Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014745.1 Kokia drynarioides strain JFW-HI SEQ_129784, 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: 532331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 76 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:421538 original size:23 final size:23
Alignment explanation
Indices: 421494--421573 Score: 115
Period size: 23 Copynumber: 3.4 Consensus size: 23
421484 TTAGCAGTGT
*
421494 GTGTGCCCTCTGTTATTAGCACTTC
1 GTGTGCCCTC--TAATTAGCACTTC
*
421519 GTGTGCCCTCTAATTAGCACCTC
1 GTGTGCCCTCTAATTAGCACTTC
*
421542 GTGTGCCCTCTAATTAGCACTTT
1 GTGTGCCCTCTAATTAGCACTTC
421565 GTGTGCCCT
1 GTGTGCCCT
421574 TTATTACCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 41 0.80
25 10 0.20
ACGTcount: A:0.14, C:0.30, G:0.20, T:0.36
Consensus pattern (23 bp):
GTGTGCCCTCTAATTAGCACTTC
Found at i:423705 original size:52 final size:52
Alignment explanation
Indices: 423625--423873 Score: 322
Period size: 52 Copynumber: 4.8 Consensus size: 52
423615 ATTTCACTTC
* * ** * * *
423625 ATTCATAAACTCACGATGATAAATAGTCATCGGACCTTATAATCCACAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAGG
* * *
423677 ATTCATATACTCACAATGACA-TAGAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACT-TAGTCATCGGACCTTTTAATCCATAAAGG
* ** *
423729 A-TCTATATACTCACAATGACACTTAGTCATCGGACCTTTTAATCTGTAAAAG
1 ATTC-ATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAGG
*
423781 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAGG
*
423833 ATTCATATACTCACGATGACACTTAGTCATCAGACCTTTTA
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTA
423874 GTCTATGGCT
Statistics
Matches: 175, Mismatches: 18, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.01
52 170 0.97
53 3 0.02
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAGG
Found at i:430149 original size:21 final size:21
Alignment explanation
Indices: 430125--430182 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
430115 TGGTACAGAT
*
430125 TTCTACCGGTACATGTACT-AG
1 TTCTACCGATACATGTA-TAAG
* *
430146 TTCTACCGATACAAGTATAAT
1 TTCTACCGATACATGTATAAG
430167 TTCTACCGATACATGT
1 TTCTACCGATACATGT
430183 CATGCATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCTACCGATACATGTATAAG
Found at i:430194 original size:21 final size:21
Alignment explanation
Indices: 430168--430220 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
430158 AAGTATAATT
430168 TCTACCGATACATGTCATGCA
1 TCTACCGATACATGTCATGCA
* *
430189 TGTACCGATATATGTCATGCA
1 TCTACCGATACATGTCATGCA
*
430210 TCTAACGATAC
1 TCTACCGATAC
430221 TGAAAACTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (21 bp):
TCTACCGATACATGTCATGCA
Found at i:431043 original size:52 final size:52
Alignment explanation
Indices: 430853--431045 Score: 242
Period size: 52 Copynumber: 3.7 Consensus size: 52
430843 CACTTCATTT
* * * * *
430853 ATATACTCACGATGACACATAGCCACCGGACCTTATAATCCACAAGGGATTC
1 ATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTC
* * *
430905 ATATACTCACGATGACACAGAGTCATCGGACCTATTAATCCATAAAGGATCC
1 ATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTC
* * * * * *
430957 ATATACTCATGATGACACTTAGTCATCGGACCTTTTAATTCGTAAAAGATTT
1 ATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTC
* *
431009 ATATACTCACGATGACACTTAATCATCGGACCTTTTA
1 ATATACTCACGATGACACATAGTCATCGGACCTTTTA
431046 GTCTATGGCT
Statistics
Matches: 122, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 122 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ATATACTCACGATGACACATAGTCATCGGACCTTTTAATCCATAAAGGATTC
Found at i:434050 original size:52 final size:52
Alignment explanation
Indices: 433972--434210 Score: 218
Period size: 52 Copynumber: 4.6 Consensus size: 52
433962 TAAATGAAAA
433972 AGGTCCGATGACTT-TGTGTCATCGTGAGTATATGAATCCTTCATGGATTATG
