Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015263.1 Kokia drynarioides strain JFW-HI SEQ_130308, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1369056
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 871 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:317447 original size:5 final size:5
Alignment explanation
Indices: 317412--317446 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
317402 CAAGATTATA
*
317412 AAATC AAATC AAATC AAATC AAATC AAATC TAATC
1 AAATC AAATC AAATC AAATC AAATC AAATC AAATC
317447 TTAAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (5 bp):
AAATC
Found at i:322989 original size:6 final size:6
Alignment explanation
Indices: 322974--323003 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
322964 ATTTCGACTC
*
322974 TCTTCT TCTTCA TCTTCA TCTTCA TCTTCA
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA
323004 CCTCGACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.33, G:0.00, T:0.53
Consensus pattern (6 bp):
TCTTCA
Found at i:334160 original size:30 final size:30
Alignment explanation
Indices: 334125--334184 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
334115 TTATTTATAT
334125 AAATAAAAGAGTTATTAATTAAAAAATTAA
1 AAATAAAAGAGTTATTAATTAAAAAATTAA
* * * *
334155 AAATAATATATTTATTAATTAAAACATTAA
1 AAATAAAAGAGTTATTAATTAAAAAATTAA
334185 TTAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (30 bp):
AAATAAAAGAGTTATTAATTAAAAAATTAA
Found at i:347325 original size:3 final size:3
Alignment explanation
Indices: 347311--347348 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
347301 AATTGCTTGT
*
347311 TGC TGT TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
347349 TTGTTGATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.29, G:0.34, T:0.37
Consensus pattern (3 bp):
TGC
Found at i:347421 original size:12 final size:12
Alignment explanation
Indices: 347404--347437 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
347394 AAGAAATTGT
347404 TGTTGCTGCTGC
1 TGTTGCTGCTGC
* *
347416 TGTTGCTGTTGT
1 TGTTGCTGCTGC
347428 TGTTGCTGCT
1 TGTTGCTGCT
347438 TCTGCAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.32, T:0.50
Consensus pattern (12 bp):
TGTTGCTGCTGC
Found at i:348308 original size:9 final size:8
Alignment explanation
Indices: 348273--348307 Score: 61
Period size: 8 Copynumber: 4.2 Consensus size: 8
348263 AAACATTCTT
348273 TTTAAAAA
1 TTTAAAAA
348281 TTTAAAAA
1 TTTAAAAA
348289 TTTAAAAA
1 TTTAAAAA
348297 TTATAAAAA
1 TT-TAAAAA
348306 TT
1 TT
348308 AAGAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.69
9 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTAAAAA
Found at i:352197 original size:3 final size:3
Alignment explanation
Indices: 352189--352220 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
352179 CTTATTCGAT
352189 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
352221 TAAAAGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:355470 original size:14 final size:14
Alignment explanation
Indices: 355433--355480 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
355423 TTTTTATTAG
355433 TATATTGTTTATATT
1 TATATT-TTTATATT
355448 TA-A--TTTATATT
1 TATATTTTTATATT
355459 TATATTTTTATATT
1 TATATTTTTATATT
*
355473 TATCTTTT
1 TATATTTT
355481 AGAGTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.34
12 1 0.03
14 16 0.55
15 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (14 bp):
TATATTTTTATATT
Found at i:361841 original size:6 final size:6
Alignment explanation
Indices: 361830--361887 Score: 62
Period size: 6 Copynumber: 9.5 Consensus size: 6
361820 AACCCAATTA
** * * *
361830 TTTTAT TTTTAT TTTTAT TCTTTCC CTTTAT TTATAT TTATAT TTTTAT
1 TTTTAT TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTTAT
361879 TTTTAT TTT
1 TTTTAT TTT
361888 CTTATTTGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 40 0.93
7 3 0.07
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:361883 original size:14 final size:13
Alignment explanation
Indices: 361830--361894 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 13
361820 AACCCAATTA
361830 TTTTATTTTTA-T
1 TTTTATTTTTATT
*
361842 TTTTATTCTTTCCCTT
1 TTTTATT-TTT--ATT
*
361858 TATTTATATTTATAT
1 T-TTTATTTTTAT-T
361873 TTTTATTTTTATT
1 TTTTATTTTTATT
361886 TTCTTATTT
1 TT-TTATTT
361895 GTTCAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 7 0.17
13 6 0.14
14 17 0.40
15 2 0.05
16 5 0.12
17 5 0.12
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:363612 original size:27 final size:27
Alignment explanation
Indices: 363573--363639 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
363563 TGTTTTGCTT
* *
363573 TTTTTTTTTAAATCAGTTTATTCAGTC
1 TTTTTTTTAAAATCAGTTTATTCAATC
363600 TTTTTTTTAAAATCAGTTTATTCAATC
1 TTTTTTTTAAAATCAGTTTATTCAATC
363627 TTTTTTTTAAAAT
1 TTTTTTTTAAAAT
363640 TAGCAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTTTTTAAAATCAGTTTATTCAATC
Found at i:363953 original size:26 final size:25
Alignment explanation
Indices: 363912--363961 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
363902 TTTATTTAAC
363912 CCTTTTTATATCATTTTAGTTAAAT
1 CCTTTTTATATCATTTTAGTTAAAT
* *
363937 CCTTTTTATTATTATTTTATTTAAA
1 CCTTTTTA-TATCATTTTAGTTAAA
363962 ATAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.28, C:0.10, G:0.02, T:0.60
Consensus pattern (25 bp):
CCTTTTTATATCATTTTAGTTAAAT
Found at i:363971 original size:27 final size:25
Alignment explanation
Indices: 363914--363971 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
363904 TATTTAACCC
**
363914 TTTTTATATCATTTTAGTTAAATCC
1 TTTTTATATCATTTTAGTTAAATAA
* *
363939 TTTTTATTATTATTTTATTTAAAATAA
1 TTTTTA-TATCATTTTAGTT-AAATAA
363966 TTTTTA
1 TTTTTA
363972 ATTCTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 6 0.22
26 11 0.41
27 10 0.37
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTATATCATTTTAGTTAAATAA
Found at i:371588 original size:50 final size:50
Alignment explanation
Indices: 371531--371625 Score: 190
Period size: 50 Copynumber: 1.9 Consensus size: 50
371521 TTCTCACATT
371531 TCACAATTCTATTTATTTTTGCCAAGTTTGACAAATATTTTATACGATTC
1 TCACAATTCTATTTATTTTTGCCAAGTTTGACAAATATTTTATACGATTC
371581 TCACAATTCTATTTATTTTTGCCAAGTTTGACAAATATTTTATAC
1 TCACAATTCTATTTATTTTTGCCAAGTTTGACAAATATTTTATAC
371626 AATTAACCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (50 bp):
TCACAATTCTATTTATTTTTGCCAAGTTTGACAAATATTTTATACGATTC
Found at i:376205 original size:38 final size:38
Alignment explanation
Indices: 376139--376625 Score: 144
Period size: 38 Copynumber: 12.6 Consensus size: 38
376129 TTGAAGGCAG
* * * * *
376139 TCAATCTTTTACTCCGATCACAGAGCAGATTGAAACAT
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAAACAA
* *
376177 TCAATCTTTTACCCCAATCATGGGGCAGATT-AAAGAA
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAAACAA
** * *
376214 TCTAATCTTTTACCTTAATCAAAAGGCAGATTGAAAACACA
1 TC-AATCTTTTACCCCAATCATAGGGCAGATTG-AAACA-A
* * * * *
376255 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-AT
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAA-ACAA
* *** * * * * *
376293 TCAATCTTCTACCTTGATCAGAAGACAAATTGAAGA-AT
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAA-ACAA
* ** * * * *
376331 TCAATCTCTTACCTTAATCAAAAGGTAAATTGAACACACA
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAA-ACA-A
* * * *** * * *
376371 CCGATCTCTTACTTTAATCAAAAGGCAGAGTGAAGACACA
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAA-ACA-A
* * * * * *
376411 TCGATCTCTTACCTCGATCATAAGGTAGATTGAAA-AA
1 TCAATCTTTTACCCCAATCATAGGGCAGATTGAAACAA
* ** * * *
376448 TTCAATCTCTTACCTTAATC-TAAAGGCAAATTGAAGACAG
1 -TCAATCTTTTACCCCAATCAT-AGGGCAGATTGAA-ACAA
** * * *
376488 TCAATCTTTTACTTCGATCAT-GGAACAGATTGAAACAT
1 TCAATCTTTTACCCCAATCATAGG-GCAGATTGAAACAA
* * *
376526 TCAATCTTTTACCCCGATCAT-GAGACAGATT-AAAAAA
1 TCAATCTTTTACCCCAATCATAG-GGCAGATTGAAACAA
* ** * *
376563 TCCAATCTCTTACCTTAATCAGAAGGCAGATTGAAAACACA
1 T-CAATCTTTTACCCCAATCATAGGGCAGATTG-AAACA-A
* * *
376604 CCAATCTCTTACCCCGATCATA
1 TCAATCTTTTACCCCAATCATA
376626 AGATAAATTT
Statistics
Matches: 345, Mismatches: 85, Indels: 36
0.74 0.18 0.08
Matches are distributed among these distances:
37 13 0.04
38 188 0.54
39 30 0.09
40 111 0.32
41 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (38 bp):
TCAATCTTTTACCCCAATCATAGGGCAGATTGAAACAA
Found at i:376278 original size:78 final size:79
Alignment explanation
Indices: 376178--376984 Score: 346
Period size: 78 Copynumber: 10.4 Consensus size: 79
376168 TTGAAACATT
* * *
376178 CAATCTTTTACCCCAATCATGGGGCAGATT-AAAGAATCTAATCTTTTACCTTAATCAAAAGGCA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCTAATCTCTTACCTTAATCAAAAGGCA
376242 GATTGAAAACACAC
66 GATTGAAAACACAC
* * *
376256 CAATCTCTTACCCCGATCATGGGGCAGATTG-AAGAAT-TCAATCT-TCTACCTTGATCAGAAGA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCT-AATCTCT-TACCTTAATCAAAAGG
* * **
376318 CAAATTGAAGA-A-TT
64 CAGATTGAAAACACAC
*** *** * * * ** *
376332 CAATCTCTTACCTTAATCAAAAGGTAAATTGAACACACA-CCGATCTCTTACTTTAATCAAAAGG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAA-AGA-ATCTAATCTCTTACCTTAATCAAAAGG
* * *
376396 CAGAGTGAAGACACAT
64 CAGATTGAAAACACAC
* * ** * *
376412 CGATCTCTTACCTCGATCATAAGGTAGATTGAAA-AAT-TCAATCTCTTACCTTAATCTAAAGGC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCT-AATCTCTTACCTTAATCAAAAGGC
* * **
376475 AAATTGAAGACA-GT
65 AGATTGAAAACACAC
* ** ** * * * *** ** *
376489 CAATCTTTTACTTCGATCATGGAACAGATTGAAACATTC-AATCTTTTACCCCGATCATGAGACA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCTAATCTCTTACCTTAATCAAAAGGCA
376553 GATT-AAAA-A-ATC
66 GATTGAAAACACA-C
*** * * * *** *
376565 CAATCTCTTACCTTAATCA-GAAGGCAGATTGAAA-ACACACCAATCTCTTACCCCGATCATAAG
1 CAATCTCTTACCCCGATCATG-GGGCAGATTGAAAGA-A-TCTAATCTCTTACCTTAATCAAAAG
** * *
376628 ATAAATTTAAAA-ATCA-
63 GCAGATTGAAAACA-CAC
* * * ** * * * ***
376644 -AATCTTTTACTCCGATTATGAAGCAGATT-AAAGCATCCAATCTCTTATGCC--GATCATGGGG
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCTAATCTCTTA--CCTTAATCAAAAGG
*
376705 CAGATTGAAAA-A-TC
64 CAGATTGAAAACACAC
* * * ** * *
376719 TAATATTTTACCTTGATCA-GAAGGCAAATTG-AAGAAT-TCAATCTCTTACCTTAATCAAAAGG
1 CAATCTCTTACCCCGATCATG-GGGCAGATTGAAAGAATCT-AATCTCTTACCTTAATCAAAAGG
* *
376781 CAAATTGAAGACACAC
64 CAGATTGAAAACACAC
* ** *
376797 CGATCTCTTACCCCGATCATGGGATAGATTGAAAG-ATCCAATCTCTTACCTTAATCAGAAA-GC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCTAATCTCTTACCTTAATCA-AAAGGC
* *
376860 AGATTGAAGATACAC
65 AGATTGAAAACACAC
** * *
376875 TGATCTCTTACCCCGATCATGGGGTAGATTGAAA-AAT-TCAATCTCTTACCTTAATCAAAAGAC
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCT-AATCTCTTACCTTAATCAAAAGGC
