Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008743.1 Hibiscus syriacus cultivar Beakdansim tig00111832_pilon, 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: 979257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:500984 original size:2 final size:2
Alignment explanation
Indices: 500979--501033 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
500969 ATAAAATCAA
500979 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501021 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
501034 CACCCACGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:504998 original size:60 final size:60
Alignment explanation
Indices: 504917--505046 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 60
504907 TATCCCCCCG
* * * * **
504917 ACTATAGGGTATTATTATTTTAAGTCCCTCAACTATTAAACA-TTACAAAATGGTCCTCTA
1 ACTATAGGATACTATGATTTTAACTCCCAAAACTATTAAA-AGTTACAAAATGGTCCTCTA
* *
504977 ACTATAGGATACTATGATTTTAACTCCCAAAACTATTAAAAGTTACAAAGTGGTCCTCTG
1 ACTATAGGATACTATGATTTTAACTCCCAAAACTATTAAAAGTTACAAAATGGTCCTCTA
505037 ACTATAGGAT
1 ACTATAGGAT
505047 GTTGCTTTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.02
60 60 0.98
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (60 bp):
ACTATAGGATACTATGATTTTAACTCCCAAAACTATTAAAAGTTACAAAATGGTCCTCTA
Found at i:505444 original size:60 final size:60
Alignment explanation
Indices: 505308--505444 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
505298 ATAATCGGGT
* * * *
505308 GATCATTTTGTAACTTTTAATAGTCGATGGACTTAACGAATCAACATTCTAAAGTTGAAG
1 GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAACAAAACAACATTCTAAAGTTGAAG
* * * *
505368 GATGATTTTGTAACTTTTAATAGTCAAAGGACTTAATAAAACAATA-TCATATAGTT-AAGG
1 GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAACAAAACAACATTC-TAAAGTTGAA-G
505428 GATCATTTGTGT-ACTTT
1 GATCATTT-TGTAACTTT
505445 ACCCTCTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 4 0.06
60 58 0.89
61 3 0.05
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (60 bp):
GATCATTTTGTAACTTTTAATAGTCAAAGGACTTAACAAAACAACATTCTAAAGTTGAAG
Found at i:505527 original size:19 final size:18
Alignment explanation
Indices: 505482--505526 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
505472 TAATATATGA
505482 AAAATTATAATTTATTTTTG
1 AAAA-TATAATTTA-TTTTG
505502 AAAATATAATTTA-TTTG
1 AAAATATAATTTATTTTG
*
505519 AAATTATA
1 AAAATATA
505527 TTTTTGTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
19 9 0.38
20 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
AAAATATAATTTATTTTG
Found at i:506452 original size:19 final size:19
Alignment explanation
Indices: 506428--506498 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
506418 AATGCATTTC
506428 ATGCATCGATGCACATACT
1 ATGCATCGATGCACATACT
506447 ATGCATCGATGCACATACT
1 ATGCATCGATGCACATACT
506466 ATGCATCGATGCACATACT
1 ATGCATCGATGCACATACT
506485 ATGCATCGATGCAC
1 ATGCATCGATGCAC
506499 TCAGAGTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (19 bp):
ATGCATCGATGCACATACT
Found at i:506537 original size:65 final size:63
Alignment explanation
Indices: 506466--506608 Score: 182
Period size: 65 Copynumber: 2.2 Consensus size: 63
506456 TGCACATACT
*
506466 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
506529 TG
62 TC
* * *
506531 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAATATCGAATGCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
506595 ATGCATCGATGCAC
1 ATGCATCGATGCAC
506609 TAAGGGTCCA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
63 1 0.01
64 30 0.43
65 34 0.49
66 5 0.07
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:512381 original size:21 final size:20
Alignment explanation
Indices: 512316--512390 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
512306 TTATGCTTAA
512316 TGCATCGATACACCT-AACAG
1 TGCATCGATACACCTGAA-AG
* * *
512336 AGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CC-TGAAAG
*
512358 TGCATCGATACACCATGAAGG
1 TGCATCGATACACC-TGAAAG
*
512379 TGCACCGATACA
1 TGCATCGATACA
512391 TGCCTTGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.23
21 20 0.45
22 12 0.27
23 2 0.05
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (20 bp):
TGCATCGATACACCTGAAAG
Found at i:512405 original size:23 final size:22
Alignment explanation
Indices: 512337--512410 Score: 87
Period size: 21 Copynumber: 3.4 Consensus size: 22
512327 ACCTAACAGA
*
512337 GCATCGATGCATCCTTGAATGT
1 GCATCGATACATCCTTGAATGT
* *
512359 GCATCGATACA-CCATGAAGGT
1 GCATCGATACATCCTTGAATGT
* *
512380 GCACCGATACATGCCTTGAATAT
1 GCATCGATACAT-CCTTGAATGT
512403 GCATCGAT
1 GCATCGAT
512411 GCACACTGCC
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 18 0.43
22 10 0.24
23 14 0.33
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (22 bp):
GCATCGATACATCCTTGAATGT
Found at i:512407 original size:44 final size:42
Alignment explanation
Indices: 512315--512410 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 42
512305 TTTATGCTTA
* *
512315 ATGCATCGATACACCTAACAGAGCATCGATGCATCCTTGAAT
1 ATGCATCGATACACCTAACAGAGCACCGATACATCCTTGAAT
* * *
512357 GTGCATCGATACACCATGAA-GGTGCACCGATACATGCCTTGAAT
1 ATGCATCGATACACC-T-AACAGAGCACCGATACAT-CCTTGAAT
512401 ATGCATCGAT
1 ATGCATCGAT
512411 GCACACTGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 14 0.31
43 12 0.27
44 19 0.42
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (42 bp):
ATGCATCGATACACCTAACAGAGCACCGATACATCCTTGAAT
Found at i:513311 original size:13 final size:13
Alignment explanation
Indices: 513293--513317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
513283 CATTTCACAT
513293 TTGATTATGAATA
1 TTGATTATGAATA
513306 TTGATTATGAAT
1 TTGATTATGAAT
513318 CTAATGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGAATA
Found at i:513961 original size:65 final size:63
Alignment explanation
Indices: 513844--514051 Score: 226
Period size: 65 Copynumber: 3.2 Consensus size: 63
513834 TTTCAAAGTG
* * * **
513844 ATGCATTGATGCACCAATCCATGCATCGATGTAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATT
513907 TC
62 TC
*
513909 ATGCATCGATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATT
*
513972 TG
62 TC
* *
513974 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATTTC
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
514038 ATGCATCGATGCAC
1 ATGCATCGATGCAC
514052 TCTTAGTGCA
Statistics
Matches: 124, Mismatches: 10, Indels: 20
0.81 0.06 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 48 0.39
65 66 0.53
66 5 0.04
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTC
Found at i:518448 original size:15 final size:17
Alignment explanation
Indices: 518414--518446 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
518404 GAAAATAACG
*
518414 TAAGTAATATTTTATTT
1 TAAGTAATATTATATTT
518431 TAAGTAAT-TTATATTT
1 TAAGTAATATTATATTT
518447 AAAATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
TAAGTAATATTATATTT
Found at i:519086 original size:18 final size:18
Alignment explanation
Indices: 519063--519097 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
519053 TTTATGTTTA
519063 AGTTATCAATTTAGTTCG
1 AGTTATCAATTTAGTTCG
519081 AGTTATCAATTTAGTTC
1 AGTTATCAATTTAGTTC
519098 ATCCGTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (18 bp):
AGTTATCAATTTAGTTCG
Found at i:520278 original size:49 final size:49
Alignment explanation
Indices: 520200--520294 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
520190 GATACTTGTG
* ** *
520200 GAGGGGTTGTCTGGGATACCTTGGGCACCATGGAGGTCCGCCCCTAGAT
1 GAGGGGTTGCCTGGGATACCCCGGACACCATGGAGGTCCGCCCCTAGAT
*
520249 GAGGGGTTGCCTGGGATACCCCGGACACCATGGAGGTCTGCCCCTA
1 GAGGGGTTGCCTGGGATACCCCGGACACCATGGAGGTCCGCCCCTA
520295 TTTAGAGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (49 bp):
GAGGGGTTGCCTGGGATACCCCGGACACCATGGAGGTCCGCCCCTAGAT
Found at i:521290 original size:23 final size:23
Alignment explanation
Indices: 521264--521321 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
521254 TTATATGTTT
521264 GACAACATGTTTGTTTAGCCTTC
1 GACAACATGTTTGTTTAGCCTTC
521287 GACAACATGTTTGTTTAGCCTTC
1 GACAACATGTTTGTTTAGCCTTC
*
521310 AACAACATGTTT
1 GACAACATGTTT
521322 AGTCATATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (23 bp):
GACAACATGTTTGTTTAGCCTTC
Found at i:522078 original size:19 final size:20
Alignment explanation
Indices: 522054--522105 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
522044 AAATAACCAA
* *
522054 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACACGAACTC
522073 CAAATTCGCAACACGAACTC
1 CAAATTCGCAACACGAACTC
*
522093 CAATTTCGCAACA
1 CAAATTCGCAACA
522106 AAGTTTCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.37, C:0.33, G:0.12, T:0.19
Consensus pattern (20 bp):
CAAATTCGCAACACGAACTC
Found at i:522721 original size:15 final size:15
Alignment explanation
Indices: 522703--522735 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
522693 CTTGAAACTT
522703 AAATTCGTAACACGA
1 AAATTCGTAACACGA
*
522718 AAA-TCGTAACTCGA
1 AAATTCGTAACACGA
522732 AAAT
1 AAAT
522736 AAAATTCGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.81
15 3 0.19
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (15 bp):
AAATTCGTAACACGA
Found at i:523096 original size:81 final size:81
Alignment explanation
Indices: 523009--523172 Score: 328
