1 CATTTCAC-ATTTCATATTC
*
25476913 CATTTCACATTTCA-CTTC
1 CATTTCACATTTCATATTC
25476931 CATTTCACA
1 CATTTCACA
25476940 CCATTTGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
19 6 0.23
20 8 0.31
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (19 bp):
CATTTCACATTTCATATTC
Found at i:25480660 original size:42 final size:43
Alignment explanation
Indices: 25480561--25480719 Score: 157
Period size: 43 Copynumber: 3.7 Consensus size: 43
25480551 GGCTCGTACA
* *
25480561 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCAAATAACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACGTAATCAAATAACG
* *
25480604 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCATAT-ACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
* * *
25480646 ATGCCAATGCCCCAGACATGGTCTTACACGTTAATCTTAAAT--TG
1 ATGCCAATGTCCCAGACAGGGTCTTACACG-TAATC--AAATAACG
* *
25480690 ATGCCAACGTCCTAGAC-GTGGTCTTACACG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACG
25480720 ATAACACATT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
42 30 0.31
43 38 0.39
44 27 0.28
45 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACGTAATCAAATAACG
Found at i:25485991 original size:16 final size:16
Alignment explanation
Indices: 25485964--25485998 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
25485954 AATTTGAATC
25485964 TAATAATAAATT-ATT
1 TAATAATAAATTAATT
25485979 TAATAAGTAAATTAATT
1 TAATAA-TAAATTAATT
25485996 TAA
1 TAA
25485999 ATATGGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TAATAATAAATTAATT
Found at i:25487075 original size:19 final size:20
Alignment explanation
Indices: 25487030--25487084 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 20
25487020 ATCTTCAAGG
*
25487030 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATAT-AC
25487051 ATATGCAATCTTAGATAT-C
1 ATATGCAATCTTAGATATAC
25487070 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
25487085 AAAGATGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (20 bp):
ATATGCAATCTTAGATATAC
Found at i:25487855 original size:3 final size:3
Alignment explanation
Indices: 25487847--25487878 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
25487837 GATTTGTTTT
*
25487847 TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25487879 TTTGTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:25494422 original size:45 final size:45
Alignment explanation
Indices: 25494373--25494922 Score: 681
Period size: 45 Copynumber: 12.4 Consensus size: 45
25494363 GGAGTAGGTT
* * *
25494373 GAAGATAACAGATTTTGTCTTCCTGTATTGGCAGCGGAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
25494418 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAATTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
25494463 GAAGATAGCAGATCTTGTCTTCCTATGTTGGCAACGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * *
25494508 GAAGGTAGTAGATCTTGTCTTCCTGTATTGGTAGCAAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
25494553 GAAGATAGCAGATCTTGTCTTCCTGTACTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
*
25494598 GAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
** *
25494643 GAAGATAGCAGGCCTTGTCTTCCTCTATTGGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
25494688 GAAGATAGCATATATTGTCTTCCTGTATTGGCAAG-GAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGC-AGCGAAGTAGATC
* *
25494733 GAAGATAGCAAATCTTGTCTTCCTGTACT---AGC-----AG--C
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * *
25494768 GAAGATAGCAAATCTTGTTTTCCTGTATTAGCAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* *
25494813 AAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
* * * * * *
25494858 GAATATAGCAGATCCTGTCTTTCTGTATTGACAGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
***
25494903 GAAGATTTAAGATCTTGTCT
1 GAAGATAGCAGATCTTGTCT
25494923 CCCTAAGCAG
Statistics
Matches: 436, Mismatches: 57, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
35 28 0.06
37 2 0.00
38 3 0.01
41 2 0.00
43 2 0.00
45 397 0.91
46 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (45 bp):
GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
Found at i:25494778 original size:35 final size:35
Alignment explanation
Indices: 25494732--25494806 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
25494722 GGAAGTAGAT
25494732 CGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
* *
25494767 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGCAG
1 CGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
25494802 CGAAG
1 CGAAG
25494807 TAGATCAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (35 bp):
CGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
Found at i:25494820 original size:80 final size:80
Alignment explanation
Indices: 25494687--25494851 Score: 242
Period size: 80 Copynumber: 2.1 Consensus size: 80
25494677 CGAAGTAGAT
* * *
25494687 CGAAGATAGCATATATTGTCTTCCTGTATTGGCAAGGAAGTAGATCGAAGATAGCAAATCTTGTC
1 CGAAGATAGCAAATATTGTCTTCCTGTATTAGCAAGGAAGTAGATCAAAGATAGCAAATCTTGTC
25494752 TTCCTGTACTAGCAG
66 TTCCTGTACTAGCAG
* * *
25494767 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGC-AGCGAAGTAGATCAAAGATAGCAGATCTTGT
1 CGAAGATAGCAAATATTGTCTTCCTGTATTAGCAAG-GAAGTAGATCAAAGATAGCAAATCTTGT
* *
25494831 CTTCCTGTATTGGCAG
65 CTTCCTGTACTAGCAG
25494847 CGAAG
1 CGAAG
25494852 TAGATTGAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
79 2 0.03
80 74 0.97
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (80 bp):
CGAAGATAGCAAATATTGTCTTCCTGTATTAGCAAGGAAGTAGATCAAAGATAGCAAATCTTGTC
TTCCTGTACTAGCAG
Found at i:25494866 original size:125 final size:125
Alignment explanation
Indices: 25494521--25494884 Score: 372
Period size: 125 Copynumber: 2.8 Consensus size: 125