*
376938 AGATTAAAAACACAC
65 AGATTGAAAACACAC
*** **
376953 CAATCT-TTGTTCAAATCATGGGGCAGATTGAA
1 CAATCTCTTACCCCGATCATGGGGCAGATTGAA
376985 GCATCTGATA
Statistics
Matches: 554, Mismatches: 133, Indels: 85
0.72 0.17 0.11
Matches are distributed among these distances:
74 2 0.00
75 4 0.01
76 127 0.23
77 81 0.15
78 293 0.53
79 17 0.03
80 29 0.05
81 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (79 bp):
CAATCTCTTACCCCGATCATGGGGCAGATTGAAAGAATCTAATCTCTTACCTTAATCAAAAGGCA
GATTGAAAACACAC
Found at i:376288 original size:116 final size:117
Alignment explanation
Indices: 376064--376690 Score: 508
Period size: 116 Copynumber: 5.4 Consensus size: 117
376054 TAAAGACAGG
* * * * * * * * *
376064 CAATCTCTTACCCCGATTATGAG-TAGATTGAAGCATCCAATCTCTTACGTTAATCAGAAGACAA
1 CAATCTTTTACCCCGATCATGAGACAGATTAAAGAATTCAATCTCTTACCTTAATCAAAAGGCAA
** ** * *
376128 ATTGAAGGCA-GTCAATCTTTTACTCCGATCACAGAGCAGATTGAA-ACATT
66 ATTGAAAACACACCAATCTCTTACTCCGATCATAGAGCAGATTGAAGACATT
* * * *
376178 CAATCTTTTACCCCAATCATGGGGCAGATTAAAGAA-TCTAATCTTTTACCTTAATCAAAAGGCA
1 CAATCTTTTACCCCGATCATGAGACAGATTAAAGAATTC-AATCTCTTACCTTAATCAAAAGGCA
* * * *
376242 GATTGAAAACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGA-ATT
65 AATTGAAAACACACCAATCTCTTACTCCGATCATAGAGCAGATTGAAGACATT
* ** * * *
376294 CAATCTTCTACCTTGATCA-GAAGACAAATTGAAGAATTCAATCTCTTACCTTAATCAAAAGGTA
1 CAATCTTTTACCCCGATCATG-AGACAGATTAAAGAATTCAATCTCTTACCTTAATCAAAAGGCA
* * *** * * *
376358 AATTGAACACACACCGATCTCTTACTTTAATCA-AAAGGCAGAGTGAAGACACAT
65 AATTGAAAACACACCAATCTCTTACTCCGATCATAGA-GCAGATTGAAGACA-TT
* * * * ** *
376412 CGATCTCTTACCTCGATCATAAGGTAGATTGAAA-AATTCAATCTCTTACCTTAATCTAAAGGCA
1 CAATCTTTTACCCCGATCATGAGACAGATT-AAAGAATTCAATCTCTTACCTTAATCAAAAGGCA
* ** * * * *
376476 AATTGAAGACA-GTCAATCTTTTACTTCGATCATGGAACAGATTGAA-ACATT
65 AATTGAAAACACACCAATCTCTTACTCCGATCATAGAGCAGATTGAAGACATT
* * * *
376527 CAATCTTTTACCCCGATCATGAGACAGATTAAAAAATCCAATCTCTTACCTTAATCAGAAGGCAG
1 CAATCTTTTACCCCGATCATGAGACAGATTAAAGAATTCAATCTCTTACCTTAATCAAAAGGCAA
* * * * *
376592 ATTGAAAACACACCAATCTCTTACCCCGATCATA-AGATAAATTTAA-A-AAT
66 ATTGAAAACACACCAATCTCTTACTCCGATCATAGAG-CAGATTGAAGACATT
* * * *
376642 CAAATCTTTTACTCCGATTATGA-AGCAGATTAAAGCATCCAATCTCTTA
1 C-AATCTTTTACCCCGATCATGAGA-CAGATTAAAGAATTCAATCTCTTA
376691 TGCCGATCAT
Statistics
Matches: 403, Mismatches: 93, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
114 23 0.06
115 105 0.26
116 185 0.46
117 27 0.07
118 61 0.15
119 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (117 bp):
CAATCTTTTACCCCGATCATGAGACAGATTAAAGAATTCAATCTCTTACCTTAATCAAAAGGCAA
ATTGAAAACACACCAATCTCTTACTCCGATCATAGAGCAGATTGAAGACATT
Found at i:376388 original size:40 final size:39
Alignment explanation
Indices: 376334--376482 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 39
376324 GAAGAATTCA
* *
376334 ATCTCTTACCTTAATCAAAAGGTAAATTGAACACACACCG
1 ATCTCTTACCTTAATCAAAAGGCAAATTGAA-ACACATCG
* * *
376374 ATCTCTTACTTTAATCAAAAGGCAGAGTGAAGACACATCG
1 ATCTCTTACCTTAATCAAAAGGCAAATTGAA-ACACATCG
** * * * *
376414 ATCTCTTACCTCGATCATAAGGTAGATTGAAA-A-ATTCA
1 ATCTCTTACCTTAATCAAAAGGCAAATTGAAACACA-TCG
*
376452 ATCTCTTACCTTAATCTAAAGGCAAATTGAA
1 ATCTCTTACCTTAATCAAAAGGCAAATTGAA
376483 GACAGTCAAT
Statistics
Matches: 89, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
37 1 0.01
38 28 0.31
39 1 0.01
40 59 0.66
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (39 bp):
ATCTCTTACCTTAATCAAAAGGCAAATTGAAACACATCG
Found at i:376431 original size:156 final size:157
Alignment explanation
Indices: 376218--376499 Score: 390
Period size: 156 Copynumber: 1.8 Consensus size: 157
376208 AAAGAATCTA
* * **
376218 ATCTTTTACCTTAATCAAAAGGCAGATTGAAAACACACCAATCTCTTACCCCGATCATGGGGCAG
1 ATCTCTTACCTTAATCAAAAGGCAGAGTGAAAACACACCAATCTCTTACCCCGATCATAAGGCAG
* * *
376283 ATTGAAGAATTCAATCT-TCTACCTTGATC-AGAAGACAAATTGAAGA-ATTCAATCTCTTACCT
66 ATTGAAAAATTCAATCTCT-TACCTTAATCTA-AAGACAAATTGAAGACAGTCAATCTCTTACCT
376345 TAATCAAAAGGTAAATTGAACACACACCG
129 TAATCAAAAGGTAAATTGAACACACACCG
* * * * * *
376374 ATCTCTTACTTTAATCAAAAGGCAGAGTGAAGACACATCGATCTCTTACCTCGATCATAAGGTAG
1 ATCTCTTACCTTAATCAAAAGGCAGAGTGAAAACACACCAATCTCTTACCCCGATCATAAGGCAG
* *
376439 ATTGAAAAATTCAATCTCTTACCTTAATCTAAAGGCAAATTGAAGACAGTCAATCTTTTAC
66 ATTGAAAAATTCAATCTCTTACCTTAATCTAAAGACAAATTGAAGACAGTCAATCTCTTAC
376500 TTCGATCATG
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
156 94 0.87
157 14 0.13
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.28
Consensus pattern (157 bp):
ATCTCTTACCTTAATCAAAAGGCAGAGTGAAAACACACCAATCTCTTACCCCGATCATAAGGCAG
ATTGAAAAATTCAATCTCTTACCTTAATCTAAAGACAAATTGAAGACAGTCAATCTCTTACCTTA
ATCAAAAGGTAAATTGAACACACACCG
Found at i:376862 original size:192 final size:191
Alignment explanation
Indices: 376374--376916 Score: 562
Period size: 192 Copynumber: 2.8 Consensus size: 191
376364 ACACACACCG
* * * *
376374 ATCTCTTACTTTAATCAAAAGGCAGAGTGAAGACACATCGATCTCTTACCTCGATCATAAGG-TA
1 ATCTCTTACCTTAATCAAAAGGCAGATTGAAGACACACCGATCTCTTACCCCGATCAT-AGGATA
* * * *
376438 GATTGAAAAATTCAATCTCTTACCTTAATCTA-AAGGCAAATTGAAGACAGT-CAATCTTTTACT
65 GATTGAAAAATCCAATCTCTTACCTTAATC-AGAAAGCAGATTGAAG-CA-TCCAATCTCTTA-T
* ** * * *
376501 TCGATCATGGAACAGATTGAAACATTCAATCTTTTACCCCGATCATGAGACAGATTAAAAAATCC
126 CCGATCATGGGGCAGATTGAAAAATTCAATATTTTACCCCGATCATGAGACAAATTAAAAAATCC
376566 A
191 A
* * * * *
376567 ATCTCTTACCTTAATCAGAAGGCAGATTGAAAACACACCAATCTCTTACCCCGATCATAAGATAA
1 ATCTCTTACCTTAATCAAAAGGCAGATTGAAGACACACCGATCTCTTACCCCGATCATAGGATAG
* * * ** * *
376632 ATTTAAAAATCAAATCTTTTA-CTCCGATTATG-AAGCAGATTAAAGCATCCAATCTCTTATGCC
66 ATTGAAAAATCCAATCTCTTACCT-TAATCA-GAAAGCAGATTGAAGCATCCAATCTCTTAT-CC
** * * * *
376695 GATCATGGGGCAGATTGAAAAA-TCTAATATTTTACCTTGATCA-GAAGGCAAATTGAAGAATTC
128 GATCATGGGGCAGATTGAAAAATTC-AATATTTTACCCCGATCATG-AGACAAATTAAAAAATCC
376758 A
191 A
* *
376759 ATCTCTTACCTTAATCAAAAGGCAAATTGAAGACACACCGATCTCTTACCCCGATCATGGGATAG
1 ATCTCTTACCTTAATCAAAAGGCAGATTGAAGACACACCGATCTCTTACCCCGATCATAGGATAG
* * *
376824 ATTGAAAGATCCAATCTCTTACCTTAATCAGAAAGCAGATTGAAG-ATACACTGATCTCTTACCC
66 ATTGAAAAATCCAATCTCTTACCTTAATCAGAAAGCAGATTGAAGCAT-C-C-AATCTCTTA-TC
*
376888 CGATCATGGGGTAGATTGAAAAATTCAAT
127 CGATCATGGGGCAGATTGAAAAATTCAAT
376917 CTCTTACCTT
Statistics
Matches: 285, Mismatches: 50, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
191 8 0.03
192 156 0.55
193 85 0.30
194 34 0.12
195 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (191 bp):
ATCTCTTACCTTAATCAAAAGGCAGATTGAAGACACACCGATCTCTTACCCCGATCATAGGATAG
ATTGAAAAATCCAATCTCTTACCTTAATCAGAAAGCAGATTGAAGCATCCAATCTCTTATCCGAT
CATGGGGCAGATTGAAAAATTCAATATTTTACCCCGATCATGAGACAAATTAAAAAATCCA
Found at i:376864 original size:38 final size:38
Alignment explanation
Indices: 376201--376942 Score: 138
Period size: 38 Copynumber: 19.2 Consensus size: 38
376191 CAATCATGGG
* * *
376201 GCAGATT-AAAGAATCTAATCTTTTACCTTAATCA-AAA
1 GCAGATTGAAAG-ATCCAATCTCTTACCTTGATCAGAAA
* * ** **
376238 GGCAGATTGAAAACACACCAATCTCTTACCCCGATCATG-GG
1 -GCAGATTG-AAAGA-TCCAATCTCTTACCTTGATCA-GAAA
*
376279 GCAGATTG-AAGAATTCAATCT-TCTACCTTGATCAG-AA
1 GCAGATTGAAAG-ATCCAATCTCT-TACCTTGATCAGAAA
* * *
376316 GACAAATTG-AAGAATTCAATCTCTTACCTTAATCA-AAA
1 G-CAGATTGAAAG-ATCCAATCTCTTACCTTGATCAGAAA
* * * * * * *
376354 GGTAAATTGAACACACACCGATCTCTTACTTTAATCA-AAA
1 -GCAGATTGAA-AGA-TCCAATCTCTTACCTTGATCAGAAA
* * * *
376394 GGCAGAGTG-AAGA-CACATCGATCTCTTACCTCGATCATAAG
1 -GCAGATTGAAAGATC-CA---ATCTCTTACCTTGATCAGAAA
* * * * *
376435 GTAGATTGAAAAATTCAATCTCTTACCTTAATCTA-AAG
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATC-AGAAA
* * * *
376473 GCAAATTGAAGACAGT-CAATCTTTTA-CTTCGATCATGGAA
1 GCAGATTGAA-AGA-TCCAATCTCTTACCTT-GATCA-GAAA
* * * ** *
376513 -CAGATTGAAACATTCAATCTTTTACCCCGATCATGAGA
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATCA-GAAA
* * * *
376551 -CAGATTAAAAAATCCAATCTCTTACCTTAATCAGAAG
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATCAGAAA
* * ** *
376588 GCAGATTGAAAACACACCAATCTCTTACCCCGATCA-TAA
1 GCAGATTG-AAAGA-TCCAATCTCTTACCTTGATCAGAAA
* * * * * * * *
376627 GATAAATTTAAAAATCAAATCTTTTA-CTCCGATTATG-AA
1 G-CAGATTGAAAGATCCAATCTCTTACCT-TGATCA-GAAA
**
376666 GCAGATT-AAAGCATCCAATCTCTTATGCC--GATCATG-GG
1 GCAGATTGAAAG-ATCCAATCTCTTA--CCTTGATCA-GAAA
* * * * *
376704 GCAGATTGAAAAATCTAATATTTTACCTTGATCAGAAG
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATCAGAAA
* * *
376742 GCAAATTG-AAGAATTCAATCTCTTACCTTAATCA-AAA
1 GCAGATTGAAAG-ATCCAATCTCTTACCTTGATCAGAAA
* * * * ** **
376779 GGCAAATTGAAGACACACCGATCTCTTACCCCGATCATGGGA
1 -GCAGATTGAA-AGA-TCCAATCTCTTACCTTGATCA-GAAA
* *
376821 -TAGATTGAAAGATCCAATCTCTTACCTTAATCAGAAA
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATCAGAAA
* ** **
376858 GCAGATTG-AAGATACACTGATCTCTTACCCCGATCATG-GG
1 GCAGATTGAAAGAT-C-C-AATCTCTTACCTTGATCA-GAAA
* * * *
376898 GTAGATTGAAAAATTCAATCTCTTACCTTAATCA-AAA
1 GCAGATTGAAAGATCCAATCTCTTACCTTGATCAGAAA
376935 GACAGATT
1 G-CAGATT
376943 AAAAACACAC
Statistics
Matches: 511, Mismatches: 134, Indels: 118
0.67 0.18 0.15
Matches are distributed among these distances:
36 3 0.01
37 24 0.05
38 277 0.54
39 53 0.10
40 140 0.27
41 13 0.03
42 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (38 bp):
GCAGATTGAAAGATCCAATCTCTTACCTTGATCAGAAA
Found at i:378917 original size:25 final size:25
Alignment explanation
Indices: 378866--378934 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
378856 ATTGCCTTTA
* *
378866 TTTTCTTACTAATTTTATTTAACCCT
1 TTTTATTA-TAATTTTATTAAACCCT
*
378892 TTTTA-TATAATTTTAGTTAAATCCT
1 TTTTATTATAATTTTA-TTAAACCCT
*
378917 TTTTATTATTATTTTATT
1 TTTTATTATAATTTTATT
378935 TAAAATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 8 0.22
25 16 0.43
26 13 0.35
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.62
Consensus pattern (25 bp):
TTTTATTATAATTTTATTAAACCCT
Found at i:378920 original size:26 final size:24
Alignment explanation
Indices: 378866--378934 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 24
378856 ATTGCCTTTA
* *
378866 TTTTCTTACTAATTTTATTTAACCCT
1 TTTTATTA-TAATTTTA-TTAAACCT
378892 TTTTA-TATAATTTTAGTTAAATCCT
1 TTTTATTATAATTTTA-TTAAA-CCT
*
378917 TTTTATTATTATTTTATT
1 TTTTATTATAATTTTATT
378935 TAAAATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 12 0.32
25 12 0.32
26 13 0.35
ACGTcount: A:0.26, C:0.10, G:0.01, T:0.62
Consensus pattern (24 bp):
TTTTATTATAATTTTATTAAACCT
Found at i:378937 original size:26 final size:25
Alignment explanation
Indices: 378875--378938 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 25
378865 ATTTTCTTAC
378875 TAATTTTATTT-AACCCTTTTTATA
1 TAATTTTATTTAAACCCTTTTTATA
* *
378899 TAATTTTAGTTAAATCCTTTTTATTA
