Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002341.1 Hibiscus syriacus cultivar Beakdansim tig00004779_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: 1266629
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:535652 original size:15 final size:15
Alignment explanation
Indices: 535611--535655 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
535601 CAGCTTTCCT
*
535611 CCCTAGAGCAGCTTC
1 CCCTAGAGCTGCTTC
* * *
535626 TCCAAGAACTGCTTC
1 CCCTAGAGCTGCTTC
535641 CCCTAGAGCTGCTTC
1 CCCTAGAGCTGCTTC
535656 TCCACCTCCT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.38, G:0.18, T:0.24
Consensus pattern (15 bp):
CCCTAGAGCTGCTTC
Found at i:535689 original size:15 final size:15
Alignment explanation
Indices: 535616--535690 Score: 50
Period size: 15 Copynumber: 5.2 Consensus size: 15
535606 TTCCTCCCTA
* *
535616 GAGCAGCTTCTCCAA
1 GAGCTGCTTCTCCAC
* *
535631 GAACTGCTTCCCCTA-
1 GAGCTGCTTCTCC-AC
535646 GAGCTGCTTCTCCAC
1 GAGCTGCTTCTCCAC
* * *
535661 ---CTCCTCCCCCAC
1 GAGCTGCTTCTCCAC
535673 GAGCTGCTTCTCCAC
1 GAGCTGCTTCTCCAC
535688 GAG
1 GAG
535691 TAGTTTCTCC
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
12 9 0.20
14 1 0.02
15 33 0.75
16 1 0.02
ACGTcount: A:0.17, C:0.43, G:0.17, T:0.23
Consensus pattern (15 bp):
GAGCTGCTTCTCCAC
Found at i:538477 original size:12 final size:12
Alignment explanation
Indices: 538460--538484 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
538450 AATATTTTAG
538460 TAAAATATTATT
1 TAAAATATTATT
538472 TAAAATATTATT
1 TAAAATATTATT
538484 T
1 T
538485 TTTTTATTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:538478 original size:25 final size:27
Alignment explanation
Indices: 538421--538482 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
538411 ATGCTGTCAA
*
538421 AAAATATTATCGTAAATATTATTATTT
1 AAAATATTATAGTAAATATTATTATTT
** *
538448 TTAATATTTTAGTAAA-A-TATTATTT
1 AAAATATTATAGTAAATATTATTATTT
538473 AAAATATTAT
1 AAAATATTAT
538483 TTTTTTTATT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 15 0.54
26 1 0.04
27 12 0.43
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (27 bp):
AAAATATTATAGTAAATATTATTATTT
Found at i:538539 original size:25 final size:24
Alignment explanation
Indices: 538511--538588 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
538501 AGTAGAAAAA
538511 TAATATTTTAGGTAGCGTCTAATAT
1 TAATATTTTAGGTAGCGT-TAATAT
* *
538536 TAATATTTCT-GGTA--G--AAAAA
1 TAATATTT-TAGGTAGCGTTAATAT
538556 TAATATTTTAGGTAGCGTATAATAT
1 TAATATTTTAGGTAGCGT-TAATAT
538581 TAATATTT
1 TAATATTT
538589 CTAGTAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 1 0.02
20 15 0.36
22 1 0.02
23 1 0.02
25 23 0.55
26 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (24 bp):
TAATATTTTAGGTAGCGTTAATAT
Found at i:538557 original size:45 final size:45
Alignment explanation
Indices: 538500--538611 Score: 188
Period size: 45 Copynumber: 2.5 Consensus size: 45
538490 ATTTAAAAAT
*
538500 TAGTAGAAAAATAATATTTTAGGTAGCGTCTAATATTAATATTTC
1 TAGTAGAAAAATAATATTTTAGGTAGCGTATAATATTAATATTTC
*
538545 TGGTAGAAAAATAATATTTTAGGTAGCGTATAATATTAATATTTC
1 TAGTAGAAAAATAATATTTTAGGTAGCGTATAATATTAATATTTC
*
538590 TAGTAAAAAATATAATATTTTA
1 TAGTAGAAAA-ATAATATTTTA
538612 AATAATATTT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 51 0.82
46 11 0.18
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.40
Consensus pattern (45 bp):
TAGTAGAAAAATAATATTTTAGGTAGCGTATAATATTAATATTTC
Found at i:538569 original size:20 final size:20
Alignment explanation
Indices: 538502--538570 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
538492 TTAAAAATTA
538502 GTAGAAAAATAATATTTTAG
1 GTAGAAAAATAATATTTTAG
* *
538522 GTAGCGTCTAATATTAATATTTCT-G
1 GTA--G---AAAAATAATATTT-TAG
538547 GTAGAAAAATAATATTTTAG
1 GTAGAAAAATAATATTTTAG
538567 GTAG
1 GTAG
538571 CGTATAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 1 0.03
20 19 0.50
22 1 0.03
23 1 0.03
25 15 0.39
26 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.17, T:0.38
Consensus pattern (20 bp):
GTAGAAAAATAATATTTTAG
Found at i:539001 original size:26 final size:25
Alignment explanation
Indices: 538972--539021 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
538962 TATTTTTGAG
* *
538972 AAAATTTATTTTTAAAATAATATTTT
1 AAAATTTA-TTTAAAAATAAAATTTT
538998 AAAATTTATTTAAAAATAAAATTT
1 AAAATTTATTTAAAAATAAAATTT
539022 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTTATTTAAAAATAAAATTTT
Found at i:539013 original size:12 final size:12
Alignment explanation
Indices: 538972--539014 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
538962 TATTTTTGAG
538972 AAAATTTATTTTT
1 AAAATTTA-TTTT
*
538985 AAAATAATATTTT
1 AAAAT-TTATTTT
*
538998 AAAATTTATTTA
1 AAAATTTATTTT
539010 AAAAT
1 AAAAT
539015 AAAATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 14 0.54
14 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAAATTTATTTT
Found at i:539485 original size:20 final size:20
Alignment explanation
Indices: 539430--539490 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
539420 ATTCGACTCA
*
539430 GTTTTT-AAATTCGCAACGC
1 GTTTTTCAAATTCGTAACGC
* * **
539449 GATTCTCCAAAACCGTAACGC
1 G-TTTTTCAAATTCGTAACGC
539470 GTTTTTCAAATTCGTAACGC
1 GTTTTTCAAATTCGTAACGC
539490 G
1 G
539491 AATTTCGTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.03
20 19 0.61
21 11 0.35
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (20 bp):
GTTTTTCAAATTCGTAACGC
Found at i:549007 original size:8 final size:8
Alignment explanation
Indices: 548994--549031 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
548984 CTTAGATATT
548994 TACATACG
1 TACATACG
549002 TACATACG
1 TACATACG
549010 TACATACG
1 TACATACG
*
549018 TACGTACG
1 TACATACG
549026 TACATA
1 TACATA
549032 TGTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (8 bp):
TACATACG
Found at i:558434 original size:15 final size:15
Alignment explanation
Indices: 558414--558443 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
558404 AAATTAAAAT
558414 AAAAAGAAGAAGAAG
1 AAAAAGAAGAAGAAG
558429 AAAAAGAAGAAGAAG
1 AAAAAGAAGAAGAAG
558444 CAGCTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAAGAAGAAGAAG
Found at i:561058 original size:29 final size:29