1 AGGTCCGATGA-TTCTGTGTCATCGTGAGTATATGAATCCTTCATGGATTATG
* *
434024 AGGTCCGATGATTCTGTATCATCGTGAGTATATGAATCCTAT-ACGGATTATG
1 AGGTCCGATGATTCTGTGTCATCGTGAGTATATGAATCCT-TCATGGATTATG
* * * * * * *
434076 GGGTCGGATGACTCTATGTCATCTTGAGTATATGAATCTTTTACAT--ATTATA
1 AGGTCCGATGATTCTGTGTCATCGTGAGTATATGAATC-CTT-CATGGATTATG
* * * * * * * *
434128 AGGTTCGATGACTAC-GTGTCATCGTGAGTGTATGATTCCTTTAAGGAATAAG
1 AGGTCCGATGA-TTCTGTGTCATCGTGAGTATATGAATCCTTCATGGATTATG
* * *
434180 AGGTCCGATGACTATATGTCATCGTGAGTAT
1 AGGTCCGATGATTCTGTGTCATCGTGAGTAT
434211 TAAAGGAAAT
Statistics
Matches: 146, Mismatches: 32, Indels: 18
0.74 0.16 0.09
Matches are distributed among these distances:
50 1 0.01
51 4 0.03
52 137 0.94
53 3 0.02
54 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGATTCTGTGTCATCGTGAGTATATGAATCCTTCATGGATTATG
Found at i:434162 original size:104 final size:103
Alignment explanation
Indices: 433972--434210 Score: 275
Period size: 104 Copynumber: 2.3 Consensus size: 103
433962 TAAATGAAAA
* * * *
433972 AGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATCCTTCATGGATTATGAGGTCCGATGATT
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTCAT-GATTATAAGGTCCGATGATA
* * *
434037 CTGTATCATCGTGAGTATATGAATCCTATACGGATTATG
65 CTGTATCATCGTGAGTATATGAATCCTATAAGGAATAAG
* * * * * *
434076 GGGTCGGATGACTCTATGTCATCTTGAGTATATGAATCTTTTACAT-ATTATAAGGTTCGATGAC
1 AGGTCCGATGACTATATGTCATCGTGAGTATATGAATC-CTT-CATGATTATAAGGTCCGATGA-
* * * *
434140 TAC-GTGTCATCGTGAGTGTATGATTCCTTTAAGGAATAAG
63 TACTGTATCATCGTGAGTATATGAATCCTATAAGGAATAAG
434180 AGGTCCGATGACTATATGTCATCGTGAGTAT
1 AGGTCCGATGACTATATGTCATCGTGAGTAT
434211 TAAAGGAAAT
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
104 105 0.94
105 4 0.04
106 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.36
Consensus pattern (103 bp):
AGGTCCGATGACTATATGTCATCGTGAGTATATGAATCCTTCATGATTATAAGGTCCGATGATAC
TGTATCATCGTGAGTATATGAATCCTATAAGGAATAAG
Found at i:435113 original size:21 final size:21
Alignment explanation
Indices: 435089--435129 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
435079 TGTATTGTTA
*
435089 GAACTATCACTTGTACCGATG
1 GAACCATCACTTGTACCGATG
*
435110 GAACCATCACTTGTATCGAT
1 GAACCATCACTTGTACCGAT
435130 AGAAATCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (21 bp):
GAACCATCACTTGTACCGATG
Found at i:436215 original size:32 final size:27
Alignment explanation
Indices: 436143--436197 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
436133 AAAATTACCA
436143 ATCCAAAATTTAATCCACCTATAATAT
1 ATCCAAAATTTAATCCACCTATAATAT
436170 ATCCAAAATTTAATCCACCTATAATAT
1 ATCCAAAATTTAATCCACCTATAATAT
436197 A
1 A
436198 ACTCCGTAAA
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:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (27 bp):
ATCCAAAATTTAATCCACCTATAATAT
Found at i:437798 original size:60 final size:60
Alignment explanation
Indices: 437705--437835 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
437695 TTAATATAAT
* * *
437705 ATTTGGTACCTGAACTTGACACTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGCACCTAAACTTTTTTTAGACCCA
** * * **
437765 ATTTGGTACCTGAACTTGGTATTTTTTCCTAATTTGGCACCTAAGCTTTTTTTAGATTCA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGCACCTAAACTTTTTTTAGACCCA
437825 ATTTGGTACCT
1 ATTTGGTACCT
437836 AAATTTATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGCACCTAAACTTTTTTTAGACCCA
Found at i:438077 original size:32 final size:31
Alignment explanation
Indices: 438060--438178 Score: 133
Period size: 32 Copynumber: 3.9 Consensus size: 31
438050 CCAACTTTTT
438060 AAAAAAGTGTCAAGTTTAGATACCAAATTAGG
1 AAAAAAGTGTCAAGTTTAG-TACCAAATTAGG
*
438092 AAAAAAGTGTCAAGTTTGAGTATCAAATTA-G
1 AAAAAAGTGTCAAGTTT-AGTACCAAATTAGG
*
438123 ACAAAAA----AAAGTTTAGATACCAAATTAGG
1 A-AAAAAGTGTCAAGTTTAG-TACCAAATTAGG