1 TAATTTTATTTAAACCCTTTTTA-TA
*
378925 TTATTTTATTTAAA
1 TAATTTTATTTAAA
378939 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 10 0.29
25 10 0.29
26 14 0.41
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (25 bp):
TAATTTTATTTAAACCCTTTTTATA
Found at i:378948 original size:27 final size:25
Alignment explanation
Indices: 378891--378948 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
378881 TATTTAACCC
**
378891 TTTTTATATAATTTTAGTTAAATCC
1 TTTTTATATAATTTTAGTTAAATAA
* *
378916 TTTTTATTATTATTTTATTTAAAATAA
1 TTTTTA-TATAATTTTAGTT-AAATAA
378943 TTTTTA
1 TTTTTA
378949 ATTCTCTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 6 0.22
26 11 0.41
27 10 0.37
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTATATAATTTTAGTTAAATAA
Found at i:383261 original size:6 final size:6
Alignment explanation
Indices: 383252--383289 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
383242 ATTAGGATAT
383252 TATTTA TATTTA -ATTTA TATTTA TATTTTTA TATTTA T
1 TATTTA TATTTA TATTTA TATTTA TA--TTTA TATTTA T
383290 CTTTTAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
8 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:383267 original size:11 final size:12
Alignment explanation
Indices: 383252--383289 Score: 51
Period size: 11 Copynumber: 3.1 Consensus size: 12
383242 ATTAGGATAT
383252 TATTTATATTTA
1 TATTTATATTTA
383264 -ATTTATATTTA
1 TATTTATATTTA
383275 TATTTTTATATTTA
1 TA--TTTATATTTA
383289 T
1 T
383290 CTTTTAGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.48
12 1 0.04
14 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTATATTTA
Found at i:383284 original size:14 final size:14
Alignment explanation
Indices: 383248--383294 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
383238 TATTATTAGG
383248 ATATTATTTATATTT
1 ATATT-TTTATATTT
383263 A-A--TTTATATTT
1 ATATTTTTATATTT
383274 ATATTTTTATATTT
1 ATATTTTTATATTT
*
383288 ATCTTTT
1 ATATTTT
383295 AGAGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 10 0.36
12 1 0.04
14 16 0.57
15 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
ATATTTTTATATTT
Found at i:389891 original size:20 final size:18
Alignment explanation
Indices: 389863--389910 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
389853 TCACGTCAGT
*
389863 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
389883 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
389903 AAATTATT
1 AAATTATT
389911 AAATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:390474 original size:121 final size:121
Alignment explanation
Indices: 390293--390526 Score: 378
Period size: 121 Copynumber: 1.9 Consensus size: 121
390283 GTCTACAATG
*
390293 GATACCCTCAACCTTCCTACTTTCACCATTTCAATTTGGGTTCCTTTTGGTCTTCTTCATTATCT
1 GATACCCTCAACCTTCCTACTTTCACCATTTCAATTTGGGTTCCTTTTGGTCGTCTTCATTATCT
* * *
390358 GACTTTTGAGATCTAGGTTTTCAACACTTATTGTTTGCTGGTTGTAGTCAATAATC
66 GACCTTTGAGATCTAGGTTTTCAACACTTATTGCTTACTGGTTGTAGTCAATAATC
* * *
390414 GATACTCTCAACCTTCCTTCTTTCACCATTTCAGTTTGGGTTCCTTTTGGTCGTCTTCATTATCT
1 GATACCCTCAACCTTCCTACTTTCACCATTTCAATTTGGGTTCCTTTTGGTCGTCTTCATTATCT
* * *
390479 GACCTTTGAGATTTGGGTTTTCAACATTTATTGCTTACTGGTTGTAGT
66 GACCTTTGAGATCTAGGTTTTCAACACTTATTGCTTACTGGTTGTAGT
390527 GTAAGTAAGA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
121 103 1.00
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (121 bp):
GATACCCTCAACCTTCCTACTTTCACCATTTCAATTTGGGTTCCTTTTGGTCGTCTTCATTATCT
GACCTTTGAGATCTAGGTTTTCAACACTTATTGCTTACTGGTTGTAGTCAATAATC
Found at i:390981 original size:40 final size:39
Alignment explanation
Indices: 390921--391027 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 39
390911 GATGATGATT
* *
390921 ATAATTTTAAAATAAATTTAATAAATTTATATTTTAAAAA
1 ATAATTTTAAAAT-AATTTAATAATTTTATATTTGAAAAA
390961 ATAATTTTAAAATAATTTTAATAATTTTATATTTGAAAAA
1 ATAATTTTAAAATAA-TTTAATAATTTTATATTTGAAAAA
391001 ATAATTTTAAAA-AATTTAATAATTTTA
1 ATAATTTTAAAATAATTTAATAATTTTA
391028 AAATCATTTG
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
38 13 0.20
39 4 0.06
40 47 0.73
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (39 bp):
ATAATTTTAAAATAATTTAATAATTTTATATTTGAAAAA
Found at i:390983 original size:20 final size:19
Alignment explanation
Indices: 390960--391036 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 19
390950 TATTTTAAAA
390960 AATAATTTTAAAATAATTTT
1 AATAATTTTAAAATAA-TTT
** **
390980 AATAATTTTATATTTGAA-AA
1 AATAATTTTA-AAAT-AATTT
391000 AATAATTTTAAAA-AATTT
1 AATAATTTTAAAATAATTT
*
391018 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
391037 GCTGACGTGG
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
17 2 0.05
18 13 0.30
19 5 0.11
20 20 0.45
21 2 0.05
22 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (19 bp):
AATAATTTTAAAATAATTT
Found at i:391030 original size:29 final size:28
Alignment explanation
Indices: 390960--391036 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
390950 TATTTTAAAA
*
390960 AATAATTTTAAAATAATTTTAATAATTT
1 AATAATTTTAAAATAATTTTAAAAATTT
* *
390988 TAT-ATTTGAAAAAATAATTTTAAAAAATTT
1 AATAATTT--TAAAATAATTTT-AAAAATTT
*
391018 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
391037 GCTGACGTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.10
28 2 0.05
29 20 0.51
30 9 0.23
31 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
AATAATTTTAAAATAATTTTAAAAATTT
Found at i:391693 original size:3 final size:3
Alignment explanation
Indices: 391685--391760 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
391675 CTTGGGCACT
* * * *
391685 AGA AGA AGA AG- AGA AAA AGA AGA ATA AG- AGA AGA A-A TGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
391730 AGA AGA A-A AGA AGA AG- AGG AGG AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
391761 GAAAATGGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
2 9 0.15
3 50 0.85
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:391717 original size:25 final size:25
Alignment explanation
Indices: 391687--391747 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
391677 TGGGCACTAG
*
391687 AAGAAGAAGAGAAAAAGAAGAATAA
1 AAGAAGAAGAGAAAAAGAAGAAGAA
*
391712 GAGAAGAA-ATGAAAAAGAAGAAGAA
1 AAGAAGAAGA-GAAAAAGAAGAAGAA
391737 AAGAAGAAGAG
1 AAGAAGAAGAG
391748 GAGGAGAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (25 bp):
AAGAAGAAGAGAAAAAGAAGAAGAA
Found at i:391744 original size:11 final size:11
Alignment explanation
Indices: 391685--391746 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
391675 CTTGGGCACT
391685 AGAAGAAGAAG-
1 AGAA-AAGAAGA
391696 AGAAAAAGAAGA
1 AG-AAAAGAAGA
* *
391708 ATAAGAGAAGAA
1 AGAAAAGAAG-A
391720 ATGAAAAAGAAGA
1 A-G-AAAAGAAGA
391733 AGAAAAGAAGA
1 AGAAAAGAAGA
391744 AGA
1 AGA
391747 GGAGGAGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 27 0.64
12 6 0.14
13 2 0.05
14 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.03
Consensus pattern (11 bp):
AGAAAAGAAGA
Found at i:392761 original size:21 final size:21
Alignment explanation
Indices: 392731--392770 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
392721 CGTGGCAAGC
392731 TAACTAGCCACATTAGTTAGT
1 TAACTAGCCACATTAGTTAGT
* *
392752 TAACTGGCCACGTTAGTTA
1 TAACTAGCCACATTAGTTA
392771 TCCCCTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (21 bp):
TAACTAGCCACATTAGTTAGT
Found at i:393602 original size:20 final size:21
Alignment explanation
Indices: 393569--393608 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
393559 TTTTACTCTT
*
393569 GGAAAAATG-GAAAATTGAAA
1 GGAAAAATGAAAAAATTGAAA
*
393589 GGAAAGATGAAAAAATTGAA
1 GGAAAAATGAAAAAATTGAA
393609 GAAAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (21 bp):
GGAAAAATGAAAAAATTGAAA
Found at i:395133 original size:31 final size:31
Alignment explanation
Indices: 395098--395165 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
395088 TACAAAATAC
*
395098 TCATTAAACTATTCGAAAA-TTTTCATTTAAG
1 TCATTAAACTATT-GAAAATTTTTCATTTAAA
* *
395129 TCATTAAACTATTTAAAATTTTTTATTTAAA
1 TCATTAAACTATTGAAAATTTTTCATTTAAA
395160 TCATTA
1 TCATTA
395166 CATTATACGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (31 bp):
TCATTAAACTATTGAAAATTTTTCATTTAAA
Found at i:398086 original size:41 final size:41
Alignment explanation
Indices: 398036--398120 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 41
398026 ACATGGCCGC
** * ** *
398036 GTGACGCACACAACCTGGCACACGGCTTGTCACACGGTCAT
1 GTGACGCACACAACCTACCACACGGCCTAACACACAGTCAT
* *
398077 GTGATGCACACGACCTACCACACGGCCTAACACACAGTCAT
1 GTGACGCACACAACCTACCACACGGCCTAACACACAGTCAT
398118 GTG
1 GTG
398121 GCATCAACAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.27, C:0.34, G:0.22, T:0.16
Consensus pattern (41 bp):
GTGACGCACACAACCTACCACACGGCCTAACACACAGTCAT
Found at i:400242 original size:29 final size:29
Alignment explanation
Indices: 400210--400266 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
400200 TGAGCTGTTT
*
400210 GTGTGCTATTATTTTGA-GTTATGTTATCA
1 GTGTGATATTATTTT-ATGTTATGTTATCA
* *
400239 GTGTGATCTTATTTTATGTTGTGTTATC
1 GTGTGATATTATTTTATGTTATGTTATC
400267 GCATGTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.18, C:0.07, G:0.21, T:0.54
Consensus pattern (29 bp):
GTGTGATATTATTTTATGTTATGTTATCA
Found at i:405843 original size:43 final size:42
Alignment explanation
Indices: 405797--405980 Score: 197
Period size: 43 Copynumber: 4.3 Consensus size: 42
405787 AAACTTGATA
* * *
405797 TATAAATGGAAGACTCATGTCTCGGGATGAGCATGATATTAT
1 TATAAATGGAAGACTCATGTCTCGGGAAGAGCATAAGATTAT
* * * * *
405839 ATATAAATGAAAGACTCATATCTCGAGATGAGCATGAGATTAT
1 -TATAAATGGAAGACTCATGTCTCGGGAAGAGCATAAGATTAT
* *
405882 GTATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATTAT
1 -TATAAATGGAAGACTCATGTCTCGGGAAGAGCATAAGATTAT
* * * * *
405925 TGTAAATGGAAGAACTTATGTCTCAGTAAGAGCATAATATTAT
1 TATAAATGGAAG-ACTCATGTCTCGGGAAGAGCATAAGATTAT
*
405968 TTTAAATGGAAGA
1 TATAAATGGAAGA
405981 ACTTATGACT
Statistics
Matches: 124, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 12 0.10
43 112 0.90
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (42 bp):
TATAAATGGAAGACTCATGTCTCGGGAAGAGCATAAGATTAT
Found at i:405958 original size:86 final size:85
Alignment explanation
Indices: 405797--406005 Score: 224
Period size: 86 Copynumber: 2.4 Consensus size: 85
405787 AAACTTGATA
* * * * *
405797 TATAAATGGAAGACTCATGTCTCGGGATGAGCATGATATTATATATAAATGAAAGACTCATATCT
1 TATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATTATATATAAATGAAAGACTCATATCT
* *
405862 CGAGATGAGCATGAGATTAT
66 CGAGAAGAGCATAAGATTAT
* * * *
405882 GTATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATTAT-TGTAAATGGAAGAACTTATGT