25494511 GGTAGTAGAT
* * * * ** * *
25494521 CTTGTCTTCCTGTATTGGTAGCAAAGTAGATTGAAGATAGCAGATCTTGTCTTCCTGTACTGGC-
1 CTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTCTTCCTGTATTGGCA
* * * *
25494585 AGCGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATA
66 AG-GAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTACT---AGC-----AG--CGAAGATA
**
25494650 GCAGGC
120 GCAAAC
* * *
25494656 CTTGTCTTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTCTTCCTGTATTGGCA
1 CTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTCTTCCTGTATTGGCA
* *
25494721 AGGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAGCGAAGATAGCAAAT
66 AGGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTACTAGCAGCGAAGATAGCAAAC
* * *
25494781 CTTGTTTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTGTATTGGC-
1 CTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTCTTCCTGTATTGGCA
* * * *
25494845 AGCGAAGTAGATTGAATATAGCAGATCCTGTCTTTCTGTA
66 AG-GAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTA
25494885 TTGACAGTGA
Statistics
Matches: 203, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
124 2 0.01
125 101 0.50
127 2 0.01
132 3 0.01
135 93 0.46
136 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (125 bp):
CTTGTCTTCCTCTATTAGCAGCGAAGTAGATCAAAGATAGCAGATATTGTCTTCCTGTATTGGCA
AGGAAGTAGATCGAAGATAGCAAATCCTGTCTTCCTGTACTAGCAGCGAAGATAGCAAAC
Found at i:25494922 original size:170 final size:170
Alignment explanation
Indices: 25494597--25494908 Score: 464
Period size: 170 Copynumber: 1.8 Consensus size: 170
25494587 CGAAGTAGAT
* * * *
25494597 CGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAGGCCTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
* * *
25494662 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCATATATTGTCTTCCTGTATTGGCAAGGAAG
66 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCAGATACTGTCTTCCTGTATTGACAAGGAAG
25494727 TAGATCGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
131 TAGATCGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
* * *
25494767 CGAAGATAGCAAATCTTGTTTTCCTGTATTAGCAGCGAAGTAGATCAAAGATAGCAGATCTTGTC
1 CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
* * * * *
25494832 TTCCTGTATTGGCAGCGAAGTAGATTGAATATAGCAGATCCTGTCTTTCTGTATTGAC-AGTGAA
66 TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCAGATACTGTCTTCCTGTATTGACAAG-GAA
*
25494896 GTAGATTGAAGAT
130 GTAGATCGAAGAT
25494909 TTAAGATCTT
Statistics
Matches: 125, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
169 2 0.02
170 123 0.98
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (170 bp):
CGAAGATAGCAAATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGATAGCAGACCTTGTC
TTCCTCTATTGGCAGCGAAGTAGATCGAAGATAGCAGATACTGTCTTCCTGTATTGACAAGGAAG
TAGATCGAAGATAGCAAATCTTGTCTTCCTGTACTAGCAG
Found at i:25495094 original size:44 final size:44
Alignment explanation
Indices: 25495046--25495217 Score: 107
Period size: 44 Copynumber: 3.9 Consensus size: 44
25495036 AAGATTGTAG
25495046 ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAACAA
1 ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAACAA
* * ** * *
25495090 ATCCTATCTTCCC-AAGGCACTAG-GGAAGCAGATTTAA-GCCACCA
1 ATCCTGTC-TCCCTAA-GCAGTAGTGG-AGCAGATCGAAGGCAACAA
* * * * * * ****** *
25495134 ATCCTTTTTCCCTGAGCAGCAGTGGAGTAGGTCGAATATTGTAG
1 ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAACAA
* *
25495178 ATCATGTATCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
1 ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
25495218 GCGAATCTTA
Statistics
Matches: 89, Mismatches: 33, Indels: 12
0.66 0.25 0.09
Matches are distributed among these distances:
43 16 0.18
44 54 0.61
45 19 0.21
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (44 bp):
ATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCAACAA
Found at i:25495230 original size:132 final size:132
Alignment explanation
Indices: 25494889--25495230 Score: 438
Period size: 132 Copynumber: 2.6 Consensus size: 132
25494879 TCTGTATTGA
* * * *
25494889 CAGTGAAGTAGATTGAAGATT-TAAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAA-G-
1 CAGTGGAGTAGGTCGAAGATTGT-AGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGC
* * * * *
25494951 ATGATAAATCTTATCTTGCTAAGGTAATAGGGAAGCAAATTTAAGCCACCAGTCCTATCTCCCTG
65 A-G-CAAATCTTATCTTCCCAAGGCAATAGGGAAGCAAATTTAAGCCACCAATCCTATCTCCCTG
*
25495016 AGTAG
128 AGCAG
* * *
25495021 CGGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
1 CAGTGGAGTAGGTCGAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
* * * * * *
25495086 ACAAATCCTATCTTCCCAAGGCACTAGGGAAGCAGATTTAAGCCACCAATCCTTTTTCCCTGAGC
66 GCAAATCTTATCTTCCCAAGGCAATAGGGAAGCAAATTTAAGCCACCAATCCTATCTCCCTGAGC
25495151 AG
131 AG
* *
25495153 CAGTGGAGTAGGTCGAATATTGTAGATCATGTATCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
1 CAGTGGAGTAGGTCGAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
*
25495218 GCGAATCTTATCT
66 GCAAATCTTATCT
25495231 CCTTGGTGTT
Statistics
Matches: 183, Mismatches: 24, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
132 180 0.98
133 2 0.01
134 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (132 bp):
CAGTGGAGTAGGTCGAAGATTGTAGATCATGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGGCA
GCAAATCTTATCTTCCCAAGGCAATAGGGAAGCAAATTTAAGCCACCAATCCTATCTCCCTGAGC
AG
Found at i:25495405 original size:44 final size:45
Alignment explanation
Indices: 25495312--25495405 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 45
25495302 AGATCAAGAC
* *
25495312 TGAAGATAACCAACCTTATCTCATTGAAGTTACAGTGGAGCCGGT
1 TGAAGATAACCAACCTTATCTCATTGAAGTTACAGTGGAGCAGGG
* * * *
25495357 TGAAGAT-ATCAATCTTATCTC-TCTGAAGTTGCAGTGGAGTAGGG
1 TGAAGATAACCAACCTTATCTCAT-TGAAGTTACAGTGGAGCAGGG