Period size: 81 Copynumber: 2.0 Consensus size: 81
522999 ATCAAAACAA
523009 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGTTATATTTACCAACTCTTCTTC
1 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGTTATATTTACCAACTCTTCTTC
523074 CGGTATCTGAAGTAAT
66 CGGTATCTGAAGTAAT
523090 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGTTATATTTACCAACTCTTCTTC
1 TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGTTATATTTACCAACTCTTCTTC
523155 CGGTATCTGAAGTAAT
66 CGGTATCTGAAGTAAT
523171 TC
1 TC
523173 TGGCATATTC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (81 bp):
TCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGTTATATTTACCAACTCTTCTTC
CGGTATCTGAAGTAAT
Found at i:524750 original size:23 final size:26
Alignment explanation
Indices: 524713--524781 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
524703 TTCTCTTGTG
524713 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
524737 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
524762 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
524782 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:524763 original size:12 final size:12
Alignment explanation
Indices: 524746--524781 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
524736 TATCATGTTC
524746 TCATATCACATG
1 TCATATCACATG
*
524758 TCATATCACATA
1 TCATATCACATG
524770 TCATATCACATG
1 TCATATCACATG
524782 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:525112 original size:11 final size:11
Alignment explanation
Indices: 525096--525150 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
525086 GGTATGCATC
525096 GATGCACTACT
1 GATGCACTACT
525107 GATGCA-T-C-
1 GATGCACTACT
525115 GATGCACTACT
1 GATGCACTACT
525126 GATGCA-T-C-
1 GATGCACTACT
*
525134 AATGCACTACT
1 GATGCACTACT
525145 GATGCA
1 GATGCA
525151 TCGGTGCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
8 11 0.31
9 4 0.11
10 4 0.11
11 17 0.47
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (11 bp):
GATGCACTACT
Found at i:525113 original size:19 final size:19
Alignment explanation
Indices: 525089--525158 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
525079 TAATGAAGGT
525089 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
525108 ATGCATCGATGCACTACTG
1 ATGCATCGATGCACTACTG
*
525127 ATGCATCAATGCACTACTG
1 ATGCATCGATGCACTACTG
*
525146 ATGCATCGGTGCA
1 ATGCATCGATGCA
525159 TAAAAGGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACTACTG
Found at i:525235 original size:64 final size:63
Alignment explanation
Indices: 525126--525280 Score: 150
Period size: 64 Copynumber: 2.4 Consensus size: 63
525116 ATGCACTACT
* * ** ** **
525126 GATGCATCAATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTTT-CATTATTAATGG
1 GATGCATCGATGCACTACTAATGCATCAATGCATAAAAGACATTCGATGTTTGCATT-TTAA-AA
* * ** *
525190 GATGCATCGATGCACTACTTATGCATCAATGCATGAATTACATTCGATGTTTGTATTTTAAAA
1 GATGCATCGATGCACTACTAATGCATCAATGCATAAAAGACATTCGATGTTTGCATTTTAAAA
*
525253 GAGTGCATCGATGCACTACCAATGCATC
1 GA-TGCATCGATGCACTACTAATGCATC
525281 GATACACCTT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 2 0.03
64 70 0.93
65 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (63 bp):
GATGCATCGATGCACTACTAATGCATCAATGCATAAAAGACATTCGATGTTTGCATTTTAAAA
Found at i:542767 original size:23 final size:26
Alignment explanation
Indices: 542730--542782 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 26
542720 TTCTCTTGTG
542730 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
542754 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
542779 ATCA
1 ATCA
542783 CATGAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 11 0.41
24 8 0.30
25 8 0.30
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:543170 original size:64 final size:64
Alignment explanation
Indices: 543097--543250 Score: 168
Period size: 64 Copynumber: 2.4 Consensus size: 64
543087 TGAAGGTATA
* * * * *
543097 CATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATG-TTTCATTATT-AATGGGAT
1 CATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATT-TTAAAAGAG-T
543160 G
64 G
* * * ** *
543161 CATCGATGCACTACTTATACATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAGTG
1 CATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAGAGTG
*
543225 CATCGATGCACTACCAATGCATCGAT
1 CATCGATGCACTACTAATGCATCGAT
543251 ACACCTTTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 65 0.87
65 10 0.13
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (64 bp):
CATCGATGCACTACTAATGCATCGATGCATAAAAGGCATTCGATGTTTTCATTTTAAAAGAGTG
Found at i:544745 original size:98 final size:100
Alignment explanation
Indices: 544522--544778 Score: 245
Period size: 98 Copynumber: 2.6 Consensus size: 100
544512 AAACATTTGT
* * * *
544522 GTTGCGAAAACAAAATTCGTGTTGCGAATCAGAAAATCTTGTTGCGAATTTAAAAATTGCGTTGC
1 GTTGCGAAAATAAAATTCGTGTTGCGAATCACAAAATCTCGTTGCGAATTTAAAAACTGCGTTGC
*
544587 TAAAAAGAAATTCGCCTTGCGAATTCAGAAATCGA
66 TAAAAAGAAATTCGCATTGCGAATTCAGAAATCGA
** * * **
544622 GTTGCGAATTTGAAATTCCGTGTTGCGAAT-ACCAAAT-TCG-TGCGAATTTGGAAACTGCGTTG
1 GTTGCGAAAATAAAATT-CGTGTTGCGAATCACAAAATCTCGTTGCGAATTTAAAAACTGCGTTG
* * * * * *
544684 -TAAAATTGGAGTTCGTATTGCGAATTTAGAAAATCGC
65 CTAAAA-AGAAATTCGCATTGCGAATTCAG-AAATCGA
* ** * *
544721 GTTGCGAAAATAAAATTCGAGTTGCGAATTTCAAAA-CTGAGTTGCGAATTTAGAAACT
1 GTTGCGAAAATAAAATTCGTGTTGCGAATCACAAAATCT-CGTTGCGAATTTAAAAACT
544779 TTGTTGCGAA
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
97 5 0.04
98 47 0.38
99 27 0.22
100 19 0.15
101 27 0.22
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (100 bp):
GTTGCGAAAATAAAATTCGTGTTGCGAATCACAAAATCTCGTTGCGAATTTAAAAACTGCGTTGC
TAAAAAGAAATTCGCATTGCGAATTCAGAAATCGA
Found at i:544777 original size:20 final size:20
Alignment explanation
Indices: 544701--544812 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
544691 GGAGTTCGTA
* *
544701 TTGCGAATTTAGAAAATCGCG
1 TTGCGAATTTAGAAACT-GAG
** *
544722 TTGCGAAAATA-AAATTCGAG
1 TTGCGAATTTAGAAACT-GAG
544742 TTGCGAATTTCA-AAACTGAG
1 TTGCGAATTT-AGAAACTGAG
**
544762 TTGCGAATTTAGAAACTTTG
1 TTGCGAATTTAGAAACTGAG
* * * * *
544782 TTGCGAAATTGGAGATTGCG
1 TTGCGAATTTAGAAACTGAG
544802 TTGCGAATTTA
1 TTGCGAATTTA
544813 TTGATTATTT
Statistics
Matches: 72, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
19 1 0.01
20 57 0.79
21 14 0.19
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGAATTTAGAAACTGAG
Found at i:548042 original size:20 final size:20
Alignment explanation
Indices: 548019--548070 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
548009 AACGCGATCC
548019 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
548039 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
548059 CCAAAATCGCAA
1 CCAGAATCGCAA
548071 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:548087 original size:21 final size:20
Alignment explanation
Indices: 548060--548158 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
548050 AATCAGTTTC
548060 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
548081 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
548102 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
548122 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
548143 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
548159 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:548187 original size:20 final size:20
Alignment explanation
Indices: 548125--548318 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
548115 CGATTTTCCA
* ** *
548125 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
548145 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
548165 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
548185 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
548205 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
548225 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
548245 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
548265 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
548285 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
548306 AAATCGCAACGCG
1 AAATCGCAACGCG
548319 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:548209 original size:60 final size:60
Alignment explanation
Indices: 548125--548318 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
548115 CGATTTTCCA
* ** * *
548125 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
548185 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
548245 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
548306 AAATCGCAACGCG
1 AAATCGCAACGCG
548319 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:548735 original size:32 final size:32
Alignment explanation
Indices: 548697--548765 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
548687 ATTTCACTTA
*
548697 GATTTCATTTCGCGTTACGATTCTGTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
548729 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
548761 GATTT
1 GATTT
548766 TCAAGTTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:548746 original size:18 final size:18
Alignment explanation
Indices: 548697--548746 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
548687 ATTTCACTTA
*
548697 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