1 -TATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATTATATATAAATGAAAG-ACTCATAT
*
405946 CTC-AGTAAGAGCATAATATTAT
64 CTCGAG-AAGAGCATAAGATTAT
* * **
405968 TTTAAATGGAAGAACTTATGACTCGGTGGGAGCATAAG
1 TATAAATGGAAG-ACTTATGTCTCGGTAAGAGCATAAG
406006 GTTAATTCAG
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
85 23 0.22
86 81 0.78
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (85 bp):
TATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATTATATATAAATGAAAGACTCATATCT
CGAGAAGAGCATAAGATTAT
Found at i:405981 original size:43 final size:43
Alignment explanation
Indices: 405794--406005 Score: 196
Period size: 43 Copynumber: 4.9 Consensus size: 43
405784 TAAAAACTTG
* * * * * *
405794 ATATATAAATGGAAGACTCATGTCTCGGGATGAGCATGATATT
1 ATATATAAATGGAAGACTTATGTCTCAGTAAGAGCATAAGATT
* * * * *
405837 ATATATAAATGAAAGACTCATATCTCGAG-ATGAGCATGAGATT
1 ATATATAAATGGAAGACTTATGTCTC-AGTAAGAGCATAAGATT
* *
405880 ATGTATAAATGGAAGACTTATGTCTCGGTAAGAGCATAAGATT
1 ATATATAAATGGAAGACTTATGTCTCAGTAAGAGCATAAGATT
* *
405923 AT-TGTAAATGGAAGAACTTATGTCTCAGTAAGAGCATAATATT
1 ATATATAAATGGAAG-ACTTATGTCTCAGTAAGAGCATAAGATT
* * * **
405966 AT-TTTAAATGGAAGAACTTATGACTCGGTGGGAGCATAAG
1 ATATATAAATGGAAG-ACTTATGTCTCAGTAAGAGCATAAG
406006 GTTAATTCAG
Statistics
Matches: 146, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 12 0.08
43 133 0.91
44 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (43 bp):
ATATATAAATGGAAGACTTATGTCTCAGTAAGAGCATAAGATT
Found at i:407479 original size:26 final size:26
Alignment explanation
Indices: 407450--407643 Score: 83
Period size: 26 Copynumber: 7.5 Consensus size: 26
407440 TACCAATTCC
* * * *
407450 ACTAGTTATTCACTGGTTCAAAGTCT
1 ACTAGTTAATCACTAGCTCAAAGCCT
*
407476 ACTATTTAATCACTAGCTCAAAGCCT
1 ACTAGTTAATCACTAGCTCAAAGCCT
* *
407502 ACTA-TATAATCAC-CGACTCAAGGCCT
1 ACTAGT-TAATCACTAG-CTCAAAGCCT
* * ** *
407528 GCTA-TATAATCACTGGCTTGAAGCAT
1 ACTAGT-TAATCACTAGCTCAAAGCCT
* * **
407554 GCTATTTAATCACCGGCTCAAAGCCT
1 ACTAGTTAATCACTAGCTCAAAGCCT
* ** *
407580 GCTA-TCTAATCACCGGCTCAAGGCCT
1 ACTAGT-TAATCACTAGCTCAAAGCCT
* * * *
407606 GCTA-TATAATCACCAGCTCGAAGCAT
1 ACTAGT-TAATCACTAGCTCAAAGCCT
*
407632 ACTATTTAATCA
1 ACTAGTTAATCA
407644 TCGGCTCGAA
Statistics
Matches: 138, Mismatches: 24, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
25 3 0.02
26 132 0.96
27 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (26 bp):
ACTAGTTAATCACTAGCTCAAAGCCT
Found at i:407590 original size:78 final size:78
Alignment explanation
Indices: 407475--407697 Score: 320
Period size: 78 Copynumber: 2.9 Consensus size: 78
407465 GTTCAAAGTC
** * *
407475 TACTATTTAATCACTAGCTCAAAGCCTACTATATAATCACCGACTCAAGGCCTGCTATATAATCA
1 TACTATTTAATCACCGGCTCAAAGCCTGCTATATAATCACCGGCTCAAGGCCTGCTATATAATCA
** *
407540 CTGGCTTGAAGCA
66 CCAGCTCGAAGCA
* *
407553 TGCTATTTAATCACCGGCTCAAAGCCTGCTATCTAATCACCGGCTCAAGGCCTGCTATATAATCA
1 TACTATTTAATCACCGGCTCAAAGCCTGCTATATAATCACCGGCTCAAGGCCTGCTATATAATCA
407618 CCAGCTCGAAGCA
66 CCAGCTCGAAGCA
* * * * *
407631 TACTATTTAATCATCGGCTCGAAGCTTGCTATTTAATCATCGGCTCAAGGCCTGCTATATAATCA
1 TACTATTTAATCACCGGCTCAAAGCCTGCTATATAATCACCGGCTCAAGGCCTGCTATATAATCA
407696 CC
66 CC
407698 TCTTTTCCAA
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 130 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (78 bp):
TACTATTTAATCACCGGCTCAAAGCCTGCTATATAATCACCGGCTCAAGGCCTGCTATATAATCA
CCAGCTCGAAGCA
Found at i:407650 original size:26 final size:26
Alignment explanation
Indices: 407477--407697 Score: 214
Period size: 26 Copynumber: 8.5 Consensus size: 26
407467 TCAAAGTCTA
** * *
407477 CTATTTAATCACTAGCTCAAAGCCTA
1 CTATTTAATCACCGGCTCGAAGCCTG
* *
407503 CTATATAATCACCGACTC-AAGGCCTG
1 CTATTTAATCACCGGCTCGAA-GCCTG
* * * *
407529 CTATATAATCACTGGCTTGAAGCATG
1 CTATTTAATCACCGGCTCGAAGCCTG
*
407555 CTATTTAATCACCGGCTCAAAGCCTG
1 CTATTTAATCACCGGCTCGAAGCCTG
*
407581 CTATCTAATCACCGGCTC-AAGGCCTG
1 CTATTTAATCACCGGCTCGAA-GCCTG
* * * *
407607 CTATATAATCACCAGCTCGAAGCATA
1 CTATTTAATCACCGGCTCGAAGCCTG
* *
407633 CTATTTAATCATCGGCTCGAAGCTTG
1 CTATTTAATCACCGGCTCGAAGCCTG
*
407659 CTATTTAATCATCGGCTC-AAGGCCTG
1 CTATTTAATCACCGGCTCGAA-GCCTG
*
407685 CTATATAATCACC
1 CTATTTAATCACC
407698 TCTTTTCCAA
Statistics
Matches: 163, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
25 6 0.04
26 153 0.94
27 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (26 bp):
CTATTTAATCACCGGCTCGAAGCCTG
Found at i:409514 original size:20 final size:20
Alignment explanation
Indices: 409478--409527 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
409468 ATCAGCATGA
409478 TTTATATTAAGTGTAAATAG-G
1 TTTA-ATTAAGTGTAAA-AGAG
409499 TTTAATTAAGAT-TAAAAGAG
1 TTTAATTAAG-TGTAAAAGAG
*
409519 GTTAATTAA
1 TTTAATTAA
409528 ATCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (20 bp):
TTTAATTAAGTGTAAAAGAG
Found at i:413828 original size:41 final size:41
Alignment explanation
Indices: 413748--413868 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 41
413738 GTGTCGATTT
* * * *
413748 GAGCATGAGAATTTATATGAATGGAAGACTCGTGACTCAAAAC
1 GAGCATGAGAA--TATATTAAAGGAAGACTCATGTCTCAAAAC
* * * *
413791 GAGCATGAGAATATATTTAAGGAATACTCATGTCTCAAGAT
1 GAGCATGAGAATATATTAAAGGAAGACTCATGTCTCAAAAC
*
413832 GAGAATGAGAATATGATTAAAGGAAGACTCATGTCTC
1 GAGCATGAGAATAT-ATTAAAGGAAGACTCATGTCTC
413869 GGGATGAGGA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 35 0.53
42 20 0.30
43 11 0.17
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (41 bp):
GAGCATGAGAATATATTAAAGGAAGACTCATGTCTCAAAAC
Found at i:413866 original size:42 final size:42
Alignment explanation
Indices: 413770--413906 Score: 141
Period size: 42 Copynumber: 3.3 Consensus size: 42
413760 TTATATGAAT
* * * * * *
413770 GGAAGACTCGTGACTCAAAACGAGCATGAGAATAT-ATTTAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATTAAA
*
413811 GGAATACTCATGTCTCAAGATGAGAATGAGAATATGATTAAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATTAAA
** * * * * *
413853 GGAAGACTCATGTCTCGGGATGAGGATAAGCATACGACTAAA
1 GGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATTAAA
413895 GGAAGACTCATG
1 GGAAGACTCATG
413907 ACTCGGAATG
Statistics
Matches: 80, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 29 0.36
42 51 0.64
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (42 bp):
GGAAGACTCATGTCTCAAGATGAGAATGAGAATATGATTAAA
Found at i:420984 original size:42 final size:42
Alignment explanation
Indices: 420925--421063 Score: 197
Period size: 42 Copynumber: 3.3 Consensus size: 42
420915 GATATATTTT
420925 AGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATTAA
1 AGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATTAA
* * *
420967 AGGAAGACTCCTATCTCAGGATGAGAATTAGAATATGATTAA
1 AGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATTAA
* ** * *
421009 AGAAAGTTTCATGTCTCGGGATGAGAATGAGAATACGATTAA
1 AGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATTAA
*
421051 AGTAAGACTCATG
1 AGGAAGACTCATG
421064 ACTCGGAATG
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 83 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (42 bp):
AGGAAGACTCATGTCTCAGGATGAGAATGAGAATATGATTAA
Found at i:425474 original size:21 final size:21
Alignment explanation
Indices: 425448--425499 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
425438 AGTGTGTGTG
425448 AAAACCCAAT-ACCCAAATCCT
1 AAAACCCAATCACCCAAA-CCT
* *
425469 AAAACCAAATCACCTAAACCT
1 AAAACCCAATCACCCAAACCT
*
425490 TAAACCCAAT
1 AAAACCCAAT
425500 TCGATTTGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAACCCAATCACCCAAACCT
Found at i:432348 original size:24 final size:24
Alignment explanation
Indices: 432303--432362 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
432293 GATTTGACCC
* *
432303 ACCTATTGACCGAACACGACCCGA
1 ACCTCTTGACCGAACACAACCCGA
*
432327 ACC-CGTTGACCGAAC-CTAACCCGG
1 ACCTC-TTGACCGAACAC-AACCCGA
432351 ACCTCTTGACCG
1 ACCTCTTGACCG
432363 TTGACTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.27, C:0.40, G:0.18, T:0.15
Consensus pattern (24 bp):
ACCTCTTGACCGAACACAACCCGA
Found at i:436671 original size:26 final size:27
Alignment explanation
Indices: 436620--436682 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
436610 TATGAATAAA
436620 CTAAATTGATTTATATATGACAATTAG
1 CTAAATTGATTTATATATGACAATTAG
*
436647 -TAAATTGATTTA-A-ATTACATTATTAG
1 CTAAATTGATTTATATATGACA--ATTAG
436673 CTAAATTGAT
1 CTAAATTGAT
436683 CATATGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.16
25 1 0.03
26 17 0.53
27 9 0.28
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (27 bp):
CTAAATTGATTTATATATGACAATTAG
Found at i:436950 original size:24 final size:24
Alignment explanation
Indices: 436914--437076 Score: 220
Period size: 24 Copynumber: 6.8 Consensus size: 24
436904 TTTTGTCTAT
* *
436914 AGTGGCTGACGAGCGTAAACGTAA
1 AGTGGCTGGCGAGCATAAACGTAA
* *
436938 AGTGGCTAGCGAGCATAAACATAA
1 AGTGGCTGGCGAGCATAAACGTAA
* *
436962 AGTGGTTGGCGAGCTTAAACGTAA
1 AGTGGCTGGCGAGCATAAACGTAA
* *
436986 AGTGTCTGGCGAGCATAAACATAA
1 AGTGGCTGGCGAGCATAAACGTAA
437010 AGTGGCTGGCGAGCATAAACGTAA
1 AGTGGCTGGCGAGCATAAACGTAA
* *
437034 AGT-GTTGGCGAGCATAAACGTAT
1 AGTGGCTGGCGAGCATAAACGTAA
*
437057 AGTGGCTGACGAGCATAAAC
1 AGTGGCTGGCGAGCATAAAC
437077 ATAACTGAAA
Statistics
Matches: 120, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
23 21 0.17
24 99 0.82
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (24 bp):
AGTGGCTGGCGAGCATAAACGTAA
Found at i:436999 original size:72 final size:71
Alignment explanation
Indices: 436914--437080 Score: 253
Period size: 72 Copynumber: 2.3 Consensus size: 71
436904 TTTTGTCTAT
* * *
436914 AGTGGCTGACGAGCGTAAACGTAAAGTGGCTAGCGAGCATAAACATAAAGTGGTTGGCGAGCTTA
1 AGTGGCTGACGAGCATAAACATAAAGTGGCTAGCGAGCATAAACATAAAGT-GTTGGCGAGCATA
436979 AACGTAA
65 AACGTAA
* * * *
436986 AGTGTCTGGCGAGCATAAACATAAAGTGGCTGGCGAGCATAAACGTAAAGTGTTGGCGAGCATAA
1 AGTGGCTGACGAGCATAAACATAAAGTGGCTAGCGAGCATAAACATAAAGTGTTGGCGAGCATAA
*
437051 ACGTAT
66 ACGTAA
437057 AGTGGCTGACGAGCATAAACATAA
1 AGTGGCTGACGAGCATAAACATAA
437081 CTGAAACTTG
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 40 0.47
72 45 0.53
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (71 bp):
AGTGGCTGACGAGCATAAACATAAAGTGGCTAGCGAGCATAAACATAAAGTGTTGGCGAGCATAA
ACGTAA
Found at i:439231 original size:28 final size:28
Alignment explanation
Indices: 439181--439246 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
439171 TACAAATGAG
*
439181 TAAATTGGAAATTTTGTGAAAGTTGGGGAC
1 TAAATT-G-AATTTTGTGAAAGTTGAGGAC
*
439211 TAAATTGAATTTTAGTG-AAGTTTAGGAC
1 TAAATTGAATTTT-GTGAAAGTTGAGGAC
439239 TAAATTGA
1 TAAATTGA
439247 GCTTTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 23 0.70
29 4 0.12