25495401 TGAAG
1 TGAAG
25495406 GAAGTGAGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 34 0.81
45 7 0.17
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (45 bp):
TGAAGATAACCAACCTTATCTCATTGAAGTTACAGTGGAGCAGGG
Found at i:25495766 original size:22 final size:23
Alignment explanation
Indices: 25495738--25495782 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
25495728 ATGCAATCTT
25495738 AGATATGATATT-CAATCTTAGA
1 AGATATGATATTGCAATCTTAGA
* *
25495760 AGATATGATTTTGTAATCTTAGA
1 AGATATGATATTGCAATCTTAGA
25495783 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (23 bp):
AGATATGATATTGCAATCTTAGA
Found at i:25498530 original size:20 final size:18
Alignment explanation
Indices: 25498492--25498539 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 18
25498482 GACCAATATT
*
25498492 ATATTATTTTTCTTGTCAA
1 ATATT-TTTTTATTGTCAA
*
25498511 CAGTATTTTTTTATTTTCAA
1 -A-TATTTTTTTATTGTCAA
25498531 ATATTTTTT
1 ATATTTTTT
25498540 AAATTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
20 12 0.48
21 4 0.16
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.62
Consensus pattern (18 bp):
ATATTTTTTTATTGTCAA
Found at i:25499662 original size:32 final size:32
Alignment explanation
Indices: 25499616--25499686 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
25499606 TCTAAATTTC
* ** *
25499616 TAATCAATCCTAATTTCTTTGAGGGTTTGTAT
1 TAATCAATACTAATTTCTTCAAGGATTTGTAT
*
25499648 TAATCAATATTAATTTCTTCAAGGATTTGTAT
1 TAATCAATACTAATTTCTTCAAGGATTTGTAT
25499680 TAATCAA
1 TAATCAA
25499687 CCTCTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (32 bp):
TAATCAATACTAATTTCTTCAAGGATTTGTAT
Found at i:25501005 original size:38 final size:38
Alignment explanation
Indices: 25500923--25501017 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
25500913 ATACAGAAAT
* * * *
25500923 AGTAGACATGCTTAACATGTAATCAATTCAATAGTAGC
1 AGTAAACATGCTTAACATGTAATCAATTAAACAATAGC
* *
25500961 AATAAACATGCTTAACATGTATTCAATTAAACAATCA-C
1 AGTAAACATGCTTAACATGTAATCAATTAAACAAT-AGC
*
25500999 AGTAAACATGCTTCACATG
1 AGTAAACATGCTTAACATG
25501018 CTTTCAGTTC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 47 0.98
39 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (38 bp):
AGTAAACATGCTTAACATGTAATCAATTAAACAATAGC
Found at i:25506922 original size:18 final size:19
Alignment explanation
Indices: 25506888--25506923 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25506878 ATCTCATGCC
*
25506888 ACAGTTCAAATAAAACATT
1 ACAGTTCAAACAAAACATT
25506907 ACAGTTC-AACAAAACAT
1 ACAGTTCAAACAAAACAT
25506924 AAATTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.19, G:0.06, T:0.22
Consensus pattern (19 bp):
ACAGTTCAAACAAAACATT
Found at i:25507583 original size:38 final size:38
Alignment explanation
Indices: 25507532--25507674 Score: 175
Period size: 38 Copynumber: 3.8 Consensus size: 38
25507522 AAAAACAATG
* *
25507532 GACATGCTTAACATGTAATCAGTTCAAC-GATAGCATTA
1 GACATGCTTAACATGTATTCAGTTCAACAG-TAGCAGTA
*
25507570 GACATGCTTAACATGTATTCAGTTCAACAGTCGCAGTA
1 GACATGCTTAACATGTATTCAGTTCAACAGTAGCAGTA
*
25507608 GACATGCTTAACATGTATTCAGGTCAACAGTCA-CAGTA
1 GACATGCTTAACATGTATTCAGTTCAACAGT-AGCAGTA
* * *
25507646 GGCATGCTTCACATGCT-TTCAGGTCAACA
1 GACATGCTTAACATG-TATTCAGTTCAACA
25507675 ATTGCAGTGT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
38 93 0.98
39 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (38 bp):
GACATGCTTAACATGTATTCAGTTCAACAGTAGCAGTA
Found at i:25518583 original size:44 final size:44
Alignment explanation
Indices: 25518482--25518583 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
25518472 AGAACCTACT
25518482 TTTGGCTGTGGATTACACAACAACTAACCACAGATGGAATCTATC
1 TTTGGCTGTGGA-TACACAACAACTAACCACAGATGGAATCTATC
* *** * * * *
25518527 TCTAATTATGGATACACAACAAGTACCCACAGATGGAATCTGTC
1 TTTGGCTGTGGATACACAACAACTAACCACAGATGGAATCTATC
25518571 TTTGGCTGTGGAT
1 TTTGGCTGTGGAT
25518584 GTACAGCAAA
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
44 37 0.84
45 7 0.16
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (44 bp):
TTTGGCTGTGGATACACAACAACTAACCACAGATGGAATCTATC
Found at i:25523367 original size:64 final size:64
Alignment explanation
Indices: 25523266--25523398 Score: 223
Period size: 64 Copynumber: 2.1 Consensus size: 64
25523256 TAAAAGCCCT
*
25523266 CAAATATGCATTTAAAAACTCCAATAGTTTTAGTCAAAATATGCCAAT-CAAATAAGATAAAATA
1 CAAATATGCATTTAAAAACTCCAATAGTTTTAGTCAAAATATGCC-ATCCAAATAAGATAAAACA
* *
25523330 CAAATATGTATTTAAAAACTCTAATAGTTTTAGTCAAAATATGCCATCCAAATAAGATAAAACA
1 CAAATATGCATTTAAAAACTCCAATAGTTTTAGTCAAAATATGCCATCCAAATAAGATAAAACA
25523394 CAAAT
1 CAAAT
25523399 GGCTTGCAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
63 2 0.03
64 63 0.97
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.29
Consensus pattern (64 bp):
CAAATATGCATTTAAAAACTCCAATAGTTTTAGTCAAAATATGCCATCCAAATAAGATAAAACA
Found at i:25541859 original size:34 final size:35
Alignment explanation
Indices: 25541792--25541881 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 35
25541782 TTTTATAATT
* *
25541792 TATATATGTA-AT-TATTTTTTTATAATCTATATA
1 TATATATATATATATATTTTTTTATAATATATATA
* * *
25541825 TATATGTATATATCTATTTTTTTAT-ATATGTATA
1 TATATATATATATATATTTTTTTATAATATATATA
* *
25541859 TGTATATATATTTATATTTTTTT
1 TATATATATATATATATTTTTTT
25541882 TCTAAAGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 8 0.17
34 28 0.60
35 11 0.23
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.61
Consensus pattern (35 bp):
TATATATATATATATATTTTTTTATAATATATATA
Found at i:25541872 original size:24 final size:24
Alignment explanation
Indices: 25541823--25541875 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
25541813 ATAATCTATA
* * *