Alignment explanation
Indices: 561026--561142 Score: 183
Period size: 29 Copynumber: 4.2 Consensus size: 29
561016 AATCAGATAC
561026 TTATTTTTATAAAATAATAATTTAAGGAT
1 TTATTTTTATAAAATAATAATTTAAGGAT
561055 TTATTTTTATAAAATAATAATTTAAGGAT
1 TTATTTTTATAAAATAATAATTTAAGGAT
561084 TTA--TTT-T--AATAATAATTTAAGGAT
1 TTATTTTTATAAAATAATAATTTAAGGAT
*
561108 TTATTTTTATAAAATAATTATTTAAGGAT
1 TTATTTTTATAAAATAATAATTTAAGGAT
561137 TT-TTTT
1 TTATTTT
561143 CTACCAAGAT
Statistics
Matches: 82, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
24 20 0.24
26 4 0.05
27 4 0.05
28 4 0.05
29 50 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (29 bp):
TTATTTTTATAAAATAATAATTTAAGGAT
Found at i:561097 original size:53 final size:52
Alignment explanation
Indices: 561038--561142 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 52
561028 ATTTTTATAA
561038 AATAATAATTTAAGGATTTATTTTTATAAAATAATAATTTAAGGATTTATTTT
1 AATAATAATTTAAGGATTTATTTTTATAAAATAATAATTTAAGGATTT-TTTT
*
561091 AATAATAATTTAAGGATTTATTTTTATAAAATAATTATTTAAGGATTTTTTT
1 AATAATAATTTAAGGATTTATTTTTATAAAATAATAATTTAAGGATTTTTTT
561143 CTACCAAGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 4 0.08
53 47 0.92
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (52 bp):
AATAATAATTTAAGGATTTATTTTTATAAAATAATAATTTAAGGATTTTTTT
Found at i:561099 original size:24 final size:24
Alignment explanation
Indices: 561038--561119 Score: 110
Period size: 24 Copynumber: 3.2 Consensus size: 24
561028 ATTTTTATAA
561038 AATAATAATTTAAGGATTTATTTTTAT
1 AATAATAATTTAAGGATTTA--TTT-T
561065 AAAATAATAATTTAAGGATTTATTTT
1 --AATAATAATTTAAGGATTTATTTT
561091 AATAATAATTTAAGGATTTATTTT
1 AATAATAATTTAAGGATTTATTTT
*
561115 TATAA
1 AATAA
561120 AATAATTATT
Statistics
Matches: 52, Mismatches: 1, Indels: 5
0.90 0.02 0.09
Matches are distributed among these distances:
24 28 0.54
26 1 0.02
27 3 0.06
29 20 0.38
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (24 bp):
AATAATAATTTAAGGATTTATTTT
Found at i:561292 original size:154 final size:155
Alignment explanation
Indices: 560903--561321 Score: 582
Period size: 154 Copynumber: 2.7 Consensus size: 155
560893 TCAAAACCGA
560903 TTTATTAAACTATACTATCATTTTTTTAGTTAAGTAATTAAACTATTATATATAATCATATCATT
1 TTTATTAAACTATACTATCATTTTTTTAGTTAAGTAATTAAACTATTATATATAATCATATCATT
560968 TTTTAATTAGATTTTTTTTTTCTACCAAGATATTAATATATTACATAAAATCAGATACTTATTTT
66 TTTTAATTAGA--TTTTTTTTCTACCAAGATATTAATATATTACATAAAATCAGATACTTATTTT
561033 TATAAAATAATAATTTAAGGATTTATT
129 TATAAAATAATAATTTAAGGATTTATT
* * ** * * ** * * * *
561060 TTTA-TAAAATAATAATTTAAGGATTTATTTTA-ATAA-TAATTTAAGGATT-TATTTTTATAAA
1 TTTATTAAACT-AT-A-CT-ATCATTT-TTTTAGTTAAGTAATTAAACTATTATA-TATAATCAT
* * *
561121 ATAATTATTTAA--GGA-TTTTTTTCTACCAAGATATTAATATATTACATAAAATCAGATACTTA
60 ATCATTTTTTAATTAGATTTTTTTTCTACCAAGATATTAATATATTACATAAAATCAGATACTTA
561183 TTTTTATAAAATAATAATTTAAGGATTTATT
125 TTTTTATAAAATAATAATTTAAGGATTTATT
561214 TTTATTAAACTATACTATCATTTTTTTAGTTAAGTAATTAAACTATTATATATAATCATATCATT
1 TTTATTAAACTATACTATCATTTTTTTAGTTAAGTAATTAAACTATTATATATAATCATATCATT
561279 TTTTAATTAGATTTTTTTTCTACCAAGATATTAATATATTACA
66 TTTTAATTAGATTTTTTTTCTACCAAGATATTAATATATTACA
561322 ACATGGAATC
Statistics
Matches: 219, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
150 5 0.02
151 8 0.04
152 26 0.12
153 3 0.01
154 86 0.39
155 36 0.16
156 5 0.02
157 8 0.04
158 3 0.01
159 26 0.12
160 8 0.04
161 5 0.02
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (155 bp):
TTTATTAAACTATACTATCATTTTTTTAGTTAAGTAATTAAACTATTATATATAATCATATCATT
TTTTAATTAGATTTTTTTTCTACCAAGATATTAATATATTACATAAAATCAGATACTTATTTTTA
TAAAATAATAATTTAAGGATTTATT
Found at i:573815 original size:20 final size:19
Alignment explanation
Indices: 573792--573837 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
573782 CGATATACCA
573792 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
573812 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
573832 GGTAAA
1 GGTAAA
573838 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:573982 original size:20 final size:19
Alignment explanation
Indices: 573959--574005 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
573949 CGATATAACA
573959 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
573979 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
573999 GGTAAAA
1 GGTAAAA
574006 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:574007 original size:17 final size:19
Alignment explanation
Indices: 573968--574010 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
573958 AGGTAAAAAT
573968 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
573988 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
574005 ATGATA
1 ATGATA
574011 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:576259 original size:21 final size:21
Alignment explanation
Indices: 576232--576296 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
576222 AAGACAATCA
* *
576232 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTCGAG
* *
576253 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
576274 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
576295 AG
1 AG
576297 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:576372 original size:33 final size:33
Alignment explanation
Indices: 576330--576395 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
576320 AAATAGATGG
*
576330 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
576363 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
576396 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:582134 original size:16 final size:16
Alignment explanation
Indices: 582113--582152 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
582103 ATGGTCGACT
*
582113 GTTGACCGTTGACCGC
1 GTTGACCATTGACCGC
582129 GTTGACCATTGACCGC
1 GTTGACCATTGACCGC
582145 GTTGACCA
1 GTTGACCA
582153 GAACTTTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.28, T:0.25
Consensus pattern (16 bp):
GTTGACCATTGACCGC
Found at i:584232 original size:24 final size:24
Alignment explanation
Indices: 584205--584299 Score: 154
Period size: 24 Copynumber: 4.0 Consensus size: 24
584195 TTCGATCTGA
584205 ATTTTGATATGATACTTGACCTGG