438152 -AAAAAGTGTCAAGTTTAAGTACCAAAT
1 AAAAAAGTGTCAAGTTT-AGTACCAAAT
438179 ATTATATTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
27 7 0.09
28 15 0.20
29 1 0.01
31 16 0.22
32 33 0.45
33 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAAAGTGTCAAGTTTAGTACCAAATTAGG
Found at i:438156 original size:92 final size:90
Alignment explanation
Indices: 437990--438178 Score: 213
Period size: 92 Copynumber: 2.1 Consensus size: 90
437980 AAGATTAGGC
* ***
437990 ACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTGGACCCTAAAAAGTTTAAGTACCAAC
1 ACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTAGACAAAAAAAAGTTTAAGTACCAA-
* ***
438055 TTTTTAAAAAAGTGTCAAGTTT-AGAT
65 ATTAGGAAAAAGTGTCAAGTTTAAG-T
* * *
438081 ACCAAATTAGGAAAAAAGTGTCAAGTT-TGAGTATCAAATTAGACAAAAAAAAGTTT-AGATACC
1 ACCAAATTAGG-AAAAAGAGTCAAGTTCAG-GTACCAAATTAGACAAAAAAAAGTTTAAG-TACC
438144 AAATTAGGAAAAAGTGTCAAGTTTAAGT
63 AAATTAGGAAAAAGTGTCAAGTTTAAGT
438172 ACCAAAT
1 ACCAAAT
438179 ATTATATTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
91 40 0.48
92 43 0.52
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.25
Consensus pattern (90 bp):
ACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTAGACAAAAAAAAGTTTAAGTACCAAA
TTAGGAAAAAGTGTCAAGTTTAAGT
Found at i:441319 original size:22 final size:22
Alignment explanation
Indices: 441293--441334 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
441283 AATACTTTTA
441293 TAAAAATTATATAA-ATTATTTG
1 TAAAAATTA-ATAATATTATTTG
*
441315 TAAAATTTAATAATATTATT
1 TAAAAATTAATAATATTATT
441335 AGTATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAAAATTAATAATATTATTTG
Found at i:444273 original size:18 final size:19
Alignment explanation
Indices: 444235--444273 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
444225 AAATATAATG
**
444235 TAATAGTTATTTTTTAATA
1 TAATAGTTATTTTAAAATA
444254 TAATAGTTA-TTTAAAATA
1 TAATAGTTATTTTAAAATA
444272 TA
1 TA
444274 TACACTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATAGTTATTTTAAAATA
Found at i:447118 original size:23 final size:22
Alignment explanation
Indices: 447066--447126 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
447056 GCTTGATTTC
*
447066 TTTTATA-TAATTT-ATAA-TT
1 TTTTATATTAATTTGATAAGGT
447085 TTTTATATTAAATTTGATAAGGT
1 TTTTATATT-AATTTGATAAGGT
447108 TTTTAGT-TTAATTTGATAA
1 TTTTA-TATTAATTTGATAA
447127 ATTAATATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 1 0.03
21 5 0.14
22 14 0.39
23 8 0.22
24 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TTTTATATTAATTTGATAAGGT
Found at i:447280 original size:60 final size:63
Alignment explanation
Indices: 447169--447288 Score: 149
Period size: 64 Copynumber: 2.0 Consensus size: 63
447159 ATACGGAGTA
* ***
447169 GTATCTAAATATTAATTTGGTAAAAAAACGATGTTAAATAATTGTTGTATCTAAATATAAAGTG
1 GTATCTAAATATTAATTTGGTAAAAAAACGATCTTAAATAATTGCAATATCT-AATATAAAGTG
* *
447233 GTATTTAAATATTAATTT-G-AAAAAAA-TA-CTTAAATAATTGCAATATCTAATATAAA
1 GTATCTAAATATTAATTTGGTAAAAAAACGATCTTAAATAATTGCAATATCTAATATAAA
447289 TAAAGTAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 8 0.16
60 16 0.32
61 1 0.02
62 7 0.14
63 1 0.02
64 17 0.34
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (63 bp):
GTATCTAAATATTAATTTGGTAAAAAAACGATCTTAAATAATTGCAATATCTAATATAAAGTG
Found at i:447567 original size:6 final size:6
Alignment explanation
Indices: 447558--447582 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
447548 CCATATACGC
447558 ATACAT ATACAT ATACAT ATACAT A
1 ATACAT ATACAT ATACAT ATACAT A
447583 ATAGAAACAG
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:458978 original size:16 final size:16
Alignment explanation
Indices: 458959--458989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
458949 TTTTATATTG
*