25541823 TATATATGTATATATCTATTTTTT
1 TATATATGTATATATATATATATT
*
25541847 TATATATGTATATGTATATATATT
1 TATATATGTATATATATATATATT
25541871 TATAT
1 TATAT
25541876 TTTTTTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TATATATGTATATATATATATATT
Found at i:25548810 original size:21 final size:21
Alignment explanation
Indices: 25548770--25548811 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
25548760 ACGTGATGTG
*
25548770 AAAAAATGAAGAAATGAAAAT
1 AAAAAATGAAGAAATAAAAAT
25548791 AAAAAATGAA-AAAGTAAAAAT
1 AAAAAATGAAGAAA-TAAAAAT
25548812 GGAAAGGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAAAATGAAGAAATAAAAAT
Found at i:25550145 original size:44 final size:44
Alignment explanation
Indices: 25550095--25550246 Score: 128
Period size: 44 Copynumber: 3.5 Consensus size: 44
25550085 AATAGCAGAT
*
25550095 CTTGTCTTCCTGTATCAGTAGCGAAGTAGATAGAAGATACCAGC
1 CTTGTCTTCCTGTATCAGCAGCGAAGTAGATAGAAGATACCAGC
* * * * * * * * *
25550139 CTTGTCTTCTTG-AGCAGCAGTGGAGTAGGTTGAAAATAGCAGAT
1 CTTGTCTTCCTGTATCAGCAGCGAAGTAGATAGAAGATACCAG-C
* ** * *
25550183 CTTGTCTTCCTATATTGGCAGCGAAGTGGATCGAAGATACCAGC
1 CTTGTCTTCCTGTATCAGCAGCGAAGTAGATAGAAGATACCAGC
* *
25550227 CTTGTCTCCCTG-AGCAGCAG
1 CTTGTCTTCCTGTATCAGCAG
25550247 TGGAGTAGGT
Statistics
Matches: 78, Mismatches: 28, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
43 27 0.35
44 31 0.40
45 20 0.26
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (44 bp):
CTTGTCTTCCTGTATCAGCAGCGAAGTAGATAGAAGATACCAGC
Found at i:25550159 original size:88 final size:88
Alignment explanation
Indices: 25550055--25550292 Score: 352
Period size: 88 Copynumber: 2.7 Consensus size: 88
25550045 CTCAGCTTTA
* *
25550055 TCTCTCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCTTGTCTTCCTGTATCAGTAGCGAA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATCAGTAGCGAA
25550120 GTAGATAGAAGATACCAGCCTTG
66 GTAGATAGAAGATACCAGCCTTG
* * * ** *
25550143 TCTTCTTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTATATTGGCAGCGAA
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATCAGTAGCGAA
* *
25550208 GTGGATCGAAGATACCAGCCTTG
66 GTAGATAGAAGATACCAGCCTTG
* *
25550231 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAACAGATCTTGCCTTCCTGTA-CTAGTAGC
1 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATC-AGTAGC
25550293 AAAGCAAATC
Statistics
Matches: 131, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
88 131 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (88 bp):
TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGTCTTCCTGTATCAGTAGCGAA
GTAGATAGAAGATACCAGCCTTG
Found at i:25550719 original size:49 final size:49
Alignment explanation
Indices: 25550665--25550823 Score: 167
Period size: 49 Copynumber: 3.2 Consensus size: 49
25550655 GAAGTTACAA
25550665 CGGTGAATCTTGTTTCCCGACATTGCAATTAAAAAGATTGAGGCCACAG
1 CGGTGAATCTTGTTTCCCGACATTGCAATTAAAAAGATTGAGGCCACAG
** * * ** * ** * * *
25550714 CGGTGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTAC-G
1 CGGTGAATCTTGTTTCC-CGACATTGCAATTAAAAAGATTGAGGCCACAG
**
25550763 ACGACGAATCTTGTTTCCCGACATTGCAATTAAAAAGATTGAGGCCACAG
1 -CGGTGAATCTTGTTTCCCGACATTGCAATTAAAAAGATTGAGGCCACAG
25550813 CGGTGAATCTT
1 CGGTGAATCTT
25550824 ACTTCCTTGG
Statistics
Matches: 79, Mismatches: 28, Indels: 6
0.70 0.25 0.05
Matches are distributed among these distances:
49 45 0.57
50 34 0.43
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (49 bp):
CGGTGAATCTTGTTTCCCGACATTGCAATTAAAAAGATTGAGGCCACAG
Found at i:25550772 original size:50 final size:50
Alignment explanation
Indices: 25550620--25550873 Score: 174
Period size: 50 Copynumber: 5.1 Consensus size: 50
25550610 TTGAAGCCAC
* * * * * *
25550620 AATCTTACTTCCCTGGCGATGTAGTGGAACAAATTGAAGTTACAACGGTG
1 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTG
** * * ** * ** * * *
25550670 AATCTTGTTTCC-CGACATTGCAATTAAAAAGATTGAGGCCAC-AGCGGTG
1 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGA-CGGTG
**
25550719 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGACG
1 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTG
** * * ** * ** * * *
25550769 AATCTTGTTTCC-CGACATTGCAATTAAAAAGATTGAGGCCAC-AGCGGTG
1 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGA-CGGTG
25550818 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTG
1 AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTG
25550868 AATCTT
1 AATCTT
25550874 GTCTTCCCGA
Statistics
Matches: 143, Mismatches: 55, Indels: 12
0.68 0.26 0.06
Matches are distributed among these distances:
48 2 0.01
49 65 0.45
50 74 0.52
51 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (50 bp):
AATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTG
Found at i:25550772 original size:99 final size:99
Alignment explanation
Indices: 25550519--25550896 Score: 538
Period size: 99 Copynumber: 3.9 Consensus size: 99
25550509 ATATTGAAGT
* * * *
25550519 CACAACGGCGAATCTTACTTCCTTGGCGATGTAGTGGAACAGATTGAAGCTACTACGGTGAATCT
1 CACAGCGGTGAATCTTACTTCCTTGGCGATGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
* *
25550584 TGTTTCCCGACATTGCAATT-AATAGATTGAAG-
66 TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
* * * * *
25550616 C-CA-C----AATCTTACTTCCCTGGCGATGTAGTGGAACAAATTGAAGTTACAACGGTGAATCT
1 CACAGCGGTGAATCTTACTTCCTTGGCGATGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
25550675 TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
66 TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
* **
25550709 CACAGCGGTGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCT
1 CACAGCGGTGAATCTTACTTCCTTGGCGATGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
25550774 TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
66 TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