548715 GA-TTC-TGT--CGTTGC
1 GATTTCATTTCGCGTTGC
548729 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
548747 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 3 0.12
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:548908 original size:14 final size:14
Alignment explanation
Indices: 548889--548943 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
548879 AGAATGACTG
548889 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
548903 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
548922 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
548936 TCGCAACG
1 TCGCAACG
548944 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:548956 original size:33 final size:33
Alignment explanation
Indices: 548889--548959 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
548879 AGAATGACTG
***
548889 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
548922 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
548955 TCGCA
1 TCGCA
548960 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:548977 original size:19 final size:19
Alignment explanation
Indices: 548955--549052 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
548945 GAAACCAAAA
*
548955 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
548974 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
548988 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
549007 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
549021 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
549040 TCGCGTTGCGATT
1 TCGCGTTGCGATT
549053 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:548996 original size:14 final size:14
Alignment explanation
Indices: 548977--549066 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
548967 TTTCATTTCG
548977 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
548991 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
549010 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
549024 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
549041 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
549057 CGTTGCGATT
1 CGTTGCGATT
549067 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:549002 original size:33 final size:33
Alignment explanation
Indices: 548960--549074 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
548950 CAAAATCGCA
548960 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
548993 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
549026 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
549059 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
549075 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:551000 original size:185 final size:186
Alignment explanation
Indices: 550770--551151 Score: 748
Period size: 185 Copynumber: 2.1 Consensus size: 186
550760 TAGATTGCTT
550770 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550835 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
550900 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
550955 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
551020 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
551085 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
551141 AGTAAATTTAT
1 AGTAAATTTAT
551152 CCATTCAAGT
Statistics
Matches: 194, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
185 154 0.79
186 40 0.21
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:551084 original size:93 final size:93
Alignment explanation
Indices: 550770--551149 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
550760 TAGATTGCTT
*
550770 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550835 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550863 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
550927 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
550955 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
551020 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
551048 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
551113 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
551141 AGTAAATTT
1 AGTAAATTT
551150 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 193 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:551233 original size:19 final size:19
Alignment explanation
Indices: 551193--551321 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
551183 TAGTTTACTT
* *
551193 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
551213 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
551232 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
551251 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
551265 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
551284 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
551298 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
551317 TCGCA
1 TCGCA
551322 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:551272 original size:33 final size:32
Alignment explanation
Indices: 551229--551321 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
551219 CGCGAAACCA
**
551229 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
551261 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
551294 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
551322 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:551319 original size:52 final size:52
Alignment explanation
Indices: 551193--551321 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
551183 TAGTTTACTT
**
551193 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
551245 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
551298 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
551322 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:551339 original size:19 final size:19
Alignment explanation
Indices: 551317--551451 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
551307 GAAACCAAAA
*
551317 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
551336 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
551352 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
551369 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
551385 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
551402 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
551421 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
551441 TCGTGTTGCGA
1 TCGCGTTGCGA
551452 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:551358 original size:14 final size:14
Alignment explanation
Indices: 551339--551395 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
551329 TTTCATTTCG
551339 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
551353 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
551370 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
551386 CGTTGCGATT
1 CGTTGCGATT
551396 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:551364 original size:33 final size:33
Alignment explanation
Indices: 551322--551414 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
551312 CAAAATCGCA
*
551322 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
551355 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
551388 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
551415 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:553311 original size:38 final size:38
Alignment explanation
Indices: 553268--553340 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
553258 AATTGATTGT
*
553268 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
553306 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
553341 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:553327 original size:19 final size:19
Alignment explanation
Indices: 553263--553327 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
553253 AGTTTAATTG
*
553263 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
553282 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
553300 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
553320 ATTGATTT
1 ATTGATTT
553328 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:553341 original size:14 final size:14
Alignment explanation
Indices: 553322--553357 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
553312 ATTGTTTAAT
553322 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
553336 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
553350 TGATTTGT
1 TGATTTGT
553358 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:553480 original size:19 final size:19
Alignment explanation
Indices: 553464--553545 Score: 120
Period size: 19 Copynumber: 4.6 Consensus size: 19
553454 AAAAATGACT
553464 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553483 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
553502 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
553516 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
553535 ATCGCAATGCG
1 ATCGCAATGCG
553546 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 40 0.71
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:553579 original size:52 final size:52
Alignment explanation
Indices: 553552--553871 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