1 ATTTTGATATGATACTTGACCTGG
*
584229 ATTTTGATATGATATTTGACCTGG
1 ATTTTGATATGATACTTGACCTGG
*
584253 ATTTTTATATGATACTTGACCTGG
1 ATTTTGATATGATACTTGACCTGG
* *
584277 ATTCTGATATGCTACTTGACCTG
1 ATTTTGATATGATACTTGACCTG
584300 AATTATGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (24 bp):
ATTTTGATATGATACTTGACCTGG
Found at i:584326 original size:2 final size:2
Alignment explanation
Indices: 584319--584348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
584309 TTGATTTTTG
584319 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
584349 CCGTTACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587734 original size:26 final size:26
Alignment explanation
Indices: 587683--587734 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
587673 ACCCTACCTG
* * *
587683 AACCCGACCCGATATATAACTCAAAA
1 AACCCGACCCAAAATATAACTAAAAA
587709 AACCCGACCCAAAATAATAA-TAAAAA
1 AACCCGACCCAAAAT-ATAACTAAAAA
587735 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.54, C:0.27, G:0.06, T:0.13
Consensus pattern (26 bp):
AACCCGACCCAAAATATAACTAAAAA
Found at i:589892 original size:15 final size:17
Alignment explanation
Indices: 589854--589895 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
589844 TATATATATA
589854 TATTA-AATTTAGTTAT
1 TATTATAATTTAGTTAT
589870 TAATTATAATTTA-TT-T
1 T-ATTATAATTTAGTTAT
589886 TATTATAATT
1 TATTATAATT
589896 CTAATAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 6 0.25
18 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TATTATAATTTAGTTAT
Found at i:596244 original size:17 final size:17
Alignment explanation
Indices: 596202--596262 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
596192 TATATTAATA
596202 ATATAATTTTAT-ATTCTC
1 ATAT-ATTTTATAATT-TC
* *
596220 TTAAATTTTATAATTTC
1 ATATATTTTATAATTTC
* * *
596237 ATATATTTAATATTTTA
1 ATATATTTTATAATTTC
596254 ATATATTTT
1 ATATATTTT
596263 TAAAAAAAGT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTTATAATTTC
Found at i:596891 original size:2 final size:2
Alignment explanation
Indices: 596884--596941 Score: 66
Period size: 2 Copynumber: 29.0 Consensus size: 2
596874 TTTTATCATC
*
596884 TA TA TA TA TA TA TA T- TA TCA TC TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
*
596925 TA TCA TC TA TA TA TA TA
1 TA T-A TA TA TA TA TA TA
596942 GATTATAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
1 2 0.04
2 42 0.88
3 4 0.08
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:596913 original size:26 final size:26
Alignment explanation
Indices: 596884--596941 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
596874 TTTTATCATC
596884 TATATATATATATATTATCATCTATA
1 TATATATATATATATTATCATCTATA
596910 TATATATATATATATTATCATCTATA
1 TATATATATATATATTATCATCTATA
596936 TATATA
1 TATATA
596942 GATTATAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATATATATATATTATCATCTATA
Found at i:596939 original size:22 final size:22
Alignment explanation
Indices: 596864--596947 Score: 105
Period size: 22 Copynumber: 3.7 Consensus size: 22
596854 AATAAACTTC
* *
596864 TATATTTATATTTTATCATCTA
1 TATATATATATATTATCATCTA
596886 TATATATATATATTATCATCTA
1 TATATATATATATTATCATCTA
* *
596908 TATATATATATATATATTATCATC
1 TATATATATATAT-TATCATC-TA
*
596932 TATATATATAGATTAT
1 TATATATATATATTAT
596948 AAGGTAGAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
22 33 0.60
23 9 0.16
24 13 0.24
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.52
Consensus pattern (22 bp):
TATATATATATATTATCATCTA
Found at i:597619 original size:2 final size:2
Alignment explanation
Indices: 597612--597637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
597602 TATTTTCAAT
597612 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
597638 AATTTTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:612479 original size:22 final size:22
Alignment explanation
Indices: 612453--612495 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
612443 CGATTTATTA
612453 AATAGCTATATAAATATTAGTT
1 AATAGCTATATAAATATTAGTT
*
612475 AATAGCTATATAAATGTTAGT
1 AATAGCTATATAAATATTAGT
612496 ATTTTTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
AATAGCTATATAAATATTAGTT
Found at i:617103 original size:17 final size:17
Alignment explanation
Indices: 617078--617111 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
617068 CCGGTTTCGA
617078 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
617095 TTTTTAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
617112 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:617395 original size:32 final size:33
Alignment explanation
Indices: 617305--617397 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
617295 AACATAATTG
* *
617305 AATACTTAAATACTTCCAAGTTTGATAAATTCA
1 AATACTTAAAAACTTCCAAGTTCGATAAATTCA
617338 AATACTTAAAAACTTCCAAGTTCGATAAATTCA
1 AATACTTAAAAACTTCCAAGTTCGATAAATTCA
617371 AATACTTAAAAACTT-CAAGTTCGATAA
1 AATACTTAAAAACTTCCAAGTTCGATAA
617398 TTGAAACAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 12 0.21
33 46 0.79
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (33 bp):
AATACTTAAAAACTTCCAAGTTCGATAAATTCA
Found at i:617416 original size:21 final size:21
Alignment explanation
Indices: 617392--617433 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
617382 ACTTCAAGTT
617392 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
617413 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
617434 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:623442 original size:2 final size:2
Alignment explanation
Indices: 623431--623509 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
623421 AATAAATTTA
623431 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
623472 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
623510 GTGTGTGTGT
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:626404 original size:22 final size:21
Alignment explanation
Indices: 626353--626414 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
626343 TACGTTTATG
626353 ATTTTTT-TTCTTTTAT-AGC
1 ATTTTTTCTTCTTTTATGAGC
*
626372 ATTTTTCTTCTTCTTTTATGACTC
1 A-TTTT-TTCTTCTTTTATGA-GC
*
626396 ATTTTTTCTTATCTTTATG
1 ATTTTTTCTTCT-TTTATG