458959 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
458975 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
458990 ACATTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:459120 original size:13 final size:13
Alignment explanation
Indices: 459103--459136 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
459093 AATTAAAAAA
*
459103 AAAAACAATGTAAT
1 AAAAA-AATATAAT
459117 AAAAAAATATAAT
1 AAAAAAATATAAT
459130 AAAAAAA
1 AAAAAAA
459137 AATAGCGCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAAAAATATAAT
Found at i:460192 original size:46 final size:47
Alignment explanation
Indices: 460131--460236 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 47
460121 AATATAATAA
** * *
460131 TTTTGCCTTTTAACTTT-ATGGGTAAATATTTATCAAAATGATATAG
1 TTTTGCCTTTTAACTTTGAAAGGTAAACATTTATCAAAATGACATAG
*
460177 TTTTGCATTTTAACTTTGGAAAAGGTAAACATTTATCAAAATGACATAG
1 TTTTGCCTTTTAACTTT-G-AAAGGTAAACATTTATCAAAATGACATAG
460226 TTTTGCCTTTT
1 TTTTGCCTTTT
460237 CTTATTTAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
46 16 0.31
49 35 0.69
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (47 bp):
TTTTGCCTTTTAACTTTGAAAGGTAAACATTTATCAAAATGACATAG
Found at i:460370 original size:21 final size:20
Alignment explanation
Indices: 460346--460388 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
460336 CTTGAATAAC
460346 TTAAACTATTTAATTCAAAAT
1 TTAAACTATTTAA-TCAAAAT
* * *
460367 TTAAATTTTTTTATCAAAAT
1 TTAAACTATTTAATCAAAAT
460387 TT
1 TT
460389 TTTAAATCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAAACTATTTAATCAAAAT
Found at i:461517 original size:21 final size:20
Alignment explanation
Indices: 461477--461520 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
461467 TTCAAATTTA
*
461477 TTATTTTTATTTTGTAATAT
1 TTATTTTTATGTTGTAATAT
461497 TTATTTTTATAGTT-TAGATAT
1 TTATTTTTAT-GTTGTA-ATAT
461518 TTA
1 TTA
461521 AATCTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (20 bp):
TTATTTTTATGTTGTAATAT
Found at i:461770 original size:21 final size:21
Alignment explanation
Indices: 461735--461785 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
461725 GAATTATGTA
461735 ATTTAGATTTATAAACTTTAT
1 ATTTAGATTTATAAACTTTAT
* * *
461756 GTTTGGATTTCTAAACTTTAT
1 ATTTAGATTTATAAACTTTAT
461777 ATTTAGATT
1 ATTTAGATT
461786 ATGCTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.53
Consensus pattern (21 bp):
ATTTAGATTTATAAACTTTAT
Found at i:461984 original size:16 final size:15
Alignment explanation
Indices: 461960--462002 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
461950 ACGGGTCGAC
*
461960 ATTTTGAATACCTAAA
1 ATTTCGAATACCT-AA
461976 ATTTCGAATACCTAA
1 ATTTCGAATACCTAA
461991 ATCTTCGAATAC
1 AT-TTCGAATAC
462003 TCGATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.35
Consensus pattern (15 bp):
ATTTCGAATACCTAA
Found at i:463362 original size:24 final size:25
Alignment explanation
Indices: 463330--463377 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
463320 GTATGTATTT
*
463330 ATGATGATTTTATTTTAATTAAAAA
1 ATGATGATTTAATTTTAATTAAAAA
*
463355 ATGA-GATTTAATTTTAGTTAAAA
1 ATGATGATTTAATTTTAATTAAAA
463378 TTAATATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (25 bp):
ATGATGATTTAATTTTAATTAAAAA
Found at i:482753 original size:22 final size:20
Alignment explanation
Indices: 482715--482754 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
482705 TACAAGGCTC
*
482715 TAACATAATGAGTAACAAGA
1 TAACATAATGACTAACAAGA
482735 TAACACTAACTGACTAACAA
1 TAACA-TAA-TGACTAACAA
482755 ATCTTGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 3 0.18
22 9 0.53
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (20 bp):
TAACATAATGACTAACAAGA
Found at i:486106 original size:21 final size:21
Alignment explanation
Indices: 486065--486108 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