553542 TGCGTTTATA
*
553552 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
553604 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
553656 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
553713 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
553765 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
553817 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
553870 AT
1 AT
553872 GTTGGGATTT
Statistics
Matches: 257, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
52 182 0.71
53 17 0.07
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:553598 original size:19 final size:19
Alignment explanation
Indices: 553574--553899 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
553564 GATTATCTCG
553574 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
553593 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
553612 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
553626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
553645 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
553664 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
553683 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
553702 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
553721 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
553735 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
553754 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
553773 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
553787 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
553806 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
553825 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
553839 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
553859 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
553873 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
553892 TTGCGATT
1 TTGCGATT
553900 GTATTTTCCG
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
16 31 0.12
17 28 0.10
18 3 0.01
19 160 0.59
20 12 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:553736 original size:161 final size:157
Alignment explanation
Indices: 553552--553871 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
553542 TGCGTTTATA
553552 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
* *
553617 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGT
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
553682 ATTGCGATTTTAATTT-CGCATTGCGATTTTC
127 -TTGCGATTTTAATTTCCGCATTGCGATTTTC
*
553713 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
553778 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
66 ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
*
553843 GATTTTCATTTCCGCATTGCGATTTTC
131 GATTTTAATTTCCGCATTGCGATTTTC
553870 AT
1 AT
553872 GTTGGGATTT
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 14 0.09
157 17 0.11
158 4 0.03
159 3 0.02
161 116 0.75
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (157 bp):
ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
ATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTAATTTCCGCATTGCGATTTTC
Found at i:553843 original size:33 final size:33
Alignment explanation
Indices: 553593--553899 Score: 280
Period size: 33 Copynumber: 8.8 Consensus size: 33
553583 TCATTTCGCA
*
553593 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
553626 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
553662 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
553700 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
553735 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
553771 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
553806 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
553839 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
553873 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
553900 GTATTTTCCG
Statistics
Matches: 235, Mismatches: 20, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
31 9 0.04
32 5 0.02
33 87 0.37
34 29 0.12
35 13 0.06
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:556223 original size:12 final size:12
Alignment explanation
Indices: 556206--556230 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
556196 TCTTCGGGGA
556206 CTTTTTCTTCTT
1 CTTTTTCTTCTT
556218 CTTTTTCTTCTT
1 CTTTTTCTTCTT
556230 C
1 C
556231 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:556439 original size:24 final size:24
Alignment explanation
Indices: 556405--556451 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
556395 CTGAAACATC
556405 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
556429 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
556452 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:557153 original size:20 final size:20
Alignment explanation
Indices: 557125--557533 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
557115 AAATTTCAGT
* * * *
557125 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
557145 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
557165 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
557185 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
557205 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
557225 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
557245 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
557265 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
557285 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
557305 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
557325 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
557345 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
557365 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
557385 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
557405 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
557425 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
557445 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
557465 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
557485 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
557505 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
557525 GTTGCGATT
1 GTTGCGATT
557534 ATGGAAAATC
Statistics
Matches: 343, Mismatches: 36, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.02
20 331 0.97
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:563144 original size:2 final size:2
Alignment explanation
Indices: 563137--563164 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
563127 ATTAATAACT
563137 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
563165 AGAAGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:563398 original size:58 final size:58
Alignment explanation
Indices: 563308--563422 Score: 221
Period size: 58 Copynumber: 2.0 Consensus size: 58
563298 TATACGAGAA
563308 AGAGGTGAAAAACATGGATTTGAACAACAAACCATGTTGTCGTAATGGTAAGTAATAC
1 AGAGGTGAAAAACATGGATTTGAACAACAAACCATGTTGTCGTAATGGTAAGTAATAC
*
563366 AGAGGTGAAAAACATGGATTTGGACAACAAACCATGTTGTCGTAATGGTAAGTAATA
1 AGAGGTGAAAAACATGGATTTGAACAACAAACCATGTTGTCGTAATGGTAAGTAATA
563423 TAGATGTATG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.24
Consensus pattern (58 bp):
AGAGGTGAAAAACATGGATTTGAACAACAAACCATGTTGTCGTAATGGTAAGTAATAC
Found at i:565268 original size:17 final size:17
Alignment explanation
Indices: 565244--565287 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
565234 AAATGTTTAT
565244 AAAAATTAAAAATAA-A
1 AAAAATTAAAAATAATA
**
565260 AATAAATTATTAATAATA
1 AA-AAATTAAAAATAATA
565278 AAAAATTAAA
1 AAAAATTAAA
565288 TATATATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.09
17 17 0.77
18 3 0.14
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATTAAAAATAATA
Found at i:565309 original size:28 final size:29
Alignment explanation
Indices: 565250--565312 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
565240 TTATAAAAAT
565250 TAAAAA-TAAAAATAAATTATTAATAATA
1 TAAAAATTAAAAATAAATTATTAATAATA
* * *
565278 -AAAAATTAAATATATATT-TTAATTATA
1 TAAAAATTAAAAATAAATTATTAATAATA
565305 TAAAAATT
1 TAAAAATT
565313 TAGATTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
TAAAAATTAAAAATAAATTATTAATAATA
Found at i:566090 original size:16 final size:15
Alignment explanation
Indices: 566069--566099 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
566059 ATTTAAGCTT
566069 TAGGGTTTAAGATTTG
1 TAGGGTTTAA-ATTTG
566085 TAGGGTTTAAATTTG
1 TAGGGTTTAAATTTG
566100 AGACTTGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (15 bp):
TAGGGTTTAAATTTG
Found at i:570111 original size:40 final size:40
Alignment explanation
Indices: 570026--570132 Score: 112
Period size: 40 Copynumber: 2.7 Consensus size: 40
570016 AAAATGACCA
*
570026 ACAAATTCGCAACGTGATCTCAAATTTCGCAACCCAAGTT
1 ACAAATTCGCAACGTGAACTCAAATTTCGCAACCCAAGTT
* *
570066 ACAAATTCGCAACGTGAAAGTCAAA-TTCGCAACACATAAG-T
1 ACAAATTCGCAACGTG-AACTCAAATTTCGCAAC-C-CAAGTT
* * *
570107 -CAAATTCGTAACGCGAACTCCAATTT
1 ACAAATTCGCAACGTGAACTCAAATTT
570133 TTCAACTCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 6 0.11
40 39 0.70
41 8 0.14
42 3 0.05
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.23
Consensus pattern (40 bp):
ACAAATTCGCAACGTGAACTCAAATTTCGCAACCCAAGTT