*
25550808 CACAGCGGTGAATCTTACTTCCTTGGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
1 CACAGCGGTGAATCTTACTTCCTTGGCGATGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
* *
25550873 TGTCTTCCCGACATTACAGTTAAA
66 TGT-TTCCCGACATTGCAATTAAA
25550897 TAGAAGAACC
Statistics
Matches: 254, Mismatches: 18, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
91 71 0.28
92 10 0.04
93 1 0.00
94 2 0.01
95 2 0.01
96 2 0.01
97 1 0.00
99 147 0.58
100 18 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (99 bp):
CACAGCGGTGAATCTTACTTCCTTGGCGATGCAGTGGAACAGATTGAAGCTACGACGGTGAATCT
TGTTTCCCGACATTGCAATTAAAAAGATTGAGGC
Found at i:25551055 original size:45 final size:45
Alignment explanation
Indices: 25550992--25551379 Score: 245
Period size: 45 Copynumber: 8.8 Consensus size: 45
25550982 GATCGCATCC
* *
25550992 AGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGACGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * * *
25551037 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGA-TTAA-A-GCCAA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGC-A
* ** * * * *
25551080 TAATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAG-T-G-A
1 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * *
25551123 TAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCG--CAT--CT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGATGGCA
* * * * **
25551165 AGTCTTATCCCCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* *
25551210 AGTCTTATCTCCCTGAAGTTACAGTGGAGCA-AGCTG-AG-TAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGAT-GGCA
*
25551254 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCGGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTGAAGATGGCA
* * **
25551299 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
* * * *
25551344 AGTGTTATCCCCCTGAAATTGCAGTGGGGCAGACTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTG
25551380 GATAAACAAA
Statistics
Matches: 265, Mismatches: 53, Indels: 50
0.72 0.14 0.14
Matches are distributed among these distances:
40 19 0.07
41 8 0.03
42 5 0.02
43 15 0.06
44 82 0.31
45 131 0.49
46 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (45 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATGGCA
Found at i:25551135 original size:44 final size:44
Alignment explanation
Indices: 25551037--25551145 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 44
25551027 GACGATGGCA
*
25551037 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAAT
** * * **
25551081 AATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAG-TGAT
1 AATCTTATCTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAAT
*
25551124 AGATCTTATCTCTCTGAAGTTG
1 A-ATCTTATCTCCCTGAAGTTG
25551146 CAGAGAGCAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.06
44 51 0.94
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGAAGTGAAGCAGATTAAAGCCAAT
Found at i:25551218 original size:173 final size:174
Alignment explanation
Indices: 25550907--25551229 Score: 513
Period size: 173 Copynumber: 1.9 Consensus size: 174
25550897 TAGAAGAACC
* * *
25550907 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATAAAAATGATGGATCTTATCTCTCTGAAGTTG
1 AATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATAAAAATGATAGATCTTATCTCTCTGAAGTTG
* * * **
25550972 CAAAAGAGCAGATCGCATCCAGTCTTATCCTCCTGAAGTTGCAGTGGGGCAGACTGACGATGGCA
66 CAAAAGAGCAGATCGCATCCAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCA
25551037 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTAAAGCCAAT
131 AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTAAAGCCAAT
* *
25551081 AATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATTAAAGTGATAGATCTTATCTCTCTGAAGTTG
1 AATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATAAAAATGATAGATCTTATCTCTCTGAAGTTG
* * *
25551146 C-AGAGAGCAGATCGCATCTAGTCTTATCCCCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCA
66 CAAAAGAGCAGATCGCATCCAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCA
*
25551210 AGTCTTATCTCCCTGAAGTT
131 AATCTTATCTCCCTGAAGTT
25551230 ACAGTGGAGC
Statistics
Matches: 135, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
173 74 0.55
174 61 0.45
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (174 bp):
AATCCCATCTCCCTGAAGTTGAAGTGGAGCGGATAAAAATGATAGATCTTATCTCTCTGAAGTTG
CAAAAGAGCAGATCGCATCCAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCA
AATCTTATCTCCCTGAAGTTGTAGTGAAGCAGATTAAAGCCAAT
Found at i:25551275 original size:89 final size:90
Alignment explanation
Indices: 25551165--25551378 Score: 304
Period size: 89 Copynumber: 2.4 Consensus size: 90
25551155 GATCGCATCT
*
25551165 AGTCTTATCCCCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAGTT
1 AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAGTT
* * *
25551230 ACAGTGGAGCAAGCT-GAGTAAGCA
66 ACAGTGGAGCAAACTCAAGAAAGCA
* * * * **
25551254 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCGGACTGAAGATGGCAAGTCTTATCTCCCTGAAGTT
1 AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAGTT
*
25551319 GCAGTGGAGCAAACTCAAGAAAGCA
66 ACAGTGGAGCAAACTCAAGAAAGCA
* *
25551344 AGTGTTATCCCCCTGAAATTGCAGTGGGGCAGACT
1 AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT
25551379 GGATAAACAA
Statistics
Matches: 108, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 71 0.66
90 37 0.34
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (90 bp):
AGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAGTT
ACAGTGGAGCAAACTCAAGAAAGCA
Found at i:25551407 original size:134 final size:134
Alignment explanation
Indices: 25551165--25551413 Score: 315
Period size: 134 Copynumber: 1.9 Consensus size: 134
25551155 GATCGCATCT
* * * * *