486055 TAGAAGTAAG
*
486065 ACATGTATCGGTAGAGCTGTC
1 ACATGTATCGGTAAAGCTGTC
486086 ACATGTATCGGTAAAAG-TGTC
1 ACATGTATCGGT-AAAGCTGTC
486107 AC
1 AC
486109 TAGTTTTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (21 bp):
ACATGTATCGGTAAAGCTGTC
Found at i:490334 original size:9 final size:9
Alignment explanation
Indices: 490302--490393 Score: 61
Period size: 9 Copynumber: 10.2 Consensus size: 9
490292 TTAATCCTTC
490302 TTATTTT-T
1 TTATTTTAT
490310 TTATATTTAT
1 TTAT-TTTAT
490320 TTATTTGTA-
1 TTATTT-TAT
490329 TTATTTTAT
1 TTATTTTAT
*
490338 TTATTTTAG
1 TTATTTTAT
* *
490347 GTATTTAAT
1 TTATTTTAT
490356 TTGCA-TTTAT
1 TT--ATTTTAT
490366 TTATTGTT-T
1 TTATT-TTAT
490375 TTATGTTT-T
1 TTAT-TTTAT
490384 TT-TTTTAT
1 TTATTTTAT
490392 TT
1 TT
490394 GTTATTTACT
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
7 3 0.04
8 11 0.16
9 37 0.54
10 16 0.24
11 1 0.01
ACGTcount: A:0.20, C:0.01, G:0.07, T:0.73
Consensus pattern (9 bp):
TTATTTTAT
Found at i:492555 original size:12 final size:12
Alignment explanation
Indices: 492522--492557 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
492512 AAAGGACATG
492522 CAAGATCAATTA
1 CAAGATCAATTA
**
492534 CAAGCGCAATTA
1 CAAGATCAATTA
492546 CAAGATCAATTA
1 CAAGATCAATTA
492558 GCCAAAGTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (12 bp):
CAAGATCAATTA
Found at i:496588 original size:50 final size:50
Alignment explanation
Indices: 496528--496857 Score: 133
Period size: 51 Copynumber: 6.6 Consensus size: 50
496518 TAGAATGGAG
* * * *
496528 TGAAGTTACAATATCAAATCCTATATCCCTAAAGTTACAGTGGATC-AGA
1 TGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTACAGTGGAGCAAGA
* * * * ***
496577 TTTAAGCTACAAAAGCAAATCGT-TATCTCTCTAAAGTTGCAACAGAGCAAGA
1 -TGAAGCTACAAAACCAAATCCTATATC-C-CTAAAGTTACAGTGGAGCAAGA
* * *
496629 TGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTATAGTGG-GTC-GGA
1 TGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTACAGTGGAG-CAAGA
* ** * * * *
496678 TTAAAG-T-CATGAAAGAAAATCTTTATCTCCCTGAAGTTATAGTGGAGCAA-A
1 -TGAAGCTACA--AAACCAAATC-CTATATCCCTAAAGTTACAGTGGAGCAAGA
* * * * * * ***
496729 -GAAGCTACGACATCAAATCATATATCCCTGAAGTTGCAGTGGA-TTGGA
1 TGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTACAGTGGAGCAAGA
* * * * *** *
496777 TTGAAGCTA-AGAAAGCAAATTCTTATATCTCTGAAGTTACAGCATAGCAGGA
1 -TGAAGCTACA-AAACCAAA-TCCTATATCCCTAAAGTTACAGTGGAGCAAGA
*
496829 AGAAGCTACAAAACCAAATCCTATA-CCCT
1 TGAAGCTACAAAACCAAATCCTATATCCCT
496858 TGAAGTTGAA
Statistics
Matches: 205, Mismatches: 55, Indels: 41
0.68 0.18 0.14
Matches are distributed among these distances:
48 23 0.11
49 21 0.10
50 61 0.30
51 89 0.43
52 11 0.05
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (50 bp):
TGAAGCTACAAAACCAAATCCTATATCCCTAAAGTTACAGTGGAGCAAGA
Found at i:496605 original size:101 final size:100
Alignment explanation
Indices: 496500--496912 Score: 282
Period size: 101 Copynumber: 4.1 Consensus size: 100
496490 GCGGATATCA
* * * * * *
496500 ATCTCCCTAAAGTTGCAATAGA--ATGGAGTGAAGTTACAATATCAAATCCTATATCCCTAAAGT
1 ATCTCCCTAAAGTTGCAACAGAGCA-AGA-TGAAGCTACAAAACCAAATCCTATACCCCTAAAGT
* *
496563 TACAGTGGATCAGATTTAAGCTACA-AAAGCAAATCGTT
64 TACAGTGGATCAGATTAAAG-T-CAGAAAGAAAATCGTT
*
496601 ATCTCTCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTA
1 ATCTCCCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTA
* * * *
496666 TAGTGGGTCGGATTAAAGTCATGAAAGAAAATCTTT
66 CAGTGGATCAGATTAAAGTCA-GAAAGAAAATCGTT
* ** *** * * * * * * *
496702 ATCTCCCTGAAGTTATAGTGGAGCAA-A-GAAGCTACGACATCAAATCATATATCCCTGAAGTTG
1 ATCTCCCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTA
** * * *
496765 CAGTGGATTGGATTGAAGCTAAGAAAGCAAATTC-TT
66 CAGTGGATCAGATTAAAG-TCAGAAAG-AAAATCGTT
* * * * * * * * * *