30 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (28 bp):
TAAATTGAATTTTGTGAAAGTTGAGGAC
Found at i:440547 original size:29 final size:29
Alignment explanation
Indices: 440515--440572 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
440505 TGAGTTGTTT
*
440515 GTATGATATTATTCTGAT-TTGTGTTATCA
1 GTATGATATTATTCTG-TGATGTGTTATCA
440544 GTATGATATTATTCTGTGATGTGTTATCA
1 GTATGATATTATTCTGTGATGTGTTATCA
440573 CATGTTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 26 0.96
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (29 bp):
GTATGATATTATTCTGTGATGTGTTATCA
Found at i:442845 original size:66 final size:65
Alignment explanation
Indices: 442759--442890 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 65
442749 ACATTTCCAC
* * * * **
442759 TCACATAAGTAGATAACATCAAGAGTGTTTCCGTGATTATTACTCTAAACATATTTATATTATAG
1 TCACATAAGTAGATAACATCAAGAATATTCCCGTGATTATAAAACT-AACATATTTATATTATAG
442824 G
65 G
* ** * *
442825 TCACATAGGTAGATCCCATCAAGAATATTCCCGTTATTATAAAACTAACATATTTATGTTATAGG
1 TCACATAAGTAGATAACATCAAGAATATTCCCGTGATTATAAAACTAACATATTTATATTATAGG
442890 T
1 T
442891 TATTAAGAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
65 19 0.35
66 36 0.65
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (65 bp):
TCACATAAGTAGATAACATCAAGAATATTCCCGTGATTATAAAACTAACATATTTATATTATAGG
Found at i:444961 original size:22 final size:22
Alignment explanation
Indices: 444925--444985 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 22
444915 CGATTTAAGG
444925 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
444946 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
444968 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
444986 GAAAGTCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 11 0.30
22 25 0.68
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:444976 original size:15 final size:16
Alignment explanation
Indices: 444951--444980 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
444941 GAATTAAAAA
444951 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
444967 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
444981 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:446655 original size:2 final size:2
Alignment explanation
Indices: 446650--446704 Score: 87
Period size: 2 Copynumber: 28.0 Consensus size: 2
446640 TTTGGTTTTG
446650 AT AT AT AT AGT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
446691 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
446705 CAGTTAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 47 0.94
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:449441 original size:44 final size:44
Alignment explanation
Indices: 449378--449472 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
449368 GAAGTCTAAT
*
449378 GTATGTTTAGTTTTGTATACATTGGAATATTGTGTACACTATTG
1 GTATGTTCAGTTTTGTATACATTGGAATATTGTGTACACTATTG
*
449422 GTATGTTCAGTTTTGTATACATTGGAATATTGTGTACAGTATTG
1 GTATGTTCAGTTTTGTATACATTGGAATATTGTGTACACTATTG
*
449466 GGATGTT
1 GTATGTT
449473 AAGCAGGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.24, C:0.06, G:0.23, T:0.46
Consensus pattern (44 bp):
GTATGTTCAGTTTTGTATACATTGGAATATTGTGTACACTATTG
Found at i:453658 original size:76 final size:76
Alignment explanation
Indices: 453532--453672 Score: 201
Period size: 76 Copynumber: 1.9 Consensus size: 76
453522 GCAAGCAGAC
* * ** * *
453532 CAAAATAGTACACGTGTCCAACATGCATGAAACCTATTAAGAACATCAATTCCTCGTCAACTCCA
1 CAAAACAGTACACGTGTCCAACATGCATGAAACATACCAAGAACATCAATTCCACATCAACTCCA
453597 CACTCATTGCA
66 CACTCATTGCA
* * *
453608 CAAAACAGTACACGTGTCCAGCATGCATGAAGCATACCAAGAACGTCAATTCCACATCAACTCCA
1 CAAAACAGTACACGTGTCCAACATGCATGAAACATACCAAGAACATCAATTCCACATCAACTCCA
453673 TGAACAGTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.21
Consensus pattern (76 bp):
CAAAACAGTACACGTGTCCAACATGCATGAAACATACCAAGAACATCAATTCCACATCAACTCCA
CACTCATTGCA
Found at i:464091 original size:47 final size:47
Alignment explanation
Indices: 464022--464116 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
464012 TTATATTAAT
464022 CCTACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGA
1 CCTACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGA
464069 CCTACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGA
1 CCTACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGA
464116 C
1 C
464117 ATTGGTAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (47 bp):
CCTACAATTGGACAATTGAATTATAAGATAAGTAAACTTAAAAGTGA
Found at i:464787 original size:53 final size:53
Alignment explanation
Indices: 464704--464804 Score: 157
Period size: 53 Copynumber: 1.9 Consensus size: 53
464694 AGTCGCAACA
*
464704 TGGTACTTATGTGAGGTCGCGACGAACTCAAGTCAATGAGTGAGGTCGTGATG
1 TGGTACTTATGTGAGGTCGCGACGAACTCAAGTCAAAGAGTGAGGTCGTGATG
* * * *
464757 TGGTACTTATGTGCGGTTGCGATGAGCTCAAGTCAAAGAGTGAGGTCG
1 TGGTACTTATGTGAGGTCGCGACGAACTCAAGTCAAAGAGTGAGGTCG
464805 CAATATGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.27
Consensus pattern (53 bp):
TGGTACTTATGTGAGGTCGCGACGAACTCAAGTCAAAGAGTGAGGTCGTGATG
Found at i:477743 original size:31 final size:31
Alignment explanation
Indices: 477700--477758 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
477690 CACAAGTACG
477700 TAACATTCTCAAGAGTGCCATTTGTTCAACA
1 TAACATTCTCAAGAGTGCCATTTGTTCAACA
* *
477731 TAACTTTCTCAAGAGTGCCATTTTTTCA
1 TAACATTCTCAAGAGTGCCATTTGTTCA
477759 TGGAAATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (31 bp):
TAACATTCTCAAGAGTGCCATTTGTTCAACA
Found at i:481565 original size:4 final size:4
Alignment explanation
Indices: 481550--481606 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
481540 TTACAAGAAT
* * *
481550 TGTA TTTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG CGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
481598 TGCA TGTA T
1 TGTA TGTA T
481607 TAAGCCCCTG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.23, C:0.04, G:0.25, T:0.49
Consensus pattern (4 bp):
TGTA
Found at i:483909 original size:30 final size:30
Alignment explanation
Indices: 483875--483947 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
483865 CAAATTTGAT
*
483875 TTTTTGGAAACTTCACGGGTCAAATCAAAA
1 TTTTTGGAAACTTAACGGGTCAAATCAAAA
* * * * * *
483905 TTTTTAGAAAATTAAGGGGTGAAATTAGAA
1 TTTTTGGAAACTTAACGGGTCAAATCAAAA
483935 TTTTTGGAAACTT
1 TTTTTGGAAACTT
483948 TGGGGGCCTA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.36
Consensus pattern (30 bp):
TTTTTGGAAACTTAACGGGTCAAATCAAAA
Found at i:484026 original size:29 final size:30
Alignment explanation
Indices: 483963--484022 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
483953 GCCTAATTGG
** *
483963 AATTTTTAGAAAATTTGGATGTCATATTAG
1 AATTTTTAGAAAATTTGGATGTCATAAAAA
483993 AATTTTTAGAAAATTTGGA-GTC-TAAAAA
1 AATTTTTAGAAAATTTGGATGTCATAAAAA
484021 AA
1 AA
484023 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 3 0.11
30 19 0.70
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.38
Consensus pattern (30 bp):
AATTTTTAGAAAATTTGGATGTCATAAAAA
Found at i:489314 original size:31 final size:30
Alignment explanation
Indices: 489249--489316 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
489239 AGACATAGTC
* **
489249 ATTAA-ATCTTTAAAAATCGAAAATTATTT
1 ATTAATATCTTTAAAAATAGAAAATTATAA
* *
489278 TTTAATATCTTTAAAAATTATAAAATTATAA
1 ATTAATATCTTTAAAAA-TAGAAAATTATAA
489309 ATTAATAT
1 ATTAATAT
489317 AACGATAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 4 0.13
30 11 0.35
31 16 0.52
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (30 bp):
ATTAATATCTTTAAAAATAGAAAATTATAA
Found at i:489720 original size:24 final size:23
Alignment explanation
Indices: 489663--489732 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
489653 TTCATTTAAC
* *
489663 TTAATCGAACATATTCACAAACA
1 TTAATTGAACATGTTCACAAACA
* * *
489686 TTAAATGAACATGTTCATAAATA
1 TTAATTGAACATGTTCACAAACA
*
489709 TATAATTGAACATGTTCACGAACA
1 T-TAATTGAACATGTTCACAAACA
489733 ATATTAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 19 0.51
24 18 0.49
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.30
Consensus pattern (23 bp):
TTAATTGAACATGTTCACAAACA
Found at i:499712 original size:21 final size:21
Alignment explanation
Indices: 499666--499726 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
499656 CGATCTAAGG
499666 AAAAATAAAAGAAACAT-AATT
1 AAAAATAAAAGAAA-ATAAATT
499687 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATA-AATT
*
499709 AAAAGA-AATAGAAAATAA
1 AAAA-ATAAAAGAAAATAA
499727 GGAAGTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 18 0.50
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAAATAAATT
Found at i:499719 original size:15 final size:16
Alignment explanation
Indices: 499692--499721 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
499682 TAATTAAAAA
499692 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
499708 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
499722 AATAAGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:503322 original size:21 final size:21
Alignment explanation
Indices: 503296--503335 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
503286 ATAAATGCCT
*
503296 CAGTTTTCTTTCGAAAATCCA
1 CAGTTTGCTTTCGAAAATCCA
*
503317 CAGTTTGCTTTTGAAAATC
1 CAGTTTGCTTTCGAAAATC
503336 TATAAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (21 bp):
CAGTTTGCTTTCGAAAATCCA
Found at i:504683 original size:22 final size:21
Alignment explanation
Indices: 504647--504707 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
504637 TGATCTAAGG
504647 AAAAATAAAAGAAATAGAATT
1 AAAAATAAAAGAAATAGAATT
504668 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAG-AAATAGAATT
*
504690 AAAAGA-AATAGAAATAGA
1 AAAA-ATAAAAGAAATAGA
504708 GAAGTCGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 18 0.49
22 18 0.49
23 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAGAAATAGAATT
Found at i:504698 original size:15 final size:16
Alignment explanation
Indices: 504673--504702 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
504663 GAATTAAAAA
504673 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
504689 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
504703 ATAGAGAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:536301 original size:3 final size:3
Alignment explanation
Indices: 536288--536329 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
536278 CATTGGAATC
* *
536288 AAG AGAG AAG AAG ATG AAG ATG AAG AAG AAG AAG AAG -AG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
536330 TGTGTGGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.36, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:543302 original size:20 final size:20