626415 CACTTCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 4 0.11
21 2 0.06
22 15 0.43
23 11 0.31
24 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (21 bp):
ATTTTTTCTTCTTTTATGAGC
Found at i:627566 original size:181 final size:180
Alignment explanation
Indices: 627263--627619 Score: 633
Period size: 181 Copynumber: 2.0 Consensus size: 180
627253 TGTTGAGTTC
*
627263 CTCTACTATTAAAAGTTACAAAATGTTCACCGACTATTCATTATGTTCAAAACTCATCATTTTCC
1 CTCTACTATTAAAAGTTACAAAATGATCACCGACTATTCATTATGTTCAAAACTCATCATTTTCC
* * *
627328 ATTAAAAAATTAACAGTCGTCTGACTTGGACGTTAACATGCGATTGAGATATGATAGTCGTTTAA
66 ATTAAAAAATTAACAGTCGTCTAACTTGAACGTTAACATGCGACTGAGATATGATAGTCGTTTAA
*
627393 GATTATGAGATCAAATTTTATTATATCTCAGTCACCAGATTAACGTCCGG
131 GATTATGAGATCAAATTTTATCATATCTCAGTCACCAGATTAACGTCCGG
*
627443 CTCTACTATTAAAAGTTACAAAATGATCACCCGACTATTCATTATGTTCCAAACTCATCATTTTC
1 CTCTACTATTAAAAGTTACAAAATGATCA-CCGACTATTCATTATGTTCAAAACTCATCATTTTC
627508 CATTAAAAAATTAACAGTCGTCTAACTTGAACGTTAACATGCGACTGAGATATGATAGTCGTTTA
65 CATTAAAAAATTAACAGTCGTCTAACTTGAACGTTAACATGCGACTGAGATATGATAGTCGTTTA
* *
627573 AGATTATGAGATCAAATTTTATCATATCTCAGTCAGCAGGTTAACGT
130 AGATTATGAGATCAAATTTTATCATATCTCAGTCACCAGATTAACGT
627620 ACAGCTAAGA
Statistics
Matches: 168, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
180 28 0.17
181 140 0.83
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (180 bp):
CTCTACTATTAAAAGTTACAAAATGATCACCGACTATTCATTATGTTCAAAACTCATCATTTTCC
ATTAAAAAATTAACAGTCGTCTAACTTGAACGTTAACATGCGACTGAGATATGATAGTCGTTTAA
GATTATGAGATCAAATTTTATCATATCTCAGTCACCAGATTAACGTCCGG
Found at i:663915 original size:295 final size:295
Alignment explanation
Indices: 663372--664242 Score: 1613
Period size: 295 Copynumber: 3.0 Consensus size: 295
663362 ACCTAAGATT
* * * *
663372 CAAATGAGATTTATATAGAAATTTACAGGTTG-TCCATTTTTGGG-TTTACATATTGTCCGTTCT
1 CAAATGAGATTTACATAGAAATTTACAGATTGCT-TATTTTTGGGATTTACGTATTGTCCGTTCT
663435 TAAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTC
65 TAAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTC
663500 GAATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCATTTT
130 GAATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCA-TTT
*
663565 TTTTTCAAAATCAATCTTATAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCAC
194 TTTTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCAC
*
663630 TACTTAGATCTAAGGAGATTAGGGCAAATCTAATGCC
259 TACTTGGATCTAAGGAGATTAGGGCAAATCTAATGCC
663667 CAAATGAGATTTACATAGAAATTTACAGATTGCTTATTTTTGGGATTTACGTATTGTCCGTTCTT
1 CAAATGAGATTTACATAGAAATTTACAGATTGCTTATTTTTGGGATTTACGTATTGTCCGTTCTT
*
663732 AAATAGATAAAGAAAAAATATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTCG
66 AAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTCG
663797 AATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCATTTTT
131 AATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCATTTTT
663862 TTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCACTA
196 TTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCACTA
663927 CTTGGATCTAAGGAGATTAGGGCAAATCTAATGCC
261 CTTGGATCTAAGGAGATTAGGGCAAATCTAATGCC
*
663962 CAAATGAGATTTACATAGAAATTTACAGATTGCCTATTTTTGGGATTTACGTATTGTCCGTTCTT
1 CAAATGAGATTTACATAGAAATTTACAGATTGCTTATTTTTGGGATTTACGTATTGTCCGTTCTT
664027 AAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTCG
66 AAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTCG
* *
664092 AATACGATCTAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTTCA-TTTT
131 AATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCATTTTT
664156 TTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCACTA
196 TTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCACTA
664221 CTTGGATCTAAGGAGATTAGGG
261 CTTGGATCTAAGGAGATTAGGG
664243 GTAAGTAAAA
Statistics
Matches: 563, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
294 91 0.16
295 328 0.58
296 144 0.26
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (295 bp):
CAAATGAGATTTACATAGAAATTTACAGATTGCTTATTTTTGGGATTTACGTATTGTCCGTTCTT
AAATAGATAAAGAAAAATTATACTACTATCTTGTATTAGATCTAAGAATTTTTCTCTTTAATTCG
AATACGATCAAACTTGAATTTATCTTTCAAAAAACTCCATCTGACCTGATTCGAATTCCATTTTT
TTTCAAAATCAATCTTACAGGGTCGGATCAATACATGTAAGGTCCAAGTTCGATACCCATCACTA
CTTGGATCTAAGGAGATTAGGGCAAATCTAATGCC
Found at i:670756 original size:6 final size:6
Alignment explanation
Indices: 670745--670774 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
670735 TTTGTAGATA
670745 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
670775 GGCAAACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.50, T:0.17
Consensus pattern (6 bp):
AGGGAT
Found at i:673015 original size:2 final size:2
Alignment explanation
Indices: 673008--673032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
672998 TTAATTTTCA
673008 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
673033 GTCAATGGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:678057 original size:113 final size:113
Alignment explanation
Indices: 677853--678070 Score: 350
Period size: 113 Copynumber: 1.9 Consensus size: 113
677843 AAATAAATAG
*
677853 AAAATGTGAAAAATTTCAACTGGTATTTATAGGCTGCTAAGGACTGATTTTCAACTTTGTAAAAG
1 AAAATATGAAAAATTTCAACTGGTATTTATAGGCTGCTAAGGACTGATTTTCAACTTTGTAAAAG
*
677918 GGGACAAACTGTTAATATCAGAAGTTATTTGATTTAATTCCAGATGAA
66 GAGACAAACTGTTAATATCAGAAGTTATTTGATTTAATTCCAGATGAA
* * *
677966 AAAATATGAAAGATTTCAACTGGTA-TTATAGGCTGCTGAGGACTGATTTTCAGCTTTGTACAAA
1 AAAATATGAAAAATTTCAACTGGTATTTATAGGCTGCTAAGGACTGATTTTCAACTTTGTA-AAA
*
678030 GGAGATAAACTGTTAATATCATG-AGTTATTTGATTTAATTC
65 GGAGACAAACTGTTAATATCA-GAAGTTATTTGATTTAATTC
678071 TAGGGGTTAC
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
112 33 0.34
113 63 0.65
114 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (113 bp):
AAAATATGAAAAATTTCAACTGGTATTTATAGGCTGCTAAGGACTGATTTTCAACTTTGTAAAAG
GAGACAAACTGTTAATATCAGAAGTTATTTGATTTAATTCCAGATGAA
Found at i:684579 original size:6 final size:6
Alignment explanation
Indices: 684554--684602 Score: 64
Period size: 6 Copynumber: 8.0 Consensus size: 6
684544 TTTCTTTCTA
*
684554 AGCTA- AGCTTAC AGGCTAC AGCTAC AGCTAC AGCTAC AGATAC AGCTAC
1 AGCTAC AGC-TAC A-GCTAC AGCTAC AGCTAC AGCTAC AGCTAC AGCTAC