496801 ATATCTCTGAAGTTACAGCATAGCAGGAAGAAGCTACAAAACCAAATCCTATACCCTTGAAGTTG
1 ATCTCCCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTT-
* ** * *
496866 A-AGTGGGTTGGATTAAAGCCATGAAAGAAAATCTTT
65 ACAGTGGATCAGATTAAAGTCA-GAAAGAAAATCGTT
496902 ATCTCCCTAAA
1 ATCTCCCTAAA
496913 CTTGTAGTGG
Statistics
Matches: 246, Mismatches: 55, Indels: 22
0.76 0.17 0.07
Matches are distributed among these distances:
99 71 0.29
100 16 0.07
101 156 0.63
102 2 0.01
103 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (100 bp):
ATCTCCCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTA
CAGTGGATCAGATTAAAGTCAGAAAGAAAATCGTT
Found at i:496883 original size:200 final size:200
Alignment explanation
Indices: 496540--496927 Score: 548
Period size: 200 Copynumber: 1.9 Consensus size: 200
496530 AAGTTACAAT
* * *
496540 ATCAAATCCTATATCCCTAAAGTTACAGTGGATCAGATTTAAGCTACAAAAGCAAATCGTTATCT
1 ATCAAATCATATATCCCTAAAGTTACAGTGGATCAGATTGAAGCTACAAAAGCAAATCGTTATAT
* *
496605 CTCTAAAGTTGCAACAGAGCAAGATGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTATAGT
66 CTCTAAAGTTACAACAGAGCAAGAAGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTATAGT
* * *
496670 GGGTCGGATTAAAGTCATGAAAGAAAATCTTTATCTCCCTGAAGTTATAGTGGAGCAAAGAAGCT
131 GGGTCGGATTAAAGCCATGAAAGAAAATCTTTATCTCCCTAAACTTATAGTGGAGCAAAGAAGCT
496735 ACGAC
196 ACGAC
* * **
496740 ATCAAATCATATATCCCTGAAGTTGCAGTGGATTGGATTGAAGCTA-AGAAAGCAAATTC-TTAT
1 ATCAAATCATATATCCCTAAAGTTACAGTGGATCAGATTGAAGCTACA-AAAGCAAA-TCGTTAT
* * * * * *
496803 ATCTCTGAAGTTACAGCATAGCAGGAAGAAGCTACAAAACCAAATCCTATACCCTTGAAGTTGA-
64 ATCTCTAAAGTTACAACAGAGCAAGAAGAAGCTACAAAACCAAATCCTATACCCCTAAAGTT-AT
* *
496867 AGTGGGTTGGATTAAAGCCATGAAAGAAAATCTTTATCTCCCTAAACTTGTAGTGGAGCAA
128 AGTGGGTCGGATTAAAGCCATGAAAGAAAATCTTTATCTCCCTAAACTTATAGTGGAGCAA
496928 GATAAGCCAC
Statistics
Matches: 165, Mismatches: 20, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
199 1 0.01
200 161 0.98
201 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (200 bp):
ATCAAATCATATATCCCTAAAGTTACAGTGGATCAGATTGAAGCTACAAAAGCAAATCGTTATAT
CTCTAAAGTTACAACAGAGCAAGAAGAAGCTACAAAACCAAATCCTATACCCCTAAAGTTATAGT
GGGTCGGATTAAAGCCATGAAAGAAAATCTTTATCTCCCTAAACTTATAGTGGAGCAAAGAAGCT
ACGAC
Found at i:498973 original size:4 final size:4
Alignment explanation
Indices: 498954--499061 Score: 56
Period size: 4 Copynumber: 25.0 Consensus size: 4
498944 TTAATCCTTC
* * * * *
498954 TTAT TTTT TATAT TTAT TTAT TTGT ATTATT TTAT TTAT TTAG GTAT TCAAT
1 TTAT TTAT T-TAT TTAT TTAT TTAT -TTA-T TTAT TTAT TTAT TTAT T-TAT
* * *
499006 TTGCAT TTAT TTAT TGTTT TTAT GTTGT TTAT TTAT TTAT TT-G TTAT
1 TT--AT TTAT TTAT T-TAT TTAT -TTAT TTAT TTAT TTAT TTAT TTAT
499053 TTACT TTAT
1 TTA-T TTAT
499062 GTCACTCTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
3 2 0.03
4 50 0.64
5 21 0.27
6 5 0.06
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:498995 original size:8 final size:8
Alignment explanation
Indices: 498954--499061 Score: 56
Period size: 9 Copynumber: 12.5 Consensus size: 8
498944 TTAATCCTTC
*
498954 TTATTTTT
1 TTATTTAT
498962 TATATTTAT
1 T-TATTTAT
*
498971 TTATTTGT
1 TTATTTAT
498979 ATTATTTTAT
1 -TTA-TTTAT
*
498989 TTATTTAG
1 TTATTTAT
* *
498997 GTATTCAAT
1 TTATT-TAT
499006 TTGCATTTAT
1 TT--ATTTAT
*
499016 TTATTGTTT
1 TTATT-TAT
*
499025 TTATGTTGT
1 TTAT-TTAT
499034 TTATTTAT
1 TTATTTAT
*
499042 TTATTT-G
1 TTATTTAT
499049 TTATTTACT
1 TTATTTA-T
499058 TTAT
1 TTAT
499062 GTCACTCTAA
Statistics
Matches: 76, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
7 6 0.08
8 27 0.36
9 31 0.41
10 9 0.12
11 3 0.04
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (8 bp):
TTATTTAT
Found at i:499224 original size:23 final size:23
Alignment explanation
Indices: 499197--499261 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
499187 TTTTTATTAC