Alignment explanation
Indices: 543259--543303 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
543249 GTTTTCGGAA
543259 AATATTTTTTAGAAAATATT
1 AATATTTTTTAGAAAATATT
543279 --TATTTTTCTAGAAAA-ATT
1 AATATTTTT-TAGAAAATATT
543297 AATATTT
1 AATATTT
543304 GTTTTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
AATATTTTTTAGAAAATATT
Found at i:544793 original size:18 final size:19
Alignment explanation
Indices: 544747--544793 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
544737 ATTTGATTTG
544747 ATTTGTAAAATTTTAAATTA
1 ATTT-TAAAATTTTAAATTA
* *
544767 AATTAAAAATTTTAAA-TA
1 ATTTTAAAATTTTAAATTA
544785 ATTTTAAAA
1 ATTTTAAAA
544794 AATATTTACT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTTAAAATTTTAAATTA
Found at i:545423 original size:20 final size:21
Alignment explanation
Indices: 545385--545423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
545375 AATGTAAAAG
545385 ATTGTTGTTGTGATTAGTTGA
1 ATTGTTGTTGTGATTAGTTGA
545406 ATTGTTCGTTG-G-TTAGTT
1 ATTGTT-GTTGTGATTAGTT
545424 ACTGCTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.15, C:0.03, G:0.28, T:0.54
Consensus pattern (21 bp):
ATTGTTGTTGTGATTAGTTGA
Found at i:545480 original size:6 final size:6
Alignment explanation
Indices: 545469--545556 Score: 53
Period size: 6 Copynumber: 15.2 Consensus size: 6
545459 TGGGCCCAAC
* * *
545469 AAATTT AAATTT -ATTTT AAATTT AAGTTT ATA-TT AAATTT AAA--T
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
* * *
545513 CAATTT GGAATTT AAA--T ATATTAT AAATATT AAATTT AAATTT A
1 AAATTT -AAATTT AAATTT AAATT-T AAAT-TT AAATTT AAATTT A
545557 CTTAAATTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 18
0.68 0.12 0.20
Matches are distributed among these distances:
4 6 0.10
5 8 0.13
6 33 0.53
7 14 0.23
8 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:545491 original size:17 final size:17
Alignment explanation
Indices: 545469--545550 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
545459 TGGGCCCAAC
545469 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
545486 AAATTTAAGTTTATATT
1 AAATTTAAATTTATTTT
** *
545503 AAATTTAAATCAATTTG
1 AAATTTAAATTTATTTT
* * *
545520 GAATTTAAATATATTAT
1 AAATTTAAATTTATTTT
545537 AAATATTAAATTTA
1 AAAT-TTAAATTTA
545551 AATTTACTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
17 42 0.84
18 8 0.16
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:547463 original size:29 final size:29
Alignment explanation
Indices: 547419--547734 Score: 206
Period size: 30 Copynumber: 10.8 Consensus size: 29
547409 CCCTTGAACT
* *
547419 TTTCCAAAA-TTCCATTTTGACCCCAAAC
1 TTTCCAAAATTTACATTTTAACCCCAAAC
* *
547447 -TTCTCAAAATTTACATTTTTACCCTTAAAC
1 TTTC-CAAAATTTACATTTTAACCC-CAAAC
* *
547477 TTTCCAAAATTCA-ATTTTTAACCCCAAAT
1 TTTCCAAAATTTACA-TTTTAACCCCAAAC
*
547506 TCTTCCAAAA-TTACAATTTT-ACCCTTAAAC
1 T-TTCCAAAATTTAC-ATTTTAACCC-CAAAC
* * *
547536 TTTTCTAAAA-TT-CTATTTTAACCCTAAAT
1 -TTTCCAAAATTTAC-ATTTTAACCCCAAAC
* *
547565 TTTCCAAAAATTACACTTTT-TCCCTCAAAC
1 TTTCCAAAATTTACA-TTTTAACCC-CAAAC
* **
547595 TTTCCAAAATTT-CATTTTAACCACAATT
1 TTTCCAAAATTTACATTTTAACCCCAAAC
* *
547623 TTTCCAAAAATTACACTTTT-GCCCCAAAC
1 TTTCCAAAATTTACA-TTTTAACCCCAAAC
* * * *
547652 TTTCCAAAA-TTCCATTTTAACCTCGAAT
1 TTTCCAAAATTTACATTTTAACCCCAAAC
*
547680 TTTCCAAAAATTACATGTTT-ACCCCTAAAAC
1 TTTCCAAAATTTACAT-TTTAACCCC--AAAC
* *
547711 TTTCCAAAATTTCCATTTTTACCC
1 TTTCCAAAATTTACATTTTAACCC
547735 TCGAATGTTT
Statistics
Matches: 226, Mismatches: 38, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
27 7 0.03
28 49 0.22
29 68 0.30
30 77 0.34
31 25 0.11
ACGTcount: A:0.34, C:0.26, G:0.01, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTTACATTTTAACCCCAAAC
Found at i:547494 original size:58 final size:58
Alignment explanation
Indices: 547393--547734 Score: 368
Period size: 59 Copynumber: 5.8 Consensus size: 58
547383 TAAACTATCA
* * * * * *
547393 AAAAATCATATTTTGACCCTTGAACTTTTCCAAAATTCCATTTTGACCCCAAA-CTTCTC
1 AAAAATTACATTTTTACCCTTAAAC-TTTCCAAAATTCCATTTTAACCCCAAATTTTC-C
* *
547452 AAAATTTACATTTTTACCCTTAAACTTTCCAAAATTCAATTTTTAACCCCAAATTCTTCC
1 AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCA-TTTTAACCCCAAATT-TTCC
* * * *
547512 -AAAATTACAATTTTACCCTTAAACTTTTCTAAAATTCTATTTTAACCCTAAATTTTCC
1 AAAAATTACATTTTTACCCTTAAAC-TTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * * *
547570 AAAAATTACACTTTTT-CCCTCAAACTTTCCAAAATTTCATTTTAACCACAATTTTTCC
1 AAAAATTACA-TTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * * * *
547628 AAAAATTACACTTTTGCCC-CAAACTTTCCAAAATTCCATTTTAACCTCGAATTTTCC
1 AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * *
547685 AAAAATTACATGTTTACCCCTAAAACTTTCCAAAATTTCCATTTTTACCC
1 AAAAATTACATTTTTA-CCCTTAAACTTTCCAAAA-TTCCATTTTAACCC
547735 TCGAATGTTT
Statistics
Matches: 241, Mismatches: 32, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
57 51 0.21
58 60 0.25
59 98 0.41
60 29 0.12
61 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
Found at i:547749 original size:59 final size:56
Alignment explanation
Indices: 547419--547792 Score: 266
Period size: 59 Copynumber: 6.4 Consensus size: 56
547409 CCCTTGAACT
* * *
547419 TTTCCAAAATTCCATTTTGACCC-CAAACTTCTCAAAATTTACATTTTTACCCTTAAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAA-TTTTCAAAA-TTACA-TTTTACCCCTAAAC
* *
547477 TTTCCAAAATTCAATTTTTAACCC-CAAATTCTTCCAAAATTACAATTTTACCCTTAAAC
1 TTTCCAAAATTCCATTTTT-ACCCTCAAATT-TT-CAAAATTAC-ATTTTACCCCTAAAC
* * * *
547536 TTTTCTAAAATTCTATTTTAACCCT-AAATTTTCCAAAAATTACACTTTT-TCCCTCAAAC
1 -TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACA-TTTTACCCCT-AAAC
* * * * *
547595 TTTCCAAAATTTCA-TTTTAACCACAATTTTTCCAAAAATTACACTTTTGCCCC-AAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACA-TTTTACCCCTAAAC
* *
547652 TTTCCAAAATTCCA-TTTTAACCTCGAATTTTCCAAAAATTACATGTTTACCCCTAAAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACAT-TTTACCCCT-AAAC
* * *
547711 TTTCCAAAATTTCCATTTTTACCCTCGAATGTTT-AAAATT-CTATTTTTGACCCC-GAGC
1 TTTCCAAAA-TTCCATTTTTACCCTCAAAT-TTTCAAAATTAC-A-TTTT-ACCCCTAAAC
547769 TTTCCAAAAATTACCA-TTTTACCC
1 TTTCC-AAAATT-CCATTTTTACCC
547793 CCGAATGTCT
Statistics
Matches: 270, Mismatches: 24, Indels: 44
0.80 0.07 0.13
Matches are distributed among these distances:
56 1 0.00
57 56 0.21
58 79 0.29
59 85 0.31
60 33 0.12
61 13 0.05
62 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (56 bp):
TTTCCAAAATTCCATTTTTACCCTCAAATTTTCAAAATTACATTTTACCCCTAAAC
Found at i:547792 original size:29 final size:30
Alignment explanation
Indices: 547414--547906 Score: 225
Period size: 29 Copynumber: 16.8 Consensus size: 30
547404 TTTGACCCTT
*
547414 GAACTTTTCC-AAAATT-CCATTTTGACCCC
1 GAAC-TTTCCAAAAATTACCATTTTTACCCC
* * *
547443 AAAC-TTCTCAAAATTTA-CATTTTTACCCTT
1 GAACTTTC-CAAAAATTACCATTTTTACCC-C
* *
547473 AAACTTTCC-AAAATT-CAATTTTTAACCCC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
* * * *
547502 AAATTCTTCC-AAAATTA-CAATTTTACCCTT
1 GAACT-TTCCAAAAATTACCATTTTTACCC-C
* * * * * *
547532 AAACTTTTCTAAAATT-CTATTTTAACCCT
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
547561 AAATTTTCCAAAAATTA-CACTTTTT-CCCTC
1 GAACTTTCCAAAAATTACCA-TTTTTACCC-C
* * * *
547591 AAACTTTCC-AAAATT-TCATTTTAACCAC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* * *
547619 -AATTTTTCCAAAAATTA-CACTTTTGCCCC
1 GAA-CTTTCCAAAAATTACCATTTTTACCCC
* * *
547648 AAACTTTCC-AAAATT-CCATTTTAACCTC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
547676 GAATTTTCCAAAAATTA-CATGTTTACCCC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
547705 TAAAACTTTCC-AAAATTTCCATTTTTACCCTC
1 --GAACTTTCCAAAAATTACCATTTTTACCC-C
* *
547737 GAA-TGTT--TAAAATT-CTATTTTTGACCCC
1 GAACT-TTCCAAAAATTACCATTTTT-ACCCC
*
547765 GAGCTTTCCAAAAATTACCA-TTTTACCCCC
1 GAACTTTCCAAAAATTACCATTTTTA-CCCC
* ** *
547795 GAA-TGTCTGAAAA-TACCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
*
547824 GAACCTTCCAAAAATTACCA-TTTTACCCC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* * * *
547853 GAAATATCTAAAAATT-CCATTTTTAACCTC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
547883 GAACCTTT-CAAAAATTACCATTTT
1 GAA-CTTTCCAAAAATTACCATTTT
547907 GTTCCCGAAG
Statistics
Matches: 353, Mismatches: 67, Indels: 86
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.01
28 52 0.15
29 152 0.43
30 107 0.30
31 36 0.10
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACCATTTTTACCCC
Found at i:547808 original size:59 final size:59
Alignment explanation
Indices: 547708--547906 Score: 244
Period size: 59 Copynumber: 3.4 Consensus size: 59
547698 TTACCCCTAA
* * * * *
547708 AACTTTCC-AAAATTTCCATTTTTACCCTCGAATGT-TTAAAATTCTATTTTTGACCCCG
1 AACTTTCCAAAAATTACCA-TTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
* * *
547766 AGCTTTCCAAAAATTACCATTTTACCCCCGAATGTCTGAAAATACCATTTTTGACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
* * *
547825 AACCTTCCAAAAATTACCATTTTA-CCCCGAAATATCTAAAAATTCCATTTTTAACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCCCG-AATGTCTAAAAATTCCATTTTTGACCTCG
547884 AACCTTT-CAAAAATTACCATTTT
1 AA-CTTTCCAAAAATTACCATTTT
547907 GTTCCCGAAG
Statistics
Matches: 123, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 27 0.22
59 93 0.76
60 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
AACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
Found at i:554323 original size:6 final size:6
Alignment explanation
Indices: 554298--554342 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
554288 ACAATTCATA
* * *
554298 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
554343 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:556038 original size:27 final size:27
Alignment explanation
Indices: 556000--556054 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
555990 ACACAATTAC
556000 TAATTAATCCTTGAATTTTCTTAACCT
1 TAATTAATCCTTGAATTTTCTTAACCT
556027 TAATTAATCCTTGAATTTTCTTAACCT
1 TAATTAATCCTTGAATTTTCTTAACCT
556054 T
1 T
556055 TCTTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATTAATCCTTGAATTTTCTTAACCT
Found at i:558153 original size:31 final size:31
Alignment explanation
Indices: 558118--558176 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
558108 AAACAAGAAT
558118 TAACTTATTCACAA-AAATAAA-AAATAAAAAA
1 TAACTT-TT-ACAATAAATAAATAAATAAAAAA
558149 TAACTTTTACAATAAATAAATAAATAAA
1 TAACTTTTACAATAAATAAATAAATAAA
558177 TTGGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 9 0.35
31 13 0.50
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (31 bp):
TAACTTTTACAATAAATAAATAAATAAAAAA
Found at i:560036 original size:21 final size:20
Alignment explanation