684603 TAATTGAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 3 0.08
6 29 0.74
7 5 0.13
8 2 0.05
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (6 bp):
AGCTAC
Found at i:691396 original size:24 final size:25
Alignment explanation
Indices: 691377--691445 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
691367 TATGTTTAGT
691377 ATCTAAACTTTTATCTTGTTTTGAC
1 ATCTAAACTTTTATCTTGTTTTGAC
*
691402 ACCTAAACTTTTATCTTGTTTTGAC
1 ATCTAAACTTTTATCTTGTTTTGAC
691427 ATCTAAACTTTTAT-TTGTT
1 ATCTAAACTTTTATCTTGTT
691446 CTAAAATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
24 5 0.12
25 37 0.88
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (25 bp):
ATCTAAACTTTTATCTTGTTTTGAC
Found at i:693110 original size:32 final size:31
Alignment explanation
Indices: 693049--693112 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
693039 TACTAATTTT
*
693049 ATGATTATATGTTATTACATACGTCGAAATA
1 ATGATTATATGTTATTACATAAGTCGAAATA
* * *
693080 ATGATGTATATGTTGTTACATAATTTGAAATA
1 ATGAT-TATATGTTATTACATAAGTCGAAATA
693112 A
1 A
693113 GCTTTGGACC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (31 bp):
ATGATTATATGTTATTACATAAGTCGAAATA
Found at i:698446 original size:12 final size:12
Alignment explanation
Indices: 698429--698459 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
698419 TTAAATATAT
*
698429 ATACCCGGCCTG
1 ATACCCGGCCCG
698441 ATACCCGGCCCG
1 ATACCCGGCCCG
698453 ATACCCG
1 ATACCCG
698460 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:707837 original size:19 final size:20
Alignment explanation
Indices: 707809--707848 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
707799 CCTCCGGCCT
* *
707809 TAATGTATGTGTA-TAATCA
1 TAATGAATGTGCATTAATCA
707828 TAATGAATGTGCATTAATCA
1 TAATGAATGTGCATTAATCA
707848 T
1 T
707849 GTAATTATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (20 bp):
TAATGAATGTGCATTAATCA
Found at i:714435 original size:7 final size:7
Alignment explanation
Indices: 714424--714457 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
714414 TCTTCATCAC
*
714424 TCTTCTC
1 TCTTCTA
714431 TCTTCTA
1 TCTTCTA
714438 TCTTCTA
1 TCTTCTA
714445 TCTTCTA
1 TCTTCTA
714452 TCTTCT
1 TCTTCT
714458 GATGGAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.09, C:0.32, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTTCTA
Found at i:715366 original size:12 final size:12
Alignment explanation
Indices: 715349--715379 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
715339 TTAGCATAAA
715349 CGGGTATCGGGC
1 CGGGTATCGGGC
715361 CGGGTATCGGGC
1 CGGGTATCGGGC
715373 CGGGTAT
1 CGGGTAT
715380 ATATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.19
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:715414 original size:2 final size:2
Alignment explanation
Indices: 715403--715480 Score: 71
Period size: 2 Copynumber: 42.5 Consensus size: 2
715393 AAATACATAA
*
715403 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
715442 AA AT -T AA AT TT AT -T A- AT AT -T 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
715480 A
1 A
715481 ATTATTATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
1 7 0.11
2 54 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:715442 original size:54 final size:52
Alignment explanation
Indices: 715377--715480 Score: 163
Period size: 54 Copynumber: 2.0 Consensus size: 52
715367 TCGGGCCGGG
715377 TATATATATTTAAATTAAATACATAAATATTATATATATATATATATATATA
1 TATATATATTTAAATTAAATACATAAATATTATATATATATATATATATATA
** *
715429 TATATATTAATTTAAATTAAATTTATTAATATTATATATATATATATATATA
1 TATATA-T-ATTTAAATTAAATACATAAATATTATATATATATATATATATA
715481 ATTATTATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 6 0.13
53 1 0.02
54 40 0.85
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (52 bp):
TATATATATTTAAATTAAATACATAAATATTATATATATATATATATATATA
Found at i:728674 original size:19 final size:19
Alignment explanation
Indices: 728650--728697 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
728640 TTTTCAACTC
728650 TTGTATTATAGCTTGTACA
1 TTGTATTATAGCTTGTACA
*
728669 TTGTATTGTAGCTTGTACA
1 TTGTATTATAGCTTGTACA
728688 TTGTATTATA
1 TTGTATTATA
728698 TATTGCAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGTATTATAGCTTGTACA
Found at i:737013 original size:51 final size:51
Alignment explanation
Indices: 736937--737060 Score: 196
Period size: 51 Copynumber: 2.4 Consensus size: 51
736927 CACGTAGGGG
* * *
736937 TATAGCGCGGGGCAGGTACCACGACATACCTTTACTACTGACATAATTTTA
1 TATAGCGCGGGGCAAGTACCGCGACATACATTTACTACTGACATAATTTTA
*
736988 TATAGCGCGGGGCAAGTACCGCGACATACATTTACTCCTGACATAATTTTA
1 TATAGCGCGGGGCAAGTACCGCGACATACATTTACTACTGACATAATTTTA
737039 TATAGCGCGGGGC-AGATACCGC
1 TATAGCGCGGGGCAAG-TACCGC
737061 TTTTTGTATA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 2 0.03
51 66 0.97
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (51 bp):
TATAGCGCGGGGCAAGTACCGCGACATACATTTACTACTGACATAATTTTA
Found at i:742905 original size:110 final size:111
Alignment explanation
Indices: 742711--742931 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
742701 ATTACAAAAA
* * *
742711 TTAATTCTTAATCTAATAATCATGTATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * *
742776 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAAAGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
742822 TTAATTCTTAATCTAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
742886 AATTAAAAAGTTCAAATGTTACCGTATCAACAAAGTGTAGAGATAT
66 AATTAAAAAGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
742932 ATGATTTTCA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 69 0.67
111 34 0.33
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAAAGTTAAAATGTTACCGTATCAACAAAGTGTAGAGATAT
Found at i:743069 original size:12 final size:10
Alignment explanation
Indices: 743055--743095 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
743045 ACCTTAAAAA
*
743055 GAGAGTATTT
1 GAGAGAATTT
743065 GAGAGAAATTT
1 GAGAG-AATTT
743076 -AGAGAATTT
1 GAGAGAATTT
743085 GAGAGAATTT
1 GAGAGAATTT
743095 G
1 G
743096 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:750033 original size:42 final size:42
Alignment explanation
Indices: 749986--750101 Score: 178