Found at i:570173 original size:20 final size:20
Alignment explanation
Indices: 570150--570217 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
570140 CAGTTTCCAG
570150 ATTCGCAACACGATTATCAA
1 ATTCGCAACACGATTATCAA
*
570170 ATTCGCAACGCGA-TAGTCGAA
1 ATTCGCAACACGATTA-TC-AA
* * *
570191 AATCGCAACACAATT-TTAA
1 ATTCGCAACACGATTATCAA
570210 ATTCGCAA
1 ATTCGCAA
570218 TGCATTTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
19 11 0.28
20 15 0.38
21 12 0.31
22 1 0.03
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.24
Consensus pattern (20 bp):
ATTCGCAACACGATTATCAA
Found at i:570830 original size:7 final size:7
Alignment explanation
Indices: 570820--570846 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
570810 CCAACTTCCG
570820 AATGTTA
1 AATGTTA
570827 AATGTTA
1 AATGTTA
570834 AATGTTA
1 AATGTTA
570841 AATGTT
1 AATGTT
570847 TCAACTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (7 bp):
AATGTTA
Found at i:571173 original size:20 final size:20
Alignment explanation
Indices: 571093--571185 Score: 98
Period size: 20 Copynumber: 4.5 Consensus size: 20
571083 AACAAATGCA
* *
571093 TTGCGATTTTGGAGTATCGCG
1 TTGCGAATTT-GACTATCGCG
571114 TTGCGAATTTCGACTATCGCG
1 TTGCGAATTT-GACTATCGCG
* **
571135 TTACGAATCTT-AAAATCGCG
1 TTGCGAAT-TTGACTATCGCG
*
571155 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
571175 TTGCGAATTTG
1 TTGCGAATTTG
571186 GAACCTGGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 31 0.52
21 25 0.42
22 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:571198 original size:40 final size:40
Alignment explanation
Indices: 571110--571205 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
571100 TTTGGAGTAT
*
571110 CGCGTTGCGAATTTCGACTATCGCGTTACGAATCTTAAAAT
1 CGCGTTGCGAATTT-GACTATCGCGTTACGAATCTTAAAAC
* * **
571151 CGCGTTGCGAATTTGACTTTCGCGTTGCGAAT-TTGGAAC
1 CGCGTTGCGAATTTGACTATCGCGTTACGAATCTTAAAAC
*
571190 CTGGGTTGCGAATTTG
1 C-GCGTTGCGAATTTG
571206 TTGGTCATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 5 0.10
40 29 0.60
41 14 0.29
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (40 bp):
CGCGTTGCGAATTTGACTATCGCGTTACGAATCTTAAAAC
Found at i:571295 original size:3 final size:3
Alignment explanation
Indices: 571287--571314 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
571277 TTATTTTCTC
571287 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
571315 GTAAGGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:580115 original size:7 final size:7
Alignment explanation
Indices: 580099--580130 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
580089 AATATTTTAA
580099 ATAAAAT
1 ATAAAAT
*
580106 ATAAATT
1 ATAAAAT
580113 ATAAAAT
1 ATAAAAT
580120 ATAAAAT
1 ATAAAAT
580127 ATAA
1 ATAA
580131 TCCATCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAAAAT
Found at i:582166 original size:196 final size:201
Alignment explanation
Indices: 581824--582219 Score: 658
Period size: 196 Copynumber: 2.0 Consensus size: 201
581814 GAACCTTTTT
*
581824 TTGAGATAAAATTGGAACCCGATCCGACCCGACCTAAAATAATAGTAAAAAATTATTTTTATTCA
1 TTGAGATAAAATCGGAACCCGATCCGACCCGA-C-AAAATAATAG-AAAAAATTATTTTTATTCA
*
581889 ATAAAAATAGTGATTTAATTAGAAAAAAATAATATAAAGAGAGATTTTATTGTAATTATTCATAA
63 ATAAAAATAGCGATTTAATTAGAAAAAAATAATATAAAGAGAGATTTTATTGTAATTATTCATAA
**
581954 ATATATAAGGTAAAAAAATCGGGTCGGGTCTGGTATTTTTCACCCTAAACCCGAATCCAACCCGA
128 ATATATAAGGTAAAAAAATCGGGTCGGGTCTAATATTTTTCACCCTAAACCCGAATCCAACCCGA
582019 CCCGATTTG
193 CCCGATTTG
* * *
582028 TTGAGATAAAATCGGAACCTGATCCGACCC-A-AAATTAA-A-AAAATATTATTTTTATTCAATA
1 TTGAGATAAAATCGGAACCCGATCCGACCCGACAAAATAATAGAAAAAATTATTTTTATTCAATA
*
582089 AAAATAGCGATTTAATT-GGAAAAAATAATATAAAGAGAGATTTTATTGTAATTATTCATAAATA
66 AAAATAGCGATTTAATTAGAAAAAAATAATATAAAGAGAGATTTTATTGTAATTATTCATAAATA
582153 TATAAGGTAAAAAAATCGGGTCGGGTCTAATATTTTTCACCCTAAACCCGAATCCAACCCGACCC
131 TATAAGGTAAAAAAATCGGGTCGGGTCTAATATTTTTCACCCTAAACCCGAATCCAACCCGACCC
582218 GA
196 GA
582220 ACACCACCTT
Statistics
Matches: 184, Mismatches: 8, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
196 111 0.60
197 37 0.20
199 1 0.01
200 6 0.03
203 1 0.01
204 28 0.15
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (201 bp):
TTGAGATAAAATCGGAACCCGATCCGACCCGACAAAATAATAGAAAAAATTATTTTTATTCAATA
AAAATAGCGATTTAATTAGAAAAAAATAATATAAAGAGAGATTTTATTGTAATTATTCATAAATA
TATAAGGTAAAAAAATCGGGTCGGGTCTAATATTTTTCACCCTAAACCCGAATCCAACCCGACCC
GATTTG
Found at i:585994 original size:36 final size:35
Alignment explanation
Indices: 585954--586063 Score: 82
Period size: 35 Copynumber: 3.1 Consensus size: 35
585944 TAGTAGGATA
585954 ATTATTCTTTTAAATATCTCAAATTAAAAAATATTT
1 ATTATTCTTTTAAATAT-TCAAATTAAAAAATATTT
* * * *
585990 ATTA-TCTATTTAACT-TTGAATATTAAAATATAATT
1 ATTATTCT-TTTAAATATTCAA-ATTAAAAAATATTT
* * * *
586025 -CTATCCTTTCAAATATTTCAAATTAAAATAATATCT
1 ATTATTCTTTTAAATA-TTCAAATTAAAA-AATATTT
586061 ATT
1 ATT
586064 TAAGTTTGAA
Statistics
Matches: 54, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
34 10 0.19
35 25 0.46
36 18 0.33
37 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (35 bp):
ATTATTCTTTTAAATATTCAAATTAAAAAATATTT
Found at i:586093 original size:34 final size:34
Alignment explanation
Indices: 586055--586151 Score: 99
Period size: 35 Copynumber: 2.8 Consensus size: 34
586045 AATTAAAATA
*
586055 ATATCTATTTAAGTTTGAATATTAAAAGTTATCC
1 ATATCTATTTAAATTTGAATATTAAAAGTTATCC
* * **
586089 ATATCT-TTTGAATATTTCAA-ATAAAAAAGTTATTG
1 ATATCTATTT-AA-ATTTGAATAT-TAAAAGTTATCC
*
586124 TTATCTATTTAAATTTGAATATTAAAAG
1 ATATCTATTTAAATTTGAATATTAAAAG
586152 ATACATATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
33 3 0.06
34 21 0.42
35 23 0.46
36 3 0.06
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.44
Consensus pattern (34 bp):
ATATCTATTTAAATTTGAATATTAAAAGTTATCC
Found at i:586236 original size:44 final size:42
Alignment explanation
Indices: 586187--586273 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 42
586177 TAAGAATCCC
586187 TATAAATATTGTGTTAACATGTTAGGTTAAATATATATCTTTTG
1 TATAAATATTGTGTTAACATGTTAGGTT-AA-ATATATCTTTTG
586231 TATAAATATTGTGTTAACATGTTAGGTTAAATATATCTTTTG
1 TATAAATATTGTGTTAACATGTTAGGTTAAATATATCTTTTG
586273 T
1 T
586274 TTCCCTCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 13 0.30
43 2 0.05
44 28 0.65
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (42 bp):
TATAAATATTGTGTTAACATGTTAGGTTAAATATATCTTTTG
Found at i:589660 original size:50 final size:50
Alignment explanation
Indices: 589584--589709 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 50
589574 GTAGCAGTAA
*
589584 AGCGCGCCCCTTGAACCGCGCTATACGCTGATTTGACG-TCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGCTATACGCTGATTTGACGCT-ACGTGGGTAT
** * *
589634 AGCGCGCCCCCTGCCCCGCGAC-ATACGGTGATTTGGCGCTACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCG-CTATACGCTGATTTGACGCTACGTGGGTAT
*
589684 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGCTATAC
589710 CTGCGTATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
49 1 0.02
50 63 0.95
51 2 0.03
ACGTcount: A:0.16, C:0.35, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGCTATACGCTGATTTGACGCTACGTGGGTAT
Found at i:590192 original size:111 final size:111
Alignment explanation
Indices: 589998--590330 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
589988 TGGAAATCAT
* * *
589998 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGCAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
590063 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
590109 ATATCTCGACATTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
590174 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
590220 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATATAATTTAAATTATTAATAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
590285 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
590331 TTTTTGTAAT
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:591860 original size:21 final size:18
Alignment explanation
Indices: 591843--591877 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
591833 GCAGCCACCG
591843 CAACCATATATGATGCCA
1 CAACCATATATGATGCCA
*
591861 CAGCCATATATGATGCC
1 CAACCATATATGATGCC
591878 GCCATCGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (18 bp):
CAACCATATATGATGCCA
Found at i:592233 original size:6 final size:6
Alignment explanation
Indices: 592218--592279 Score: 52
Period size: 6 Copynumber: 10.3 Consensus size: 6
592208 ACCTGCTCAG
* ** * ** *
592218 GACGAT GACGAC GACGAT GACGAT GGTGAC GACGAT GGTGAT GACGAC
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
*
592266 GACGAC GACGAT GA
1 GACGAT GACGAT GA
592280 TGACAGCGAG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.37, T:0.13
Consensus pattern (6 bp):
GACGAT
Found at i:592468 original size:26 final size:24
Alignment explanation
Indices: 592397--592468 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
592387 TTATATTTGT
592397 ATTTACTTTATTTTGTTTAATTGTA
1 ATTTACTTTATTTTGTTTAATT-TA
*
592422 ATTT--TTTATTATT-TTTCATTTA
1 ATTTACTTTATT-TTGTTTAATTTA
*
592444 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTTAATTT
592469 GTTGGACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
22 4 0.11
23 12 0.32
24 4 0.11