Indices: 560007--560045 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
559997 TAATGTCACG
560007 TCAGCATTTTCATCCTTAATT
1 TCAGCATTTTCAT-CTTAATT
*
560028 TCAGGATTTTCATCTTAA
1 TCAGCATTTTCATCTTAA
560046 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
TCAGCATTTTCATCTTAATT
Found at i:560166 original size:42 final size:42
Alignment explanation
Indices: 560107--560191 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
560097 TATTGATGTG
*
560107 ACATTAAACTATTGGAAATGGATAATATCATTGTTTCATACA
1 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
560149 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
1 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
560191 A
1 A
560192 TCCTAGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (42 bp):
ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
Found at i:562511 original size:29 final size:29
Alignment explanation
Indices: 562467--562782 Score: 206
Period size: 30 Copynumber: 10.8 Consensus size: 29
562457 CCCTTGAACT
* *
562467 TTTCCAAAA-TTCCATTTTGACCCCAAAC
1 TTTCCAAAATTTACATTTTAACCCCAAAC
* *
562495 -TTCTCAAAATTTACATTTTTACCCTTAAAC
1 TTTC-CAAAATTTACATTTTAACCC-CAAAC
* *
562525 TTTCCAAAATTCA-ATTTTTAACCCCAAAT
1 TTTCCAAAATTTACA-TTTTAACCCCAAAC
*
562554 TCTTCCAAAA-TTACAATTTT-ACCCTTAAAC
1 T-TTCCAAAATTTAC-ATTTTAACCC-CAAAC
* * *
562584 TTTTCTAAAA-TT-CTATTTTAACCCTAAAT
1 -TTTCCAAAATTTAC-ATTTTAACCCCAAAC
* *
562613 TTTCCAAAAATTACACTTTT-TCCCTCAAAC
1 TTTCCAAAATTTACA-TTTTAACCC-CAAAC
* **
562643 TTTCCAAAATTT-CATTTTAACCACAATT
1 TTTCCAAAATTTACATTTTAACCCCAAAC
* *
562671 TTTCCAAAAATTACACTTTT-GCCCCAAAC
1 TTTCCAAAATTTACA-TTTTAACCCCAAAC
* * * *
562700 TTTCCAAAA-TTCCATTTTAACCTCGAAT
1 TTTCCAAAATTTACATTTTAACCCCAAAC
*
562728 TTTCCAAAAATTACATGTTT-ACCCCTAAAAC
1 TTTCCAAAATTTACAT-TTTAACCCC--AAAC
* *
562759 TTTCCAAAATTTCCATTTTTACCC
1 TTTCCAAAATTTACATTTTAACCC
562783 TCGAATGTTT
Statistics
Matches: 226, Mismatches: 38, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
27 7 0.03
28 49 0.22
29 68 0.30
30 77 0.34
31 25 0.11
ACGTcount: A:0.34, C:0.26, G:0.01, T:0.39
Consensus pattern (29 bp):
TTTCCAAAATTTACATTTTAACCCCAAAC
Found at i:562542 original size:58 final size:58
Alignment explanation
Indices: 562441--562782 Score: 368
Period size: 59 Copynumber: 5.8 Consensus size: 58
562431 TAAACTATCA
* * * * * *
562441 AAAAATCATATTTTGACCCTTGAACTTTTCCAAAATTCCATTTTGACCCCAAA-CTTCTC
1 AAAAATTACATTTTTACCCTTAAAC-TTTCCAAAATTCCATTTTAACCCCAAATTTTC-C
* *
562500 AAAATTTACATTTTTACCCTTAAACTTTCCAAAATTCAATTTTTAACCCCAAATTCTTCC
1 AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCA-TTTTAACCCCAAATT-TTCC
* * * *
562560 -AAAATTACAATTTTACCCTTAAACTTTTCTAAAATTCTATTTTAACCCTAAATTTTCC
1 AAAAATTACATTTTTACCCTTAAAC-TTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * * *
562618 AAAAATTACACTTTTT-CCCTCAAACTTTCCAAAATTTCATTTTAACCACAATTTTTCC
1 AAAAATTACA-TTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * * * *
562676 AAAAATTACACTTTTGCCC-CAAACTTTCCAAAATTCCATTTTAACCTCGAATTTTCC
1 AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
* * *
562733 AAAAATTACATGTTTACCCCTAAAACTTTCCAAAATTTCCATTTTTACCC
1 AAAAATTACATTTTTA-CCCTTAAACTTTCCAAAA-TTCCATTTTAACCC
562783 TCGAATGTTT
Statistics
Matches: 241, Mismatches: 32, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
57 51 0.21
58 60 0.25
59 98 0.41
60 29 0.12
61 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
AAAAATTACATTTTTACCCTTAAACTTTCCAAAATTCCATTTTAACCCCAAATTTTCC
Found at i:562797 original size:59 final size:56
Alignment explanation
Indices: 562467--562840 Score: 266
Period size: 59 Copynumber: 6.4 Consensus size: 56
562457 CCCTTGAACT
* * *
562467 TTTCCAAAATTCCATTTTGACCC-CAAACTTCTCAAAATTTACATTTTTACCCTTAAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAA-TTTTCAAAA-TTACA-TTTTACCCCTAAAC
* *
562525 TTTCCAAAATTCAATTTTTAACCC-CAAATTCTTCCAAAATTACAATTTTACCCTTAAAC
1 TTTCCAAAATTCCATTTTT-ACCCTCAAATT-TT-CAAAATTAC-ATTTTACCCCTAAAC
* * * *
562584 TTTTCTAAAATTCTATTTTAACCCT-AAATTTTCCAAAAATTACACTTTT-TCCCTCAAAC
1 -TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACA-TTTTACCCCT-AAAC
* * * * *
562643 TTTCCAAAATTTCA-TTTTAACCACAATTTTTCCAAAAATTACACTTTTGCCCC-AAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACA-TTTTACCCCTAAAC
* *
562700 TTTCCAAAATTCCA-TTTTAACCTCGAATTTTCCAAAAATTACATGTTTACCCCTAAAAC
1 TTTCCAAAATTCCATTTTTACCCTCAAATTTT-C-AAAATTACAT-TTTACCCCT-AAAC
* * *
562759 TTTCCAAAATTTCCATTTTTACCCTCGAATGTTT-AAAATT-CTATTTTTGACCCC-GAGC
1 TTTCCAAAA-TTCCATTTTTACCCTCAAAT-TTTCAAAATTAC-A-TTTT-ACCCCTAAAC
562817 TTTCCAAAAATTACCA-TTTTACCC
1 TTTCC-AAAATT-CCATTTTTACCC
562841 CCGAATGTCT
Statistics
Matches: 270, Mismatches: 24, Indels: 44
0.80 0.07 0.13
Matches are distributed among these distances:
56 1 0.00
57 56 0.21
58 79 0.29
59 85 0.31
60 33 0.12
61 13 0.05
62 3 0.01
ACGTcount: A:0.33, C:0.26, G:0.02, T:0.39
Consensus pattern (56 bp):
TTTCCAAAATTCCATTTTTACCCTCAAATTTTCAAAATTACATTTTACCCCTAAAC
Found at i:562840 original size:29 final size:30
Alignment explanation
Indices: 562462--562954 Score: 225
Period size: 29 Copynumber: 16.8 Consensus size: 30
562452 TTTGACCCTT
*
562462 GAACTTTTCC-AAAATT-CCATTTTGACCCC
1 GAAC-TTTCCAAAAATTACCATTTTTACCCC
* * *
562491 AAAC-TTCTCAAAATTTA-CATTTTTACCCTT
1 GAACTTTC-CAAAAATTACCATTTTTACCC-C
* *
562521 AAACTTTCC-AAAATT-CAATTTTTAACCCC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
* * * *
562550 AAATTCTTCC-AAAATTA-CAATTTTACCCTT
1 GAACT-TTCCAAAAATTACCATTTTTACCC-C
* * * * * *
562580 AAACTTTTCTAAAATT-CTATTTTAACCCT
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
562609 AAATTTTCCAAAAATTA-CACTTTTT-CCCTC
1 GAACTTTCCAAAAATTACCA-TTTTTACCC-C
* * * *
562639 AAACTTTCC-AAAATT-TCATTTTAACCAC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* * *
562667 -AATTTTTCCAAAAATTA-CACTTTTGCCCC
1 GAA-CTTTCCAAAAATTACCATTTTTACCCC
* * *
562696 AAACTTTCC-AAAATT-CCATTTTAACCTC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
562724 GAATTTTCCAAAAATTA-CATGTTTACCCC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* *
562753 TAAAACTTTCC-AAAATTTCCATTTTTACCCTC
1 --GAACTTTCCAAAAATTACCATTTTTACCC-C
* *
562785 GAA-TGTT--TAAAATT-CTATTTTTGACCCC
1 GAACT-TTCCAAAAATTACCATTTTT-ACCCC
*
562813 GAGCTTTCCAAAAATTACCA-TTTTACCCCC
1 GAACTTTCCAAAAATTACCATTTTTA-CCCC
* ** *
562843 GAA-TGTCTGAAAA-TACCATTTTTGACCTC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
*
562872 GAACCTTCCAAAAATTACCA-TTTTACCCC
1 GAACTTTCCAAAAATTACCATTTTTACCCC
* * * *
562901 GAAATATCTAAAAATT-CCATTTTTAACCTC
1 GAACTTTCCAAAAATTACCATTTTT-ACCCC
562931 GAACCTTT-CAAAAATTACCATTTT
1 GAA-CTTTCCAAAAATTACCATTTT
562955 GTTCCCGAAG
Statistics
Matches: 353, Mismatches: 67, Indels: 86
0.70 0.13 0.17
Matches are distributed among these distances:
27 5 0.01
28 52 0.15
29 152 0.43
30 107 0.30
31 36 0.10
32 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (30 bp):
GAACTTTCCAAAAATTACCATTTTTACCCC
Found at i:562856 original size:59 final size:59
Alignment explanation
Indices: 562756--562954 Score: 244
Period size: 59 Copynumber: 3.4 Consensus size: 59
562746 TTACCCCTAA
* * * * *
562756 AACTTTCC-AAAATTTCCATTTTTACCCTCGAATGT-TTAAAATTCTATTTTTGACCCCG
1 AACTTTCCAAAAATTACCA-TTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
* * *
562814 AGCTTTCCAAAAATTACCATTTTACCCCCGAATGTCTGAAAATACCATTTTTGACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
* * *
562873 AACCTTCCAAAAATTACCATTTTA-CCCCGAAATATCTAAAAATTCCATTTTTAACCTCG
1 AACTTTCCAAAAATTACCATTTTACCCCCG-AATGTCTAAAAATTCCATTTTTGACCTCG
562932 AACCTTT-CAAAAATTACCATTTT
1 AA-CTTTCCAAAAATTACCATTTT
562955 GTTCCCGAAG
Statistics
Matches: 123, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
58 27 0.22
59 93 0.76
60 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.36
Consensus pattern (59 bp):
AACTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAAAAATTCCATTTTTGACCTCG
Found at i:569371 original size:6 final size:6
Alignment explanation
Indices: 569346--569384 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
569336 ACAATTCATA
* * *
569346 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
569385 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:571080 original size:27 final size:27
Alignment explanation
Indices: 571042--571096 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
571032 ACACAATTAC
571042 TAATTAATCCTTGAATTTTCTTAACCT
1 TAATTAATCCTTGAATTTTCTTAACCT
571069 TAATTAATCCTTGAATTTTCTTAACCT
1 TAATTAATCCTTGAATTTTCTTAACCT
571096 T
1 T
571097 TCTTATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (27 bp):
TAATTAATCCTTGAATTTTCTTAACCT
Found at i:573195 original size:31 final size:31
Alignment explanation
Indices: 573160--573218 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
573150 AAACAAGAAT
573160 TAACTTATTCACAA-AAATAAA-AAATAAAAAA
1 TAACTT-TT-ACAATAAATAAATAAATAAAAAA
573191 TAACTTTTACAATAAATAAATAAATAAA
1 TAACTTTTACAATAAATAAATAAATAAA
573219 TTGGATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 9 0.35
31 13 0.50
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.27
Consensus pattern (31 bp):
TAACTTTTACAATAAATAAATAAATAAAAAA
Found at i:575078 original size:21 final size:20
Alignment explanation
Indices: 575049--575087 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
575039 TAATGTCACG
575049 TCAGCATTTTCATCCTTAATT
1 TCAGCATTTTCAT-CTTAATT
*
575070 TCAGGATTTTCATCTTAA
1 TCAGCATTTTCATCTTAA
575088 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.46
Consensus pattern (20 bp):
TCAGCATTTTCATCTTAATT
Found at i:575208 original size:42 final size:42
Alignment explanation
Indices: 575149--575233 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
575139 TATTGATGTG
*
575149 ACATTAAACTATTGGAAATGGATAATATCATTGTTTCATACA
1 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
575191 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
1 ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
575233 A
1 A
575234 TCCTAGAGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (42 bp):
ACATTAAACTATTGGAAATGGATAATATCATTGTTCCATACA
Found at i:577181 original size:98 final size:98
Alignment explanation
Indices: 577012--577210 Score: 389
Period size: 98 Copynumber: 2.0 Consensus size: 98
577002 CCTATGTGTG
577012 CAAGGTGTGTGTGCATTGTCAAAGGGTTAAGAAAGTATGAACAAATACTACTATGTAATCACACC
1 CAAGGTGTGTGTGCATTGTCAAAGGGTTAAGAAAGTATGAACAAATACTACTATGTAATCACACC
577077 TAGTTTCAAGATAATCCCATTCTAGTCTCGAGA
66 TAGTTTCAAGATAATCCCATTCTAGTCTCGAGA
577110 CAAGGTGTGTGTGCATTGTCAAAGGGTTAAGAAAGTATGAACAAATACTACTATGTAATCACACC
1 CAAGGTGTGTGTGCATTGTCAAAGGGTTAAGAAAGTATGAACAAATACTACTATGTAATCACACC
*