Period size: 42 Copynumber: 2.8 Consensus size: 42
749976 TTTCCCCGAA
749986 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATT
* * * *
750028 TTCCCGTGTTTATTTCACTTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATT
* *
750070 TTCCAGTGTTTGTTTCACGTAATTGGTTTTTC
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTC
750102 TGAACGTAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.17, C:0.17, G:0.16, T:0.49
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATATT
Found at i:750381 original size:59 final size:57
Alignment explanation
Indices: 750313--750463 Score: 134
Period size: 59 Copynumber: 2.6 Consensus size: 57
750303 ATTTATAATA
* *
750313 ATATAATATTGTAT-TTTTAATACTATATAA-AATAATCAATTATATTATAATAAGATAAG
1 ATATAATATT-TATATTTTAATAATATATAATAA-AA-AAATTATATT-TAATAAGATAAG
* *
750372 ATATTATATTTTTATTTTAATAATATATAATAAAAAAATTATATTTAATAATGA-ATA-
1 ATATAATATTTATATTTTAATAATATATAATAAAAAAATTATATTTAATAA-GATA-AG
*
750429 ATAT--TATTTATATATTTAAATAATATTTTAATAAA
1 ATATAATATTTATAT-TTT-AATAATA-TATAATAAA
750464 GATATTTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
55 8 0.10
56 3 0.04
57 18 0.23
58 22 0.28
59 26 0.33
60 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (57 bp):
ATATAATATTTATATTTTAATAATATATAATAAAAAAATTATATTTAATAAGATAAG
Found at i:750433 original size:57 final size:58
Alignment explanation
Indices: 750309--750463 Score: 151
Period size: 57 Copynumber: 2.7 Consensus size: 58
750299 TAATATTTAT
* * *
750309 AATAATATAATATTGTAT-TTTTAATACTATATAA-AATAATCAATTATATTATAATAAG
1 AATAATATTATATT-TATATTTTAATAATATATAATAA-AATAAATTATATTATAATAAG
*
750367 -ATAAGATATTATATTTTTATTTTAATAATATATAATAAAA-AAATTATATT-TAATAATG
1 AAT-A-ATATTATATTTATATTTTAATAATATATAATAAAATAAATTATATTATAATAA-G
* *
750425 AATAATATTAT-TTATATATTTAAATAATATTTTAATAAA
1 AATAATATTATATT-TATATTTTAATAATA-TATAATAAA
750464 GATATTTAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
56 2 0.02
57 28 0.34
58 22 0.27
59 28 0.34
60 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (58 bp):
AATAATATTATATTTATATTTTAATAATATATAATAAAATAAATTATATTATAATAAG
Found at i:750483 original size:23 final size:23
Alignment explanation
Indices: 750457--750501 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
750447 AATAATATTT
750457 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
750480 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
750502 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:750813 original size:14 final size:14
Alignment explanation
Indices: 750794--750834 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
750784 AAATGTAATT
*
750794 CATTTTACAGAAAA
1 CATTTTTCAGAAAA
*
750808 CATTTTTCGGAAAA
1 CATTTTTCAGAAAA
*
750822 CGTTTTTCAGAAA
1 CATTTTTCAGAAA
750835 TGTAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (14 bp):
CATTTTTCAGAAAA
Found at i:750861 original size:20 final size:20
Alignment explanation
Indices: 750824--750862 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
750814 TCGGAAAACG
**
750824 TTTTTCAGAAATGTAATTCA
1 TTTTTCAGAAATCAAATTCA
*
750844 TTTTTCAGAATTCAAATTC
1 TTTTTCAGAAATCAAATTC
750863 CAGTAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (20 bp):
TTTTTCAGAAATCAAATTCA
Found at i:755787 original size:74 final size:76
Alignment explanation
Indices: 755605--755812 Score: 260
Period size: 75 Copynumber: 2.8 Consensus size: 76
755595 CAAAGCCAAA
* * * * **
755605 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
755669 TTTGGCTCCGAG
65 TTTGGCTCCGAG
* *
755681 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
755745 TTTGTTCCGAG
66 TTGGCTCCGAG
* * * *
755756 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
755813 GTTCAGCGGT
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
74 21 0.18
75 63 0.55
76 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:761606 original size:20 final size:21
Alignment explanation
Indices: 761581--761641 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
761571 TTTTGGTGCA
761581 GAGGGAATCGATTCCCCC-TT
1 GAGGGAATCGATTCCCCCTTT
761601 GAGGGAATCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCCTTT
*
761622 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAATCGATTCCCCC
761642 CACATGGGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 1 0.03
23 15 0.41
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (21 bp):
GAGGGAATCGATTCCCCCTTT
Found at i:761656 original size:21 final size:19
Alignment explanation
Indices: 761582--761663 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 19
761572 TTTGGTGCAG
**
761582 AGGGAATCGATTCCCCCTTG
1 AGGGAATCGATTCCCCC-CA
*
761602 AGGGAATCGATTCCCCCTTTGA
1 AGGGAATCGATTCCCCC---CA
*
761624 AGGGGAACCGATTCCCCCCA
1 A-GGGAATCGATTCCCCCCA
*
761644 CATGGGAATCGATACCCCCC
1 -A-GGGAATCGATTCCCCCC
761664 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 18 0.35
21 16 0.31
22 2 0.04
23 15 0.29
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (19 bp):
AGGGAATCGATTCCCCCCA
Found at i:764431 original size:75 final size:75
Alignment explanation
Indices: 764246--764451 Score: 254
Period size: 74 Copynumber: 2.7 Consensus size: 75
764236 CAAAGCCAAA
* * * * **
764246 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAG
764311 TTTGGCTCCGAG
64 TTTGGCTCCGAG
* * *
764323 ATTTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
764387 TTGTTCCGAG
66 TGGCTCCGAG
* * *
764397 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCC
764452 CTGTTCAACG
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
74 61 0.54
75 27 0.24
76 1 0.01
77 23 0.21
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:767764 original size:19 final size:19
Alignment explanation
Indices: 767740--767780 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
767730 AAAGATATTT
*
767740 ACCCCATTTAGTCAAGTAG
1 ACCCCATTTAATCAAGTAG
767759 ACCCCATTTAATCAAGTAG
1 ACCCCATTTAATCAAGTAG
767778 ACC
1 ACC
767781 ACCTTCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.12, T:0.24
Consensus pattern (19 bp):
ACCCCATTTAATCAAGTAG
Found at i:768010 original size:2 final size:2
Alignment explanation
Indices: 768003--768040 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
767993 ATTAAAAACA