25551165 AGTCTTATCCCCCTGAGGTTGCAGTGGGGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAGTT
1 AGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
* * ** *
25551230 ACAGTGGAGCAAGCTGAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCGGACTGAAGAT
66 ACAGTGGAGCAAGCTGAGTAAACAAATCCAATCCTCCTAAAGTTGCAGTGAGGCGGACTGAAGAT
25551295 GGCA
131 GGCA
* *
25551299 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGCAAGTGTTATCCCCCTGAAATT
1 AGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
* * *
25551364 GCAGTGGGGC-AGACTG-GATAAACAAATCCAAT-CTACCTAAAGTTGTAGTG
66 ACAGTGGAGCAAG-CTGAG-TAAACAAATCCAATCCT-CCTAAAGTTGCAGTG
25551414 GAGTAGATTA
Statistics
Matches: 97, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
133 5 0.05
134 92 0.95
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (134 bp):
AGTCTTATCCCCCTGAAGTTGCAGTGGAGCAAACTCAAGAAAGCAAGTCTTATCCCCCTGAAATT
ACAGTGGAGCAAGCTGAGTAAACAAATCCAATCCTCCTAAAGTTGCAGTGAGGCGGACTGAAGAT
GGCA
Found at i:25551793 original size:33 final size:32
Alignment explanation
Indices: 25551756--25551818 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
25551746 AACAGTCCTT
* *
25551756 TTACAATAAAATGGGCCCAAAACCCAAACCCAA
1 TTACAACAAAATAGGCCC-AAACCCAAACCCAA
*
25551789 TTACAACAAAATAGGCCCAAACCCAGACCC
1 TTACAACAAAATAGGCCCAAACCCAAACCC
25551819 GATTTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.11
Consensus pattern (32 bp):
TTACAACAAAATAGGCCCAAACCCAAACCCAA
Found at i:25553055 original size:34 final size:35
Alignment explanation
Indices: 25552988--25553077 Score: 96
Period size: 34 Copynumber: 2.7 Consensus size: 35
25552978 TTTTATAATT
* *
25552988 TATATATGTA-AT-TATTTTTTTATAATCTATATA
1 TATATATATATATATATTTTTTTATAATATATATA
* * *
25553021 TATATGTATATATCTATTTTTTTAT-ATATGTATA
1 TATATATATATATATATTTTTTTATAATATATATA
* *
25553055 TGTATATATATTTATATTTTTTT
1 TATATATATATATATATTTTTTT
25553078 TCTAAAGAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 8 0.17
34 28 0.60
35 11 0.23
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.61
Consensus pattern (35 bp):
TATATATATATATATATTTTTTTATAATATATATA
Found at i:25553068 original size:24 final size:24
Alignment explanation
Indices: 25553019--25553071 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
25553009 ATAATCTATA
* * *
25553019 TATATATGTATATATCTATTTTTT
1 TATATATGTATATATATATATATT
*
25553043 TATATATGTATATGTATATATATT
1 TATATATGTATATATATATATATT
25553067 TATAT
1 TATAT
25553072 TTTTTTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.02, G:0.06, T:0.58
Consensus pattern (24 bp):
TATATATGTATATATATATATATT
Found at i:25553505 original size:27 final size:26
Alignment explanation
Indices: 25553459--25553509 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
25553449 ATGTCATTGA
*
25553459 TTATTTTTTTATGTACATTAGTTTCGT
1 TTATTTATTTATGTACATTA-TTTCGT
* *
25553486 TTATTTATTTATTTATATTATTTC
1 TTATTTATTTATGTACATTATTTC
25553510 TATACCATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.67
Consensus pattern (26 bp):
TTATTTATTTATGTACATTATTTCGT
Found at i:25555054 original size:28 final size:28
Alignment explanation
Indices: 25555004--25555057 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
25554994 TGTAATTATT
**
25555004 ATTATTACTTTTAAAATTTATATATATA
1 ATTATTACTTTTAAAATCCATATATATA
* *
25555032 ATTATTATTTTTATAATCCATATATA
1 ATTATTACTTTTAAAATCCATATATA
25555058 CAAGTGNNNN
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTATTACTTTTAAAATCCATATATATA
Found at i:25558964 original size:11 final size:11
Alignment explanation
Indices: 25558948--25558973 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25558938 AAAAATTAAA
25558948 AAAACTATTTT
1 AAAACTATTTT
25558959 AAAACTATTTT
1 AAAACTATTTT
25558970 AAAA
1 AAAA
25558974 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAACTATTTT
Found at i:25558996 original size:39 final size:39
Alignment explanation
Indices: 25558938--25559068 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 39
25558928 AATTTATTTT
25558938 AAAAATTAAAAAAACTATTTTAAAACTATTTTAAAATTAA
1 AAAAATTAAAAAAACTATTTTAAAA-TATTTTAAAATTAA
* *
25558978 AAAAATTAAAAAAA-TATTTTTAAAAAATTTTAAATTTTAA
1 AAAAATTAAAAAAACTA-TTTTAAAATATTTTAAA-ATTAA
* *
25559018 AAAATTTAAAAAAAGTATTTTAAAAGTATTTTAATAA-TAA
1 AAAAATTAAAAAAACTATTTTAAAA-TATTTTAA-AATTAA
*
25559058 AATAA-TAAAAA
1 AAAAATTAAAAA
25559069 TATTTATTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
39 16 0.20
40 53 0.67
41 9 0.11
42 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (39 bp):
AAAAATTAAAAAAACTATTTTAAAATATTTTAAAATTAA
Found at i:25559019 original size:16 final size:17
Alignment explanation
Indices: 25558995--25559027 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25558985 AAAAAAATAT
*
25558995 TTTTAAAAAATTTTAAA
1 TTTTAAAAAAATTTAAA
25559012 TTTT-AAAAAATTTAAA
1 TTTTAAAAAAATTTAAA
25559028 AAAAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAAAAAATTTAAA
Found at i:25559146 original size:11 final size:11
Alignment explanation
Indices: 25559130--25559155 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25559120 GCTAATTAAA
25559130 AAAACTATTTT
1 AAAACTATTTT
25559141 AAAACTATTTT
1 AAAACTATTTT
25559152 AAAA
1 AAAA
25559156 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAACTATTTT
Found at i:25559181 original size:40 final size:39
Alignment explanation
Indices: 25559123--25559257 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 39
25559113 AAGTTGTGCT
25559123 AATTAAAAAAACTATTTTAAAACTATTTTAAAATTAAAAA
1 AATTAAAAAAACTATTTTAAAA-TATTTTAAAATTAAAAA
* *
25559163 AATTAAAAAAA-TATTTTTAAAAAATTTTAAATTTTAAAAA
1 AATTAAAAAAACTA-TTTTAAAATATTTTAAA-ATTAAAAA
* *
25559203 ATTTAAAAAAAGTATTTTAAAAGTATTTTAAAA--AAATAA
1 AATTAAAAAAACTATTTTAAAA-TATTTTAAAATTAAA-AA
* *