25 6 0.16
26 12 0.32
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.65
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTTAATTTA
Found at i:601802 original size:23 final size:23
Alignment explanation
Indices: 601762--601825 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
601752 CATTATTATA
** *
601762 TGGCACTATGGTGTAATTCTAT-G
1 TGGCACTCCGGTGCAATTCT-TCG
*
601785 TGGCACTCCGGTTCAATTCTTCG
1 TGGCACTCCGGTGCAATTCTTCG
*
601808 TGGCACTTCGGTGCAATT
1 TGGCACTCCGGTGCAATT
601826 ATACGAGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (23 bp):
TGGCACTCCGGTGCAATTCTTCG
Found at i:606989 original size:23 final size:23
Alignment explanation
Indices: 606963--607014 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
606953 ATTATTATAT
*
606963 GGCACTATGGTGCAATTCTAAGC
1 GGCACTACGGTGCAATTCTAAGC
* * *
606986 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTAAGC
607009 GGCACT
1 GGCACT
607015 TCAGTACAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTAAGC
Found at i:607024 original size:23 final size:23
Alignment explanation
Indices: 606975--607030 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
606965 CACTATGGTG
* * *
606975 CAATTCTAAGCGGCACTCCGGTG
1 CAATTCTACGCGGCACTCCAGTA
* *
606998 CAATTCTACGTGGCACTTCAGTA
1 CAATTCTACGCGGCACTCCAGTA
*
607021 CAATTATACG
1 CAATTCTACG
607031 AGCTGTGGTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (23 bp):
CAATTCTACGCGGCACTCCAGTA
Found at i:611536 original size:23 final size:24
Alignment explanation
Indices: 611492--611539 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
611482 TAACTGCAAA
*
611492 AAATAATAAGAAAATTAGTAAATT
1 AAATAATAAGAAAATTAATAAATT
*
611516 AAATAATAA-TAAATTAATAAATT
1 AAATAATAAGAAAATTAATAAATT
611539 A
1 A
611540 TGAAATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AAATAATAAGAAAATTAATAAATT
Found at i:613613 original size:6 final size:6
Alignment explanation
Indices: 613602--613628 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
613592 CCTCTCCTTT
613602 TTCTTG TTCTTG TTCTTG TTCTTG TTC
1 TTCTTG TTCTTG TTCTTG TTCTTG TTC
613629 CCCCTCGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.15, T:0.67
Consensus pattern (6 bp):
TTCTTG
Found at i:637127 original size:18 final size:19
Alignment explanation
Indices: 637094--637131 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
637084 CCCCTGCATG
637094 CCCCATGCAACTGCTGCCA
1 CCCCATGCAACTGCTGCCA
*
637113 CCCCATGC-GCTGCTGCCA
1 CCCCATGCAACTGCTGCCA
637131 C
1 C
637132 GTTGAGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.16, C:0.50, G:0.18, T:0.16
Consensus pattern (19 bp):
CCCCATGCAACTGCTGCCA
Found at i:637364 original size:2 final size:2
Alignment explanation
Indices: 637357--637381 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
637347 GGGGTTGGGT
637357 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
637382 GGGGTGTAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:637794 original size:37 final size:37
Alignment explanation
Indices: 637751--637831 Score: 135
Period size: 37 Copynumber: 2.2 Consensus size: 37
637741 TTTTACTTAT
* *
637751 TTAAATTAAATTAGTTACTTAGTAGATTATTTTTAGA
1 TTAAATTAAATTAGTTACGTAGTAGATTATTTTTAAA
637788 TTAAATTAAATTAGTTACGTAGTAGATTATTTTTAAA
1 TTAAATTAAATTAGTTACGTAGTAGATTATTTTTAAA
*
637825 TTGAATT
1 TTAAATT
637832 CATTATAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.48
Consensus pattern (37 bp):
TTAAATTAAATTAGTTACGTAGTAGATTATTTTTAAA
Found at i:638064 original size:37 final size:37
Alignment explanation
Indices: 638014--638093 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
638004 CATCAACACA
*
638014 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGAT
1 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAAAT
638051 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAAAT
1 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAAAT
*
638088 TGAATT
1 TAAATT
638094 CATTATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (37 bp):
TAAATTAAATTAGTTACTTAGTAGATTATTTTTAAAT
Found at i:638217 original size:262 final size:262
Alignment explanation
Indices: 637752--638272 Score: 988
Period size: 262 Copynumber: 2.0 Consensus size: 262
637742 TTTACTTATT
637752 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGATTAAATTAAATTAGTTACGTAGTAGATTA
1 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGATTAAATTAAATTAGTTACGTAGTAGATTA
637817 TTTTTAAATTGAATTCATTATAATATTGTCATTATTCAACATTTAATCTACTAAACTAATTCGTT
66 TTTTTAAATTGAATTCATTATAATATTGTCATTATTCAACATTTAATCTACTAAACTAATTCGTT
* *
637882 TAAACTAGACGCATGGATAGATATTGCTTTTGTATGTAACTTGTGTGTGTTTCTTATTTGTATTG
131 TAAACTAGACGCATGGATAGATATTACTTTTGTATGTAACTTGTATGTGTTTCTTATTTGTATTG
*
637947 AATACTTAGATGTAGTTAGTAGTATTTGTTTTTTATGCAGCATTTACCTCCGAGCAGCATCAACA
196 AATACTTAGATGTAGTTAGTAGTATTTATTTTTTATGCAGCATTTACCTCCGAGCAGCATCAACA
638012 CA
261 CA
*
638014 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGATTAAATTAAATTAGTTACTTAGTAGATTA
1 TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGATTAAATTAAATTAGTTACGTAGTAGATTA
638079 TTTTTAAATTGAATTCATTATAATATTGTCATTATTCAACATTTAATCTACTAAACTAATTCGTT
66 TTTTTAAATTGAATTCATTATAATATTGTCATTATTCAACATTTAATCTACTAAACTAATTCGTT
* *
638144 TAAACTAGATGCATGGATAGATATTACTTTTGTATGTAACTTGTATGTGTTTCTTATTTGTGTTG
131 TAAACTAGACGCATGGATAGATATTACTTTTGTATGTAACTTGTATGTGTTTCTTATTTGTATTG
638209 AATACTTAGATGTAGTTAGTAGTATTTATTTTTTATGCAGCATTTACCTCCGAGCAGCATCAAC
196 AATACTTAGATGTAGTTAGTAGTATTTATTTTTTATGCAGCATTTACCTCCGAGCAGCATCAAC
638273 TTTATGTGTT
Statistics
Matches: 253, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
262 253 1.00
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (262 bp):
TAAATTAAATTAGTTACTTAGTAGATTATTTTTAGATTAAATTAAATTAGTTACGTAGTAGATTA
TTTTTAAATTGAATTCATTATAATATTGTCATTATTCAACATTTAATCTACTAAACTAATTCGTT
TAAACTAGACGCATGGATAGATATTACTTTTGTATGTAACTTGTATGTGTTTCTTATTTGTATTG
AATACTTAGATGTAGTTAGTAGTATTTATTTTTTATGCAGCATTTACCTCCGAGCAGCATCAACA
CA
Found at i:639444 original size:4 final size:4
Alignment explanation
Indices: 639435--639472 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
639425 ATAATACTAT
639435 TTAA TTAA TTTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA -TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
639473 ATGTATTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:640303 original size:21 final size:21
Alignment explanation
Indices: 640274--640314 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
640264 TCCAGGAGGG
*
640274 ATGATAGAGCAAAATGGTGGA
1 ATGAGAGAGCAAAATGGTGGA
* *
640295 ATGAGAGAGCATAGTGGTGG
1 ATGAGAGAGCAAAATGGTGG
640315 GCATATATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.39, T:0.20
Consensus pattern (21 bp):
ATGAGAGAGCAAAATGGTGGA
Found at i:643497 original size:37 final size:38
Alignment explanation
Indices: 643456--643528 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
643446 TAATATACAA
*
643456 TATAAAAATAATATTAACATAACAA-CAATCGTAAATT
1 TATAAAAATAATATTAACATAACAATCAATAGTAAATT
*
643493 TATAAAAATAATATTAACATAATAATCAATAGTAAA
1 TATAAAAATAATATTAACATAACAATCAATAGTAAA
643529 ATACCTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (38 bp):
TATAAAAATAATATTAACATAACAATCAATAGTAAATT
Found at i:643744 original size:27 final size:27
Alignment explanation
Indices: 643714--643769 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
643704 CTATTAATCT
643714 TCTTTACAATTGCTTTTGCCCCCTCTA
1 TCTTTACAATTGCTTTTGCCCCCTCTA
*
643741 TCTTTGCAATTGCTTTTGCCCCCTCTA
1 TCTTTACAATTGCTTTTGCCCCCTCTA
643768 TC
1 TC
643770 AATTTTTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.34, G:0.09, T:0.45
Consensus pattern (27 bp):
TCTTTACAATTGCTTTTGCCCCCTCTA
Found at i:649181 original size:31 final size:31
Alignment explanation
Indices: 649135--649241 Score: 153
Period size: 31 Copynumber: 3.5 Consensus size: 31
649125 TTAACTTGTG
*
649135 GTGACTATATTTTAATGAAATAAAAACGAAA
1 GTGACTATATATTAATGAAATAAAAACGAAA
*
649166 GTGACCATATATTAATGAAATAAAAACGAAA
1 GTGACTATATATTAATGAAATAAAAACGAAA
* * *
649197 GTGACTATATCTTAATTAAATAAAAATGAAA
1 GTGACTATATATTAATGAAATAAAAACGAAA
649228 GTGA-TAATATATTA
1 GTGACT-ATATATTA
649242 TATCAGTAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 1 0.01
31 67 0.99
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (31 bp):
GTGACTATATATTAATGAAATAAAAACGAAA
Found at i:649445 original size:23 final size:22
Alignment explanation
Indices: 649411--649457 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
649401 GTTTATTGAA
*
649411 ATTTTATGAATTCATCTTCTAAT
1 ATTTTATAAATTCATCTT-TAAT
*
649434 ATTTTATAAATTTATCTTTAAT
1 ATTTTATAAATTCATCTTTAAT
649456 AT
1 AT
649458 GAAATCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTTATAAATTCATCTTTAAT
Found at i:650367 original size:26 final size:27
Alignment explanation
Indices: 650317--650389 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 27
650307 TTTTAATTTT
650317 TAATATTAATTTTTTAA-A-TAAATTA
1 TAATATTAATTTTTTAATATTAAATTA
*
650342 -AATATTAATTTTTTAATATTATATTA
1 TAATATTAATTTTTTAATATTAAATTA
650368 TACATATTAA--TTTTAATATTAA
1 TA-ATATTAATTTTTTAATATTAA
650390 TTTTTTTTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
24 16 0.38
25 1 0.02
26 17 0.40
27 1 0.02
28 7 0.17