499197 AATTATATTTTCATTTTATTTGCT
1 AATTATATTTT-ATTTTATTTGCT
499221 -ATTAT-TTTTACTTTT-TGTTGCT
1 AATTATATTTTA-TTTTAT-TTGCT
*
499243 AATTATATTTAATTTTATT
1 AATTATATTTTATTTTATT
499262 CGTTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
21 2 0.06
22 13 0.37
23 15 0.43
24 5 0.14
ACGTcount: A:0.25, C:0.06, G:0.05, T:0.65
Consensus pattern (23 bp):
AATTATATTTTATTTTATTTGCT
Found at i:502422 original size:2 final size:2
Alignment explanation
Indices: 502410--502441 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
502400 GAGTTATACT
502410 CA CA TCA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA -CA CA CA CA CA CA CA CA CA CA CA CA CA C
502442 GTACACATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.50, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:503781 original size:3 final size:3
Alignment explanation
Indices: 503773--503803 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
503763 TATTTATAAC
503773 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
503804 CATTTTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:504303 original size:27 final size:29
Alignment explanation
Indices: 504237--504307 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
504227 AAACATTAAA
*
504237 AAATATTAAAATAACTATATAAAAATTTT
1 AAATATTAAAATAAATATATAAAAATTTT
* * *
504266 CAATA-AAAAAAAAAT-TAT-AAAATTATT
1 AAATATTAAAATAAATATATAAAAATT-TT
504293 AAATATTAAAATAAA
1 AAATATTAAAATAAA
504308 ACAATATAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
26 6 0.18
27 9 0.27
28 14 0.42
29 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATATTAAAATAAATATATAAAAATTTT
Found at i:510588 original size:25 final size:25
Alignment explanation
Indices: 510540--510586 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
510530 ATTTAATTTT
**
510540 TTTTCTTTTTATTTCTTTATTTTCC
1 TTTTCTTTTTATCCCTTTATTTTCC
510565 TTTTCTTTTT-TCCCTTTATTTT
1 TTTTCTTTTTATCCCTTTATTTT
510587 TCTCTCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTCTTTTTATCCCTTTATTTTCC
Found at i:513768 original size:2 final size:2
Alignment explanation
Indices: 513761--513792 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
513751 ATGGTAAAGC
513761 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
513793 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:514095 original size:17 final size:17
Alignment explanation
Indices: 514075--514119 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
514065 AAAGTGAGAG
*
514075 ATATTTGATAAAAATAT
1 ATATTCGATAAAAATAT
514092 ATATTCG--AAAAATAT
1 ATATTCGATAAAAATAT
*
514107 AT-TTGGATAAAAA
1 ATATTCGATAAAAA
514120 ATAAAATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 5 0.21
17 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATTCGATAAAAATAT
Found at i:516574 original size:18 final size:17
Alignment explanation
Indices: 516553--516591 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
516543 TCACTTTCCC
*
516553 TAAATCAATTTCTTTTTT
1 TAAAT-AATTTATTTTTT
*
516571 TAAATGATTTATTTTTT
1 TAAATAATTTATTTTTT
516588 TAAA
1 TAAA
516592 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (17 bp):
TAAATAATTTATTTTTT
Found at i:516987 original size:17 final size:18
Alignment explanation
Indices: 516948--516987 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
516938 TTTTATTTAA
516948 TATTTAAATATATAATTT
1 TATTTAAATATATAATTT
* *
516966 AATTTAAATGTAT-ATTT
1 TATTTAAATATATAATTT
516983 TATTT
1 TATTT
516988 TTGGTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTTAAATATATAATTT
Found at i:517016 original size:95 final size:95
Alignment explanation
Indices: 516837--517016 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 95
516827 TTTTTGTTTA
* **
516837 TTTATTTATTATATAATATTTAAATATATAGTTTAATTTATTTATATATTTTATTTTTGGTGGAG