25559242 AAATAAAAAAATTATT
1 AATTAAAAAAACTATT
25559258 ATAGGCCCGG
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
38 3 0.04
39 25 0.30
40 44 0.54
41 10 0.12
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (39 bp):
AATTAAAAAAACTATTTTAAAATATTTTAAAATTAAAAA
Found at i:25559201 original size:16 final size:17
Alignment explanation
Indices: 25559177--25559209 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25559167 AAAAAAATAT
*
25559177 TTTTAAAAAATTTTAAA
1 TTTTAAAAAAATTTAAA
25559194 TTTT-AAAAAATTTAAA
1 TTTTAAAAAAATTTAAA
25559210 AAAAGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAAAAAATTTAAA
Found at i:25559223 original size:23 final size:24
Alignment explanation
Indices: 25559193--25559238 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
25559183 AAAATTTTAA
25559193 ATTTTAAAA-AATTTAAAAAAAGT
1 ATTTTAAAAGAATTTAAAAAAAGT
*
25559216 ATTTTAAAAGTATTTTAAAAAAA
1 ATTTTAAAAG-AATTTAAAAAAA
25559239 TAAAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
ATTTTAAAAGAATTTAAAAAAAGT
Found at i:25563750 original size:199 final size:199
Alignment explanation
Indices: 25563527--25563912 Score: 569
Period size: 199 Copynumber: 1.9 Consensus size: 199
25563517 AGTGGAGCAG
* *
25563527 ATTGAAGCTGCAACGGCGAATCTTACTCCCCTGGCAGTATAGTGGAACAGATTGAAGCTACAACG
1 ATTGAAGCCGCAACGGCGAATCTTACTCCACTGGCAGTATAGTGGAACAGATTGAAGCTACAACG
25563592 ACGAATCTTGTTTCCCCAACATTGCAATT-AAAAGATTGAAGCCGCAACAGCGAATCTTACTTTC
66 ACGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCAACAGCGAATCTTAC-TTC
* * ** **
25563656 C-TGGTGGTGTAGTGGAGTAGATTGAAGCTACGACGGTGAATCTTGTTTCCCCAACATTGCAATT
130 CTTGGTGGTATAGTGAAACAGATTGAAGCTACGACGGCAAATCTTG-TTCCCCAACATTGCAATT
25563720 AAAAAT
194 AAAAAT
* * * * * *
25563726 ATTGAAGCCGCAACGGCGAATCTTACTTCACTGGCGGTGTAGTGGAGCAGATTGAAGCTACGATG
1 ATTGAAGCCGCAACGGCGAATCTTACTCCACTGGCAGTATAGTGGAACAGATTGAAGCTACAACG
** *
25563791 GTGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCC
66 ACGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCAACAGCGAATCTTACTTCC
* *
25563856 TTTGTGGTATAGTGAAACAGATTGAAGCTACGACGGCAAATCTTGTTCCCCGACATT
131 TTGGTGGTATAGTGAAACAGATTGAAGCTACGACGGCAAATCTTGTTCCCCAACATT
25563913 CTAGTTAAAC
Statistics
Matches: 166, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
199 99 0.60
200 67 0.40
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.27
Consensus pattern (199 bp):
ATTGAAGCCGCAACGGCGAATCTTACTCCACTGGCAGTATAGTGGAACAGATTGAAGCTACAACG
ACGAATCTTGTTTCCCCAACATTGCAATTAAAAAGATTGAAGCCGCAACAGCGAATCTTACTTCC
TTGGTGGTATAGTGAAACAGATTGAAGCTACGACGGCAAATCTTGTTCCCCAACATTGCAATTAA
AAAT
Found at i:25563778 original size:100 final size:99
Alignment explanation
Indices: 25563525--25563929 Score: 537
Period size: 100 Copynumber: 4.1 Consensus size: 99
25563515 GCAGTGGAGC
* * * *
25563525 AGATTGAAGCTGCAACGGCGAATCTTACTCCCCTGGCAGTATAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCGCAACGGCGAATCTTACT-TCCTGGCGGTATAGTGGAACAGATTGAAGCTACGA
*
25563590 CGACGAATCTTGTTTCCCCAACATTGCAATT-AAA
65 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * **
25563624 AGATTGAAGCCGCAACAGCGAATCTTACTTTCCTGGTGGTGTAGTGGAGTAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTAC-TTCCTGGCGGTATAGTGGAACAGATTGAAGCTACGA
*
25563689 CGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
65 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * *
25563724 ATATTGAAGCCGCAACGGCGAATCTTACTTCACTGGCGGTGTAGTGGAGCAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTC-CTGGCGGTATAGTGGAACAGATTGAAGCTACGA
* *
25563789 TGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
65 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * *
25563824 AGATTGAAGCCGCAACGGCGAATCTTACTTCCTTTGTGGTATAGTGAAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCC-TGGCGGTATAGTGGAACAGATTGAAGCTACGA
* * * *
25563889 CGGCAAATCTTG-TTCCCCGACATT-CTAGTTAAAC
65 CGGCGAATCTTGTTTCCCCAACATTGC-AATTAAAA
25563923 AGATTGA
1 AGATTGA
25563930 GGATATCAGG
Statistics
Matches: 273, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
98 1 0.00
99 111 0.41
100 161 0.59
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (99 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTTCCTGGCGGTATAGTGGAACAGATTGAAGCTACGAC
GGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:25563847 original size:50 final size:50
Alignment explanation
Indices: 25563575--25563849 Score: 158
Period size: 50 Copynumber: 5.5 Consensus size: 50
25563565 ATAGTGGAAC
* *
25563575 AGATTGAAGCTACAACGACGAATCTTGTTTCCCCAACATTGCAATT-AAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * ****** * * ** **
25563624 AGATTGAAGCCGCAACAGCGAATCTTACTTT-CCTGGTGGTGTAGTGGAGT
1 AGATTGAAGCCACAACGGCGAATCTT-GTTTCCCCAACATTGCAATTAAAA
* * *
25563674 AGATTGAAGCTACGACGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * ** * *** ** * * ** **
25563724 ATATTGAAGCCGCAACGGCGAATCTTACTTCACTGGCGGTGTAGTGGAGC
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
* * * *
25563774 AGATTGAAGCTACGATGGTGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
*
25563824 AGATTGAAGCCGCAACGGCGAATCTT
1 AGATTGAAGCCACAACGGCGAATCTT
25563850 ACTTCCTTTG
Statistics
Matches: 145, Mismatches: 78, Indels: 5
0.64 0.34 0.02
Matches are distributed among these distances:
49 31 0.21
50 114 0.79
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
Found at i:25564205 original size:44 final size:44
Alignment explanation
Indices: 25564155--25564261 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
25564145 GATCGCATCT
* * * * *
25564155 AGTCTTATCTCCCTGAAGTGGCAGTGGAGCAGACTGAGTAAGAA
1 AGTCTTATCTCCCTGAAATGACAGTGGAGCAGACTAAATAAAAA
* *
25564199 AGTCTTATC-CTCCTGAAATTACAGTGGGGCAGACTAAATAAAAA
1 AGTCTTATCTC-CCTGAAATGACAGTGGAGCAGACTAAATAAAAA