768003 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
768041 GTTGAGTGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:768442 original size:25 final size:25
Alignment explanation
Indices: 768411--768471 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
768401 GAAGACTTTA
*
768411 AACCGAACCGTATAATGCCAAACCG
1 AACCGAACCGTATAATACCAAACCG
768436 AACCGAACCGTATAATACCAAACCG
1 AACCGAACCGTATAATACCAAACCG
**
768461 AATTGAACCGT
1 AACCGAACCGT
768472 TTTACTCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.15
Consensus pattern (25 bp):
AACCGAACCGTATAATACCAAACCG
Found at i:768630 original size:2 final size:2
Alignment explanation
Indices: 768625--768692 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
768615 TGTAAAAAAC
768625 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
768667 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
768693 TTAAGATTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:770250 original size:21 final size:22
Alignment explanation
Indices: 770202--770251 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
770192 AAATAAATAA
*
770202 TTATAT-GATATATTCTTTTTT
1 TTATATAGATATATTCTTTCTT
*
770223 TTAATATAGATATGTTC-TTCTT
1 TT-ATATAGATATATTCTTTCTT
770245 TTATATA
1 TTATATA
770252 ACTATCGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (22 bp):
TTATATAGATATATTCTTTCTT
Found at i:777759 original size:22 final size:22
Alignment explanation
Indices: 777715--777760 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
777705 TATAAATTAT
*
777715 TTTTTATTAAATATTTTTGATA
1 TTTTTATTAAATATTTTTAATA
*
777737 TTTTTATTTAAT-TTTTTAAATA
1 TTTTTATTAAATATTTTT-AATA
777759 TT
1 TT
777761 ATGACGTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:779745 original size:31 final size:29
Alignment explanation
Indices: 779705--779808 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
779695 TCGAATTTAT
*
779705 GGGTTAAATTGATATATGATCTAAAGTTCAA
1 GGGTCAAATT-ATAT-TGATCTAAAGTTCAA
* * *
779736 AGGTCAAATTAATATTTTATCTAAAGTTTAA
1 GGGTCAAATT-ATA-TTGATCTAAAGTTCAA
* *
779767 GGGTTAAAATAGTATTGTATCTAAAGTTCAA
1 GGGTCAAATTA-TATTG-ATCTAAAGTTCAA
779798 GGGTCAAATTA
1 GGGTCAAATTA
779809 AAAATTAACT
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 3 0.05
31 54 0.93
32 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (29 bp):
GGGTCAAATTATATTGATCTAAAGTTCAA
Found at i:779912 original size:21 final size:21
Alignment explanation
Indices: 779883--779923 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
779873 TAAAACTTTA
*
779883 TAAATCAATAAAATAAGTGAC
1 TAAAACAATAAAATAAGTGAC
**
779904 TAAAACAATAATGTAAGTGA
1 TAAAACAATAAAATAAGTGA
779924 TCGAAATGTT
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:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (21 bp):
TAAAACAATAAAATAAGTGAC
Found at i:789586 original size:29 final size:29
Alignment explanation
Indices: 789544--789601 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
789534 GATGTATACC
789544 CATGACTGACACCTCAAACCCAAGTCTAA
1 CATGACTGACACCTCAAACCCAAGTCTAA
789573 CATGACTGACACCTCAAACCCAAGTCTAA
1 CATGACTGACACCTCAAACCCAAGTCTAA
789602 GTACAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.34, G:0.10, T:0.17
Consensus pattern (29 bp):
CATGACTGACACCTCAAACCCAAGTCTAA
Found at i:792676 original size:7 final size:7
Alignment explanation
Indices: 792644--792712 Score: 79
Period size: 7 Copynumber: 9.9 Consensus size: 7
792634 AAACAGGAGG
792644 CTTTTTC
1 CTTTTTC
*
792651 TTTCTTTC
1 CTT-TTTC
*
792659 TTTTCTTC
1 CTTT-TTC
792667 CTTTTTC
1 CTTTTTC
792674 CTTTTTC
1 CTTTTTC
792681 CTTTTTC
1 CTTTTTC
792688 CTTTTT-
1 CTTTTTC
*
792694 CTTTTTT
1 CTTTTTC
792701 C-TTTTC
1 CTTTTTC
792707 CTTTTT
1 CTTTTT
792713 TCTCCTTGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
6 11 0.20
7 31 0.56
8 13 0.24
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
CTTTTTC
Found at i:792715 original size:13 final size:13
Alignment explanation
Indices: 792664--792712 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
792654 CTTTCTTTTC
792664 TTCCTTTTTCCTTT
1 TTCCTTTTTCC-TT
792678 TTCCTTTTTCCTT
1 TTCCTTTTTCCTT
* *
792691 TTTCTTTTTTCTT
1 TTCCTTTTTCCTT
792704 TTCCTTTTT
1 TTCCTTTTT
792713 TCTCCTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCCTTTTTCCTT
Found at i:794818 original size:35 final size:37
Alignment explanation
Indices: 794747--794819 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
794737 GTTGGAAAAT
*
794747 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
*
794784 ATTTATATATTTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
794819 A
1 A
794820 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 13 0.39
36 7 0.21
37 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:796458 original size:35 final size:35
Alignment explanation
Indices: 796386--796458 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
796376 TTTTTTATAT
*
796386 TTTAATTTTGTAAAAAAATATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATATATAAATATTATCAA
* * *
796421 TTTAATTTTTTAAAGAAA-ATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAATATATAAATATTAT-CAA
796456 TTT
1 TTT
796459 GTAATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 12 0.36
35 21 0.64
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (35 bp):
TTTAATTTTGTAAAAAAATATATAAATATTATCAA
Found at i:798629 original size:21 final size:20
Alignment explanation
Indices: 798591--798630 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
798581 TCGCTCTTTC
**
798591 TTTCCTCCCTTTTTCTCTCG
1 TTTCCTCCCTTTCCCTCTCG
798611 TTTCTCTCCCTTTCCCTCTC
1 TTTC-CTCCCTTTCCCTCTC
798631 CCGACGACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.53
Consensus pattern (20 bp):
TTTCCTCCCTTTCCCTCTCG
Found at i:806712 original size:20 final size:20
Alignment explanation
Indices: 806687--806725 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
806677 TTTTTGTTTG
*
806687 GCCGCCGATGAACGACGGCC
1 GCCGCCGATCAACGACGGCC
*
806707 GCCGCCGATCAACGGCGGC
1 GCCGCCGATCAACGACGGC
806726 GGTGAGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.41, G:0.36, T:0.05
Consensus pattern (20 bp):
GCCGCCGATCAACGACGGCC