1 TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
**
516902 CCATATTAAATGGTACCACCCGATTAATTT
66 CCATATTAAATGACACCACCCGATTAATTT
* * * *
516932 TTTATTTTTTATTTAATATTTAAATATATAATTTAATTTAAATGTATATTTTATTTTTGGTGTAG
1 TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
* *
516997 TCAT-TCTAAATGACGCCACC
66 CCATAT-TAAATGACACCACC
517017 AATTTTTGAT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 1 0.01
95 72 0.99
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (95 bp):
TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
CCATATTAAATGACACCACCCGATTAATTT
Found at i:523535 original size:23 final size:23
Alignment explanation
Indices: 523508--523555 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
523498 TATTTAAAAA
* *
523508 TAAAATCAAAATTAGAAGGA-AAT
1 TAAAATAAAAATGA-AAGGAGAAT
523531 TAAAATAAAAATGAAAGGAGAAT
1 TAAAATAAAAATGAAAGGAGAAT
523554 TA
1 TA
523556 TAAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (23 bp):
TAAAATAAAAATGAAAGGAGAAT
Found at i:525460 original size:17 final size:18
Alignment explanation
Indices: 525425--525470 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
525415 AAAAAAGTAA
* *
525425 TATTATTTTCAAGTCTTT
1 TATTATTTTCAAATATTT
525443 TATT-TTTTCAAATATTT
1 TATTATTTTCAAATATTT
*
525460 TAGTATTTTCA
1 TATTATTTTCA
525471 TGGTATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.61
Consensus pattern (18 bp):
TATTATTTTCAAATATTT
Found at i:526023 original size:2 final size:2
Alignment explanation
Indices: 526016--526047 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
526006 ATGGTAAAGC
526016 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
526048 TGAAAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:526350 original size:17 final size:17
Alignment explanation
Indices: 526330--526374 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
526320 AAAGTGAGAG
*
526330 ATATTTGATAAAAATAT
1 ATATTCGATAAAAATAT
526347 ATATTCG--AAAAATAT
1 ATATTCGATAAAAATAT
*
526362 AT-TTGGATAAAAA
1 ATATTCGATAAAAA
526375 ATAAAATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 5 0.21
17 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATTCGATAAAAATAT
Found at i:528829 original size:18 final size:17
Alignment explanation
Indices: 528808--528846 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
528798 TCACTTTCCC
*
528808 TAAATCAATTTCTTTTTT
1 TAAAT-AATTTATTTTTT
*
528826 TAAATGATTTATTTTTT
1 TAAATAATTTATTTTTT
528843 TAAA
1 TAAA
528847 ATTAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (17 bp):
TAAATAATTTATTTTTT
Found at i:529242 original size:17 final size:18
Alignment explanation
Indices: 529203--529242 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
529193 TTTTATTTAA
529203 TATTTAAATATATAATTT
1 TATTTAAATATATAATTT
* *
529221 AATTTAAATGTAT-ATTT
1 TATTTAAATATATAATTT
529238 TATTT
1 TATTT
529243 TTGGTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTTAAATATATAATTT
Found at i:529271 original size:95 final size:95
Alignment explanation
Indices: 529092--529271 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 95
529082 TTTTTGTTTA
* **
529092 TTTATTTATTATATAATATTTAAATATATAGTTTAATTTATTTATATATTTTATTTTTGGTGGAG
1 TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
**
529157 CCATATTAAATGGTACCACCCGATTAATTT
66 CCATATTAAATGACACCACCCGATTAATTT
* * * *
529187 TTTATTTTTTATTTAATATTTAAATATATAATTTAATTTAAATGTATATTTTATTTTTGGTGTAG
1 TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
* *
529252 TCAT-TCTAAATGACGCCACC
66 CCATAT-TAAATGACACCACC
529272 AATTTTTGAT
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 1 0.01
95 72 0.99
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (95 bp):
TTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATATATATTTTATTTTTGGTGGAG
CCATATTAAATGACACCACCCGATTAATTT
Done.