577175 TAGTTTCAAGATAATCTCATTCTAGTCTCGAGA
66 TAGTTTCAAGATAATCCCATTCTAGTCTCGAGA
577208 CAA
1 CAA
577211 TGAAACATCG
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 100 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (98 bp):
CAAGGTGTGTGTGCATTGTCAAAGGGTTAAGAAAGTATGAACAAATACTACTATGTAATCACACC
TAGTTTCAAGATAATCCCATTCTAGTCTCGAGA
Found at i:580079 original size:6 final size:6
Alignment explanation
Indices: 580068--580092 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
580058 CTAGGCTCTC
580068 GGTGCT GGTGCT GGTGCT GGTGCT G
1 GGTGCT GGTGCT GGTGCT GGTGCT G
580093 CTGATTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTGCT
Found at i:587902 original size:17 final size:17
Alignment explanation
Indices: 587876--587927 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
587866 CATGTATTAG
*
587876 AAAAGTTCATCATCAGA
1 AAAAGGTCATCATCAGA
*
587893 AAAAGGTCAT-AACTAGA
1 AAAAGGTCATCATC-AGA
*
587910 ACAA-GTCATCATCAGA
1 AAAAGGTCATCATCAGA
587926 AA
1 AA
587928 GTCCAACCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.19
Consensus pattern (17 bp):
AAAAGGTCATCATCAGA
Found at i:589729 original size:30 final size:29
Alignment explanation
Indices: 589695--589796 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 29
589685 CATAATATAA
589695 AATTTGGTACCTAAACTTACATTTTTTCTT
1 AATTTGGTACCTAAACTTA-ATTTTTTCTT
*
589725 AATTTGGTACCTAAACTT--TTTTTGT-TC
1 AATTTGGTACCTAAACTTAATTTTT-TCTT
* * *
589752 AATTTGGTA-TTCAAACTTGATACTTTTTCCT
1 AATTTGGTACCT-AAACTT-A-ATTTTTTCTT
589783 AATTTGGTACCTAA
1 AATTTGGTACCTAA
589797 TTTTTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
26 1 0.02
27 21 0.36
28 1 0.02
30 19 0.33
31 15 0.26
32 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (29 bp):
AATTTGGTACCTAAACTTAATTTTTTCTT
Found at i:590315 original size:31 final size:31
Alignment explanation
Indices: 590266--590329 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
590256 TTATAAAATG
*
590266 GTCACTAAATTATGCAAAAGTTTTCATTTAA
1 GTCACTAAACTATGCAAAAGTTTTCATTTAA
* * *
590297 GTCACTCAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATGCAAAAGTTTTCATTTAA
590328 GT
1 GT
590330 TATTGGGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATGCAAAAGTTTTCATTTAA
Found at i:598189 original size:29 final size:29
Alignment explanation
Indices: 598158--598384 Score: 215
Period size: 29 Copynumber: 7.8 Consensus size: 29
598148 TTCATAAGTC
**
598158 CGAGGGTAAAATGGTAATTTTTGGATACC
1 CGAGGGTAAAATGGTAATTTTTGGATATT
* * *
598187 CGAGGGTAAAACGATAATTTTTGGATGTT
1 CGAGGGTAAAATGGTAATTTTTGGATATT
* * *
598216 C-AGGAGTAAAATAGTACTTTTTGGAAAGTT
1 CGAGG-GTAAAATGGTAATTTTTGGATA-TT
* *
598246 CGAGGTTAAAATGGTAATTTTTGGAAAGTT
1 CGAGGGTAAAATGGTAATTTTTGGATA-TT
* * * *
598276 -TAGGGTCAAAATTGTAATTTTTGGACATA
1 CGAGGGT-AAAATGGTAATTTTTGGATATT
* *
598305 CAAGGGTAAAATGGTAATTTTTGGATGTT
1 CGAGGGTAAAATGGTAATTTTTGGATATT
* *
598334 CGAGGGTAAAATGATAATTTTTGGATGTT
1 CGAGGGTAAAATGGTAATTTTTGGATATT
* * *
598363 TGGGGGTAAAATAGTAATTTTT
1 CGAGGGTAAAATGGTAATTTTT
598385 TGAAAGTTTA
Statistics
Matches: 163, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.02
29 109 0.67
30 48 0.29
31 3 0.02
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (29 bp):
CGAGGGTAAAATGGTAATTTTTGGATATT
Found at i:598266 original size:88 final size:88
Alignment explanation
Indices: 598106--598359 Score: 232
Period size: 88 Copynumber: 2.9 Consensus size: 88
598096 AACAAATGGA
* * * * *** *
598106 GTCAAAAT-GTAATTTTTGG--ATGCCGAGGGCAAAACAGTAATTTTCATAAGTCCGAGGGTAAA
1 GTCAAAATCGTAATTTTTGGACAT-ACAAGGGTAAAATAGTAATTTTTGGAAGTTCGAGGGTAAA
598168 ATGGTAATTTTTGGATACCCGAGG
65 ATGGTAATTTTTGGATACCCGAGG
** * * *
598192 GT-AAAA-CGATAATTTTTGGATGTTC-AGGAGTAAAATAGTACTTTTTGGAAAGTTCGAGGTTA
1 GTCAAAATCG-TAATTTTTGGACATACAAGG-GTAAAATAGTAATTTTTGG-AAGTTCGAGGGTA
* ****
598254 AAATGGTAATTTTTGGAAAGTTTAGG
63 AAATGGTAATTTTTGGATACCCGAGG
* * *
598280 GTCAAAATTGTAATTTTTGGACATACAAGGGTAAAATGGTAATTTTTGGATGTTCGAGGGTAAAA
1 GTCAAAATCGTAATTTTTGGACATACAAGGGTAAAATAGTAATTTTTGGAAGTTCGAGGGTAAAA
*
598345 TGATAATTTTTGGAT
66 TGGTAATTTTTGGAT
598360 GTTTGGGGGT
Statistics
Matches: 134, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
85 5 0.04
86 15 0.11
87 14 0.10
88 62 0.46
89 34 0.25
90 4 0.03
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.34
Consensus pattern (88 bp):
GTCAAAATCGTAATTTTTGGACATACAAGGGTAAAATAGTAATTTTTGGAAGTTCGAGGGTAAAA
TGGTAATTTTTGGATACCCGAGG
Found at i:598497 original size:29 final size:29
Alignment explanation
Indices: 598161--598535 Score: 176
Period size: 29 Copynumber: 12.9 Consensus size: 29
598151 ATAAGTCCGA
****
598161 GGGTAAAATGGTAATTTTTGGATACCCGA-
1 GGGTAAAATGGTAATTTTTGGA-AGTTTAG
* * * *
598190 GGGTAAAACGATAATTTTTGGATGTTCAG
1 GGGTAAAATGGTAATTTTTGGAAGTTTAG
* * * *
598219 GAGTAAAATAGTACTTTTTGGAAAG-TTCG
1 GGGTAAAATGGTAATTTTTGG-AAGTTTAG
*
598248 AGGTTAAAATGGTAATTTTTGGAAAGTTTA-
1 -GGGTAAAATGGTAATTTTTGG-AAGTTTAG
* ** *
598278 GGGTCAAAATTGTAATTTTTGGACA-TACAA
1 GGGT-AAAATGGTAATTTTTGGA-AGTTTAG
* *
598308 GGGTAAAATGGTAATTTTTGGATG-TTCG
1 GGGTAAAATGGTAATTTTTGGAAGTTTAG
* * *
598336 AGGGTAAAATGATAATTTTTGGATGTTTGG
1 -GGGTAAAATGGTAATTTTTGGAAGTTTAG
* *
598366 GGGTAAAATAGTAATTTTTTGAAAGTTTA-
1 GGGTAAAATGGTAA-TTTTTGGAAGTTTAG
** * ** ***
598395 GGGTCAAAAAAGTAATTTCTAAAAGTACGG
1 GGGT-AAAATGGTAATTTTTGGAAGTTTAG
* ** * *
598425 GGGCAAAA-CATGATTTTTGGAAGTTTAA
1 GGGTAAAATGGTAATTTTTGGAAGTTTAG
* * *
598453 GGTTAAAAAT-GCAATTTTTAGAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGAAGTTTAG
**
598482 GGGTAAAATGGTAATTTTTTAAAGTTCT-G
1 GGGTAAAATGGTAATTTTTGGAAGTT-TAG
* * *
598511 AGGCAAAAT-GTGATTTTTGGAAGTT
1 GGGTAAAATGGTAATTTTTGGAAGTT
598536 CGAGGACCTT
Statistics
Matches: 259, Mismatches: 70, Indels: 35
0.71 0.19 0.10
Matches are distributed among these distances:
28 31 0.12
29 155 0.60
30 71 0.27
31 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTAG
Found at i:600358 original size:17 final size:17
Alignment explanation
Indices: 600338--600428 Score: 110
Period size: 17 Copynumber: 5.4 Consensus size: 17
600328 AATTTTTAAT
600338 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
600355 TAAATTCAAATTTAAAA
1 TAAATTTAAATTTAAAA
* * *
600372 TGAACTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
* *
600389 TAAATTTAAATTTATAC
1 TAAATTTAAATTTAAAA
* *
600406 TAAATTCAAACTTAAAA
1 TAAATTTAAATTTAAAA
600423 TAAATT
1 TAAATT
600429 AAAAATGAGT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 60 1.00
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:602561 original size:24 final size:24
Alignment explanation
Indices: 602533--602591 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
602523 TAGATTAATA
*
602533 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAT
* * *
602557 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAT
*
602581 AGAATTTAACT
1 AGAGTTTAACT
602592 GAAAGATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAT
Found at i:602594 original size:24 final size:24
Alignment explanation
Indices: 602545--602595 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
602535 AGTTTGACTC
* * *
602545 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAACTG
602569 AAACAAATAAACAGAATTTAACTG
1 AAACAAATAAACAGAATTTAACTG
602593 AAA
1 AAA
602596 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:606834 original size:6 final size:6
Alignment explanation
Indices: 606823--606863 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
606813 ACTCCTAAAA
* **
606823 AAATTC AAATTC AACTAA AAATTC AAATTC AAATTC AAATT
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC AAATT
606864 TTTTTAGTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTC
Found at i:606863 original size:18 final size:18
Alignment explanation
Indices: 606821--606856 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
606811 TTACTCCTAA
*
606821 AAAAATTCAAATTCAACT
1 AAAAATTCAAATTCAAAT
606839 AAAAATTCAAATTCAAAT
1 AAAAATTCAAATTCAAAT
606857 TCAAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAATTCAAATTCAAAT
Found at i:607227 original size:19 final size:21
Alignment explanation
Indices: 607190--607230 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
607180 TTGAAAATTA
*
607190 GGAAGAAAAAATGTGCTCTCT
1 GGAAGAAAAAATCTGCTCTCT
607211 GGAAG-AAAAATCT-CTCTCT
1 GGAAGAAAAAATCTGCTCTCT
607230 G
1 G
607231 AAAATGATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
GGAAGAAAAAATCTGCTCTCT
Found at i:614390 original size:39 final size:38
Alignment explanation
Indices: 614346--614453 Score: 155
Period size: 37 Copynumber: 2.8 Consensus size: 38
614336 AAAAAAATAT
*
614346 TTATATTTAAAAATCACCATAAATATAATAAATGGTTTA
1 TTATA-TTAAAAATCACAATAAATATAATAAATGGTTTA
*
614385 TTATATTAAAAATCA-AATAAATATAATAAATGTTTTA
1 TTATATTAAAAATCACAATAAATATAATAAATGGTTTA
* *
614422 TTGTATTAAAAAACACAAATAAATATAATAAA
1 TTATATTAAAAATCAC-AATAAATATAATAAA
614454 ATTGTATTGT
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
37 33 0.52
38 10 0.16
39 20 0.32
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (38 bp):
TTATATTAAAAATCACAATAAATATAATAAATGGTTTA
Found at i:614617 original size:68 final size:68
Alignment explanation
Indices: 614504--614640 Score: 247
Period size: 68 Copynumber: 2.0 Consensus size: 68
614494 TGAGTTATTT
* * *
614504 AGTAGGGTAAGTTTTTTTTTTTAATATACTGGTGTGATTATATGATAGTATCTGTTCATACTTTC
1 AGTAGAGTAAGTTTTTTTTTTAAATATACTGGTGTGATTACATGATAGTATCTGTTCATACTTTC
614569 TTA
66 TTA
614572 AGTAGAGTAAGTTTTTTTTTTAAATATACTGGTGTGATTACATGATAGTATCTGTTCATACTTTC
1 AGTAGAGTAAGTTTTTTTTTTAAATATACTGGTGTGATTACATGATAGTATCTGTTCATACTTTC
614637 TTA
66 TTA
614640 A
1 A
614641 CCCTTCGACA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 66 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (68 bp):
AGTAGAGTAAGTTTTTTTTTTAAATATACTGGTGTGATTACATGATAGTATCTGTTCATACTTTC
TTA
Found at i:615962 original size:21 final size:21
Alignment explanation
Indices: 615938--616075 Score: 65
Period size: 20 Copynumber: 6.5 Consensus size: 21
615928 AAAATTATAT
615938 TGTTGTTTTGTTTTTTTTTAC
1 TGTTGTTTTGTTTTTTTTTAC
* *
615959 TGTT-TTGGTTGTTGTTTTTTGC
1 TGTTGTT--TTGTTTTTTTTTAC
* * *
615981 TATT-TTATGTTGTTTTTTAC
1 TGTTGTTTTGTTTTTTTTTAC
*
616001 TGTT-TTGGTGTTTTTTTTTA-
1 TGTTGTT-TTGTTTTTTTTTAC
* *
616021 --TTGTTTTGATTGATGTTTT-C
1 TGTTGTTTTG-TT-TTTTTTTAC
*
616041 ATGTTGTTTTAGTTATTATTTTTGC
1 -TGTTGTTTT-GTT-TT-TTTTTAC
616066 TGTTGTTTTG
1 TGTTGTTTTG
616076 ATTGTTATTT
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
18 4 0.04
19 4 0.04
20 24 0.27
21 15 0.17
22 17 0.19
23 11 0.12
24 14 0.16
25 1 0.01
ACGTcount: A:0.08, C:0.04, G:0.19, T:0.70
Consensus pattern (21 bp):
TGTTGTTTTGTTTTTTTTTAC
Done.