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATATTAATTTTTTAATATTAAATTA
Found at i:650442 original size:67 final size:64
Alignment explanation
Indices: 650296--650450 Score: 215
Period size: 66 Copynumber: 2.4 Consensus size: 64
650286 TTTATATTAT
* *
650296 ATTATATT-T-GATTTTAATTTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAAT
1 ATTATATTATAGATATTAA-TTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAAG
* *
650359 ATTATATTATACATATTAATTTTAATATTAATTTTTTTTAAATAAATTAAATATTATTTTGTTTA
1 ATTATATTATAGATATTAATTTTAATATTAA--TTTTTTAAATAAATTAAATATTAATTT-TTTA
650424 AG
63 AG
650426 ATTATATTATAGATATTTAATTTTA
1 ATTATATTATAGATA-TTAATTTTA
650451 TATCATATAA
Statistics
Matches: 81, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
63 8 0.10
64 13 0.16
65 6 0.07
66 26 0.32
67 19 0.23
68 9 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (64 bp):
ATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAAG
Found at i:650999 original size:31 final size:31
Alignment explanation
Indices: 650962--651021 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
650952 TAGTTGTATG
* *
650962 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
650993 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
651022 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:661607 original size:3 final size:3
Alignment explanation
Indices: 661599--661640 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
661589 CCTATTTCTT
661599 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
661641 AAGATTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:661830 original size:3 final size:3
Alignment explanation
Indices: 661822--661848 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
661812 TTAATCTATG
661822 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
661849 TAAAGCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:661957 original size:5 final size:5
Alignment explanation
Indices: 661940--661972 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
661930 ACACTCATCC
661940 AAGAA ACAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA A-AGAA AAGAA AAGAA AAGAA AAGAA AA
661973 TTTTGTCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:663338 original size:14 final size:15
Alignment explanation
Indices: 663321--663358 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
663311 GTCTTACGAA
*
663321 TTTAAAAGTATT-AT
1 TTTAAAAATATTAAT
663335 TTTAAAAATATTAAT
1 TTTAAAAATATTAAT
*
663350 TTTAGAAAT
1 TTTAAAAAT
663359 TAATATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (15 bp):
TTTAAAAATATTAAT
Found at i:664072 original size:2 final size:2
Alignment explanation
Indices: 664065--664118 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
664055 AATTTATGTC
664065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
664107 AT AT AT AT AT AT
1 AT AT AT AT AT AT
664119 TAATATTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:670041 original size:909 final size:905
Alignment explanation
Indices: 668100--670806 Score: 4849
Period size: 909 Copynumber: 3.0 Consensus size: 905
668090 TTTTGGACTA
* * *
668100 AAATACTCTTAAAAAAAATTTCTTACAAAAATATATTTATTCTGTCATTAAATAATAAAAATTTT
1 AAATGCTCTT-AAAAAAATTTCTTACAAAAATATACTTATTCTGTCATTGAATAATAAAAATTTT
*
668165 ACGAATGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAATCTATAATTAAAA
65 ACGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAATCTATAATTAAAA
668230 TTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCA
130 TTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCA
* *
668295 ATTTTGTAAATAAATTTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATT
195 ATTTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATT
668360 TTTCAACTTGTTAAAAATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAATA
260 TTTCAACTTGTTAAAAATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAATA
668425 ATCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACTAAACACAAAA
325 ATCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACTAAACACAAAA
668490 TATAACAATCCTAGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTTCG
390 TATAACAATCCTAGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTTCG
*
668555 TGAACCAAACACACTCTAAGTGAAGAGCACGGATGGAAGGGGGGAAAATAAAATGAAAAAAATAT
455 TGAACCAAACACACTCTAAGTGAAGAGCACAGATGGAAGGGGGGAAAATAAAATGAAAAAAATAT
668620 TAAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAAGGA
520 TAAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAAGGA
*
668685 GAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAATCCTCTAGCGTGGAAAC
585 GAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAGCGTGGAAAC
* * *
668750 TGTTGGCGTCCACGTAACCATAAACTAATAGTTTTATTAGTCAAAATGGTCAAATGTACAAATTG
650 TGTTGGCGTCCACGTAACCATAAACTAATAGTTCTGTTAGTCAAAATGGTCAAAGGTACAAATTG
*
668815 ATGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATATGAACGAAATTGATAAAT
715 ATGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATACGAACGAAATTGATAAAT
668880 TTGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAAAAC
780 TTGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAAAA-
668945 AAATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATTTAAATAAT
844 AAATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATTTAAATAAT
*
669007 AAATGCTCTTAAAAAAATTTCTTACAAAAATATACTTATTATGTCATTGAATAATAAAAATTTTA
1 AAATGCTCTTAAAAAAATTTCTTACAAAAATATACTTATTCTGTCATTGAATAATAAAAATTTTA
*
669072 CGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAGTCTATAATTAAAAT
66 CGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAATCTATAATTAAAAT
*
669137 TTTATATGAAGTTCAGGAGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAA
131 TTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAA
669202 TTTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTT
196 TTTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTT
669267 TTCAACTTGTTAAAATATATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAA
261 TTCAACTTGTT-AAA-A-ATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAA
*
669332 TAATCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCATACTAAACCAACTAAACACAA
323 TAATCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACTAAACACAA
669397 AATATAACAATCCTAGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTT
388 AATATAACAATCCTAGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTT
*
669462 CGTGAACCAAACACACTCTAAGTGAAGAGCACAGATGGAAGGGGGGGAAATAAAATGAAAAAAAT
453 CGTGAACCAAACACACTCTAAGTGAAGAGCACAGATGGAAGGGGGGAAAATAAAATGAAAAAAAT
669527 ATTAAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAAG
518 ATTAAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAAG
669592 GAGAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAGCGTGGAA
583 GAGAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAGCGTGGAA
* *
669657 ACTGTTGGCGTCCACGAAACCATAAATTAATAGTTCTGTTAGTCAAAATGGTCAAAGGTACAAAT
648 ACTGTTGGCGTCCACGTAACCATAAACTAATAGTTCTGTTAGTCAAAATGGTCAAAGGTACAAAT
* *
669722 TGATGCAATTAAATAATTTAAAGGGTAAAATTAATACGAAAATACGATAGGAACGAAATTGATAA
713 TGATGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATACGAACGAAATTGATAA
669787 ATTTGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAAA
778 ATTTGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAAA
669852 AAAATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATTTAAATAAT
843 AAAATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATTTAAATAAT
669915 AAATGCTCTTAAAAAAATTTCTTACAAAAATATACTTATTCTGTCATTGAATAATAAAAATTTTA
1 AAATGCTCTTAAAAAAATTTCTTACAAAAATATACTTATTCTGTCATTGAATAATAAAAATTTTA
* * *
669980 CGAAGGTTGAATTATAAATTTATCCTTAAACTATTTTAGATTTATAAAAAAATCAATAATTAAAA
66 CGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTA-CAAAAAATCTATAATTAAAA
670045 TTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCA
130 TTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCA
*
670110 ATTTTGGAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATT
195 ATTTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATT
670175 TTTCAACTTGTTAAAAA-A-ATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAATA
260 TTTCAACTTGTTAAAAATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAATA
* *
670238 ATCTTTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACCAAACA-AAAA
325 ATCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACTAAACACAAAA
* * * * *
670302 TACATC-ATTCTCAGTAATCCTATTCTCTGGTAATCTTTTATTCCCACTGGTAATCTTATATTCC
390 TATAACAATCCT-AGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTTC
* **
670366 GTGAACCAAACGCACTCTAAGTGAAGAGCACAGATGGAAGGGGAAAAAAATAAAATGAAAAAAAA
454 GTGAACCAAACACACTCTAAGTGAAGAGCACAGATGGAAGGGG-GGAAAATAAAATG-AAAAAAA
* * *
670431 TATTAAAACGGTGATACATATTTGATTCCAAAATTGTGTA------AGTAGTATAAGAAAGAAAA
517 TATTAAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAA
*
670490 GGAGAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAACGTGGA
582 GGAGAAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAGCGTGGA
* *
670555 AACAGTTGGCGTCCACGTAACCATAAACTAATAATTCTGTTAGTCAAAATGGTCAAAGGTACAAA
647 AACTGTTGGCGTCCACGTAACCATAAACTAATAGTTCTGTTAGTCAAAATGGTCAAAGGTACAAA
*
670620 TTGATGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATACGAAAGAAATTGATA
712 TTGATGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATACGAACGAAATTGATA
*
670685 AATTTGGTCTATTATAGGGGCATCTATAACCCAAACCTTAAAAATTTGAATTATTATATTAACAA
777 AATTTGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAA
* *
670750 CACAAATATAAAGAACAAATTACTTTTAATAAAAATAATTTTATTAAAATTTAAATT
842 -AAAAATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATT
670807 AATTATATCA
Statistics
Matches: 1739, Mismatches: 53, Indels: 23
0.96 0.03 0.01
Matches are distributed among these distances:
899 269 0.15
900 54 0.03
902 4 0.00
903 100 0.06
904 112 0.06
905 46 0.03
906 254 0.15
907 13 0.01
908 173 0.10
909 714 0.41
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (905 bp):
AAATGCTCTTAAAAAAATTTCTTACAAAAATATACTTATTCTGTCATTGAATAATAAAAATTTTA
CGAAGGTTAAATTATAAATTTATCCTTAAACTATTTTAGATTTACAAAAAATCTATAATTAAAAT
TTTATATGAAGTTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAA
TTTTGTAAAAAAAATTATATAAATTTTATGAATTTAAATTTTTTAAAGAAAATATATAAATATTT
TTCAACTTGTTAAAAATATATATATATATAATAAGGACAATTTGTTCAAATATACATTCCAATAA
TCTGTTATTCTTTTAACCAAACACGATAATCTTTACATTCCTACTAAACCAACTAAACACAAAAT
ATAACAATCCTAGTAATCCTATTCTCTGGTAATATTTTATTCCCACTGGTAATCTTATATTTCGT
GAACCAAACACACTCTAAGTGAAGAGCACAGATGGAAGGGGGGAAAATAAAATGAAAAAAATATT
AAAATGGTGATACATATTTGTTTCCAAAATTGTGTAGTTTTGGGTAGTATAAGAAAGAAAAGGAG
AAATCACAACATAAATCCTCTGAAAAAAGGAAAAATCACAAATTTAGTCCTCTAGCGTGGAAACT
GTTGGCGTCCACGTAACCATAAACTAATAGTTCTGTTAGTCAAAATGGTCAAAGGTACAAATTGA
TGCAATTAAATAATTTAAAGGGTAAAATTGATACGAAAATACGATACGAACGAAATTGATAAATT
TGGTCTATTATAGGGGCATCTATAACCCAAGCCTTAAAAATTTGAATTATTATATTAACAAAAAA
ATATAAAGAACAAATTATTTTTAATAAAAATAATTTTATTAAAATTTAAATTTAAATAAT
Found at i:670353 original size:20 final size:20
Alignment explanation
Indices: 670328--670365 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
670318 ATCCTATTCT
*
670328 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
670348 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
670366 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:671889 original size:37 final size:36
Alignment explanation
Indices: 671814--671889 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
671804 TTTTTATATT
*
671814 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
671850 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
671887 TTT
1 TTT
671890 TTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:672788 original size:13 final size:13
Alignment explanation
Indices: 672770--672803 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
672760 GATAAAAACT
672770 ATAATTTTTAGAA
1 ATAATTTTTAGAA
*
672783 ATAA-TTTTATAA
1 ATAATTTTTAGAA
672795 ATAATTTTT
1 ATAATTTTT
672804 TTTTAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATAATTTTTAGAA
Found at i:677041 original size:2 final size:2
Alignment explanation
Indices: 677034--677084 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
677024 AATTTTACGT
677034 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
677076 TA TA TA TA T
1 TA TA TA TA T
677085 CGATTTTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:681038 original size:19 final size:20
Alignment explanation
Indices: 681001--681038 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
680991 TTTTTTTTTC
681001 AAATTATAATGTTATTTAAT
1 AAATTATAATGTTATTTAAT
681021 AAATTA-AAT-TTCATTTAA
1 AAATTATAATGTT-ATTTAA
681039 ATTATAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 9 0.53
20 6 0.35
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
AAATTATAATGTTATTTAAT
Found at i:681445 original size:18 final size:18
Alignment explanation
Indices: 681422--681460 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
681412 AATGAATAAA
* *
681422 TTTTGATTCGAGTCAGGT
1 TTTTGAATCGAATCAGGT
*
681440 TTTTGAATCGAATCGGGT
1 TTTTGAATCGAATCAGGT
681458 TTT
1 TTT
681461 ACTCACCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (18 bp):
TTTTGAATCGAATCAGGT
Found at i:688761 original size:16 final size:14
Alignment explanation
Indices: 688730--688764 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
688720 TATTTTAATC
688730 TTTTATATAATTTA
1 TTTTATATAATTTA
688744 TTTTATATTAATTTTA
1 TTTTATA-TAA-TTTA
688760 TTTTA
1 TTTTA
688765 ATACATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 3 0.16
16 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATATAATTTA
Found at i:689745 original size:80 final size:80
Alignment explanation
Indices: 689590--689747 Score: 246
Period size: 80 Copynumber: 2.0 Consensus size: 80
689580 AATAGAAAAT
* *
689590 AGGGAAAAATCAAAATAAATTAAAATTTAAAGGCCTAAGTAGGTAGTTGTCCCATTATTCTTTAA
1 AGGGAAAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTGTCCCATTATTCTTTAA
689655 TGATAAAAAAATTAG
66 TGATAAAAAAATTAG
* * *
689670 AGGGAAAATTCAAGATAAATTAAAATTTAAAGGCCTAAATAGG-AATTGTCCCTTTATTCTTTAA
1 AGGGAAAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTGTCCCATTATTCTTTAA
*
689734 TTATAACAAAAATT
66 TGATAA-AAAAATT
689748 GGGGGCACCC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
79 24 0.34
80 47 0.66
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (80 bp):
AGGGAAAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTGTCCCATTATTCTTTAA
TGATAAAAAAATTAG
Found at i:692430 original size:23 final size:24
Alignment explanation
Indices: 692399--692453 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
692389 GATCCTATGT
* *
692399 AAAACTAAAAGAATTT-TAAATAA
1 AAAAATAAAAGAATTTAAAAATAA
* *
692422 AAAAATAAAATACTTTAAAAATAA
1 AAAAATAAAAGAATTTAAAAATAA
692446 AAAAATAA
1 AAAAATAA
692454 TATATGTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 13 0.48
24 14 0.52
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAATAAAAGAATTTAAAAATAA
Found at i:696428 original size:20 final size:20
Alignment explanation
Indices: 696380--696453 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
696370 GAATATGTAA
* * *
696380 ATCGCAATGCGAGTATGACT
1 ATCGCAACGCGATTCTGACT
*
696400 ATCACAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
696420 ATCGGAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
696440 ATCGCAATGCGATT
1 ATCGCAACGCGATT
696454 TTCAAAGCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:696654 original size:22 final size:22
Alignment explanation
Indices: 696629--696671 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
696619 GGCGACATCC
696629 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
696651 GTCCCCATCTCCGACGAAATC
1 GTCCCCATCTCCGACGAAATC
696672 CGTCTATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.42, G:0.14, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:697090 original size:19 final size:19
Alignment explanation
Indices: 697068--697120 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
697058 GCAATTTTAG
697068 TTTCGCGTTGTGATTTTCA
1 TTTCGCGTTGTGATTTTCA
697087 TTTCGCGTTGTGATTTTCA
1 TTTCGCGTTGTGATTTTCA
*
697106 TTTCGCGTTGCGATT
1 TTTCGCGTTGTGATT
697121 CTAACATTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.09, C:0.17, G:0.23, T:0.51
Consensus pattern (19 bp):
TTTCGCGTTGTGATTTTCA
Found at i:697152 original size:20 final size:20
Alignment explanation
Indices: 697127--697173 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
697117 GATTCTAACA
697127 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCG
** *
697147 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCAAATTCGCG
697167 TTGCGAT
1 TTGCGAT
697174 TTTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCG
Found at i:697179 original size:20 final size:20
Alignment explanation
Indices: 697141--697196 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
697131 GATAGTCAAA
* **
697141 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
697161 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
697181 TTCGTATTGCGATTTT
1 TTCGTGTTGCGATTTT
697197 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:697203 original size:20 final size:20
Alignment explanation
Indices: 697160--697203 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
697150 CGATAGTCAT
* * *
697160 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTTAAG
697180 TTTCGTATTGCGATTTTAAG
1 TTTCGTATTGCGATTTTAAG
697200 TTTC
1 TTTC
697204 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTATTGCGATTTTAAG
Found at i:699209 original size:20 final size:20
Alignment explanation
Indices: 699180--699255 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
699170 GCGATTCTCT
*
699180 CGTTGCGATAGTCATTTTCA
1 CGTTGAGATAGTCATTTTCA
* *
699200 TGTTGAGATAGTCATTTTCG
1 CGTTGAGATAGTCATTTTCA
* **
699220 CGTTGTGATAGTCATTTTGG
1 CGTTGAGATAGTCATTTTCA
*
699240 CGTTGCGATAGTCATT
1 CGTTGAGATAGTCATT
699256 CGTATTACGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.42
Consensus pattern (20 bp):
CGTTGAGATAGTCATTTTCA
Found at i:699235 original size:40 final size:40
Alignment explanation
Indices: 699180--699255 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
699170 GCGATTCTCT
*
699180 CGTTGCGATAGTCATTTTCATGTTGAGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCACGTTGAGATAGTCATTTTCG
* ** *
699220 CGTTGTGATAGTCATTTTGGCGTTGCGATAGTCATT
1 CGTTGCGATAGTCATTTTCACGTTGAGATAGTCATT
699256 CGTATTACGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.42
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTTCACGTTGAGATAGTCATTTTCG
Done.