* * *
25564243 AATCCTATCTCCCTAAAAT
1 AGTCTTATCTCCCTGAAAT
25564262 TGTAGTGGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
43 1 0.02
44 49 0.96
45 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.25
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAATGACAGTGGAGCAGACTAAATAAAAA
Found at i:25566332 original size:16 final size:16
Alignment explanation
Indices: 25566311--25566341 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25566301 TCTTTTGCTC
25566311 AAATTTAAAAATAGAA
1 AAATTTAAAAATAGAA
*
25566327 AAATTTCAAAATAGA
1 AAATTTAAAAATAGA
25566342 TATAATACTC
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:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATTTAAAAATAGAA
Found at i:25567482 original size:525 final size:526
Alignment explanation
Indices: 25566491--25567492 Score: 1579
Period size: 525 Copynumber: 1.9 Consensus size: 526
25566481 TGTCCTAATG
* * ** *
25566491 CATTGGATGTGACGTGTTGATTTCTTGAGATAAAGATTTTTTTTAAAAATTTAATAAAGGAAATG
1 CATTGGATGTGACGTATTGATTTCTCGAGATAAAGATTTTTTCCAAAAATTTAATAAAGGAAATA
25566556 TTCAACGTTTAGGATTTTGAGAAATTGTGCCCTAATTATTGGGCTGCAATTTCTTCATAAATCTC
66 TTCAACGTTTAGGATTTTGAGAAATTGTGCCCTAATTATTGGGCTGCAATTTCTTCATAAATCTC
* * *
25566621 AAACAATTGAATGTTTTTTTAAAAATTTTTATTACATGAATCTTTTGGACAAACTCATTTTTGAA
131 AAACAATTGAATGTTCTTTT-AAAATTTTTATTACATCAATCTTTTGGACAAACTCATTTTTAAA
* * * *
25566686 GAAATAAAATATCGTTCCCTAACGCATTGGGTGTGATAGTTTTTCTCCGAAATGAGAGTCTTAAT
195 GAAATAAAATATCGTGCACTAACGCATTGGGTGTGACAGTTTTTCTCCAAAATGAGAGTCTTAAT
* *
25566751 GAATAACTTGATTTAATTAAGGATCGTATTTTTCAACTCTTGACATCAAGACATTTATTAATCAA
260 CAATAACTTGATTTAATTAAGGATCGTATTTTTCAACTCTTGACATCAAGACATTAATTAATCAA
* *
25566816 CTTGGTACCAATTTTTGGGCGTTACGGGGGTGCTAATCCTTCCTCGTACGTAACTGACTCCCGAA
325 CTTGGTACCAATTTTTGGGCGTTACGGGAGTGCTAATCCTTCCTCGTACGTAACTGACTCCCAAA
* *
25566881 CCCGTTTTTCTAAAACTCGTAGACCAAAGTCGTTTTTAGGTGATCCAATCACACCTTAATAAAAG
390 CCCGTTTTTCTAAAACTCGTAGACCAAAGTCGTTTTTAGGTGATCCAATCACACATCAATAAAAG
25566946 ATTGGTGGCGACT-CCAATTTTCATCGACAACTTTTTTTTTTCAAAAAATAAAAATGAAAATGGT
455 ATTGGTGGCGACTCCCAATTTTCATCGACAACTTTTTTTTTTCAAAAAATAAAAATGAAAATGGT
25567010 TTCGACA
520 TTCGACA
* * *
25567017 CATTGGATGTGACGTATTGATTTCTCGAGATGAATATTTTTTCCAAAAA-TTAATGAAGGAAATA
1 CATTGGATGTGACGTATTGATTTCTCGAGATAAAGATTTTTTCCAAAAATTTAATAAAGGAAATA
** *
25567081 TTCGAA-GTTTAGGATTTTGAGAAATTGTGCCCTAATGTATTGGGCTGCGGTTTCTTCATAAATT
66 TTC-AACGTTTAGGATTTTGAGAAATTGTGCCCTAAT-TATTGGGCTGCAATTTCTTCATAAATC
*
25567145 TTAAACAATTGAATGTTCTTTT-AAA-TTTTATTACA-CAAGTCTTTTGGACAAACTCATTTTTA
129 TCAAACAATTGAATGTTCTTTTAAAATTTTTATTACATCAA-TCTTTTGGACAAACTCATTTTTA
* *
25567207 AAGGAATAAAATATCGTGCACTAACGCATTGGGTGTGACATTTTTTCTCCAAAATGAGAGAGTCT
193 AAGAAATAAAATATCGTGCACTAACGCATTGGGTGTGACAGTTTTTCTCCAAAAT--GAGAGTCT
* * **
25567272 TAATCAATAACTTGATTTAATTAAGGATCGTATTTTT-AACTTTTGGCATTTAGACATTAATTAA
256 TAATCAATAACTTGATTTAATTAAGGATCGTATTTTTCAACTCTTGACATCAAGACATTAATTAA
25567336 TCAACTTGGTACCAATTTTTGGGCGTTA-GGGAAGTGCTAATCCTTCCTCGTACGTAACTGACTC
321 TCAACTTGGTACCAATTTTTGGGCGTTACGGG-AGTGCTAATCCTTCCTCGTACGTAACTGACTC
* *
25567400 CCAAACCCGTTTTTTCTAAGACTCGTAGACCAAAGTCGTTTTTAGGTGATCCAATCAGACATCAA
385 CCAAACCCG-TTTTTCTAAAACTCGTAGACCAAAGTCGTTTTTAGGTGATCCAATCACACATCAA
25567465 TAAAAGATTGGTGGCGACTCCCAATTTT
449 TAAAAGATTGGTGGCGACTCCCAATTTT
25567493 TCGTTTTTAA
Statistics
Matches: 435, Mismatches: 33, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
522 2 0.00
523 84 0.19
524 92 0.21
525 160 0.37
526 97 0.22
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (526 bp):
CATTGGATGTGACGTATTGATTTCTCGAGATAAAGATTTTTTCCAAAAATTTAATAAAGGAAATA
TTCAACGTTTAGGATTTTGAGAAATTGTGCCCTAATTATTGGGCTGCAATTTCTTCATAAATCTC
AAACAATTGAATGTTCTTTTAAAATTTTTATTACATCAATCTTTTGGACAAACTCATTTTTAAAG
AAATAAAATATCGTGCACTAACGCATTGGGTGTGACAGTTTTTCTCCAAAATGAGAGTCTTAATC
AATAACTTGATTTAATTAAGGATCGTATTTTTCAACTCTTGACATCAAGACATTAATTAATCAAC
TTGGTACCAATTTTTGGGCGTTACGGGAGTGCTAATCCTTCCTCGTACGTAACTGACTCCCAAAC
CCGTTTTTCTAAAACTCGTAGACCAAAGTCGTTTTTAGGTGATCCAATCACACATCAATAAAAGA
TTGGTGGCGACTCCCAATTTTCATCGACAACTTTTTTTTTTCAAAAAATAAAAATGAAAATGGTT
TCGACA
Found at i:25567956 original size:27 final size:28
Alignment explanation
Indices: 25567926--25567987 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
25567916 ATTATTAAAA
*
25567926 ATAATATT-ACTACTTTTTATAAATTTT
1 ATAATATTAAATACTTTTTATAAATTTT
* *
25567953 ATAATTTTAAATATTTTTTATAAATTTT
1 ATAATATTAAATACTTTTTATAAATTTT
25567981 -TAATATT
1 ATAATATT
25567988 TTTTTATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (28 bp):
ATAATATTAAATACTTTTTATAAATTTT
Found at i:25567973 original size:19 final size:20
Alignment explanation
Indices: 25567949--25567991 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
25567939 TTTTTATAAA
25567949 TTTTAT-AATTTTAAATATT
1 TTTTATAAATTTTAAATATT
*
25567968 TTTTATAAATTTTTAATATT
1 TTTTATAAATTTTAAATATT
25567988 TTTT
1 TTTT
25567992 TATCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATAAATTTTAAATATT
Found at i:25568828 original size:3 final size:3
Alignment explanation
Indices: 25568808--25568863 Score: 94
Period size: 3 Copynumber: 18.0 Consensus size: 3
25568798 TTTGTAAATA
25568808 AAT ATAT AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25568855 AAT AAT AAT
1 AAT AAT AAT
25568864 GTTTAAATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:25570551 original size:10 final size:10
Alignment explanation
Indices: 25570536--25570560 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
25570526 TGCATGCATG
25570536 CAATTATTTC
1 CAATTATTTC
25570546 CAATTATTTC
1 CAATTATTTC
25570556 CAATT
1 CAATT
25570561 TCAGATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (10 bp):
CAATTATTTC
Done.