Found at i:807165 original size:19 final size:20
Alignment explanation
Indices: 807141--807179 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
807131 ATCGTTTTCA
807141 TATTG-TATATATT-CTTATT
1 TATTGTTAT-TATTACTTATT
807160 TATTGTTATTATTACTTATT
1 TATTGTTATTATTACTTATT
807180 ATCATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
TATTGTTATTATTACTTATT
Found at i:808175 original size:50 final size:51
Alignment explanation
Indices: 808095--808190 Score: 151
Period size: 50 Copynumber: 1.9 Consensus size: 51
808085 GACTGATATG
*
808095 TATGATATTTTATATTATTATTATTTAAATAATAAAGTTAAAGGAATGCCA
1 TATGATATTTTATAATATTATTATTTAAATAATAAAGTTAAAGGAATGCCA
*
808146 TATGATA-TTTATAATATT-TTGTTTGAAATAATAAAGTTAAAGGAA
1 TATGATATTTTATAATATTATTATTT-AAATAATAAAGTTAAAGGAA
808191 ATTAAGGAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
49 5 0.12
50 30 0.71
51 7 0.17
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (51 bp):
TATGATATTTTATAATATTATTATTTAAATAATAAAGTTAAAGGAATGCCA
Found at i:811552 original size:20 final size:20
Alignment explanation
Indices: 811516--811553 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
811506 ATCTTATTCC
**
811516 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
811536 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
811554 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:811902 original size:15 final size:15
Alignment explanation
Indices: 811865--811904 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
811855 ATCCTTTTTA
811865 ATTCAGATATTTT-C
1 ATTCAGATATTTTCC
811879 -TTC--ATATTTTCC
1 ATTCAGATATTTTCC
811891 ATTCAGATATTTTC
1 ATTCAGATATTTTC
811905 TTTTGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
11 7 0.32
12 1 0.05
13 6 0.27
15 8 0.36
ACGTcount: A:0.25, C:0.17, G:0.05, T:0.53
Consensus pattern (15 bp):
ATTCAGATATTTTCC
Found at i:812581 original size:24 final size:26
Alignment explanation
Indices: 812552--812603 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
812542 GCCCCCTGTT
**
812552 CGAACATAAATTAACATA-AAT-GAA
1 CGAACATAAACGAACATATAATCGAA
812576 CGAACATAAACGAACATATAATCGAA
1 CGAACATAAACGAACATATAATCGAA
812602 CG
1 CG
812604 TTCACGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 3 0.12
26 5 0.21
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (26 bp):
CGAACATAAACGAACATATAATCGAA
Found at i:814383 original size:2 final size:2
Alignment explanation
Indices: 814376--814411 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
814366 AGTTTCACAA
814376 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
814412 TCATCCTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:814477 original size:2 final size:2
Alignment explanation
Indices: 814470--814497 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
814460 GTTTCAGGTG
814470 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
814498 TCAGATAGAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:820592 original size:2 final size:2
Alignment explanation
Indices: 820585--820610 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
820575 GATGTAAACA
820585 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
820611 GGTTTAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:821907 original size:2 final size:2
Alignment explanation
Indices: 821895--821924 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
821885 TGATTAAGAT
821895 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
821925 TACAGCTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:823997 original size:17 final size:17
Alignment explanation
Indices: 823975--824013 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
823965 TGAATCAAAT
*
823975 TAATTATATATTATTTA
1 TAATTAGATATTATTTA
823992 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
824009 -AATTA
1 TAATTA
824014 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:825032 original size:33 final size:33
Alignment explanation
Indices: 824991--825060 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
824981 GCGACCTACC
*
824991 CTCGCTCGGCTTT-CCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTTCCCTCGGATGCCCTCGCATAG
825024 CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
825057 CTCG
1 CTCG
825061 TTCAGATGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.09
33 32 0.91
ACGTcount: A:0.09, C:0.40, G:0.23, T:0.29
Consensus pattern (33 bp):
CTCGCTCGGTTTCCCTCGGATGCCCTCGCATAG
Found at i:825074 original size:33 final size:33
Alignment explanation
Indices: 825004--825075 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
824994 GCTCGGCTTT
* * * *
825004 CCTCGGATTCCCTCGCATAGCTCGCTCGGTTTC
1 CCTCGGATGCCCTCGCATAGCTCGCTCAGATGC
* *
825037 CCTCGGATGCCCTCGCATAGCTCGTTCAGATGG
1 CCTCGGATGCCCTCGCATAGCTCGCTCAGATGC
825070 CCTCGG
1 CCTCGG
825076 TCGGATGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.38, G:0.25, T:0.26
Consensus pattern (33 bp):
CCTCGGATGCCCTCGCATAGCTCGCTCAGATGC
Found at i:825082 original size:14 final size:14
Alignment explanation
Indices: 825065--825113 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
825055 AGCTCGTTCA
825065 GATGGCCTCGGTCG
1 GATGGCCTCGGTCG
*
825079 GAT-GAC-C--TCG
1 GATGGCCTCGGTCG
825089 GATGGCCTCGGTCG
1 GATGGCCTCGGTCG
825103 GATGGCCTCGG
1 GATGGCCTCGG
825114 ATGCCCAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 6 0.21
11 2 0.07
12 2 0.07
13 2 0.07
14 17 0.59
ACGTcount: A:0.10, C:0.29, G:0.41, T:0.20
Consensus pattern (14 bp):
GATGGCCTCGGTCG
Found at i:825093 original size:24 final size:24
Alignment explanation
Indices: 825065--825116 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
825055 AGCTCGTTCA
825065 GATGGCCTCGGTCGGATGACCTCG
1 GATGGCCTCGGTCGGATGACCTCG
*
825089 GATGGCCTCGGTCGGATGGCCTCG
1 GATGGCCTCGGTCGGATGACCTCG
825113 GATG
1 GATG
825117 CCCAGCGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.27, G:0.40, T:0.21
Consensus pattern (24 bp):
GATGGCCTCGGTCGGATGACCTCG
Found at i:825194 original size:29 final size:29
Alignment explanation
Indices: 825161--825239 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
825151 CTCTTGTAGC
* *
825161 TCGCCGGGAAGACATGGCGACCTAGTATG
1 TCGCCCGGAAGGCATGGCGACCTAGTATG
825190 TCGCCCGGAAGGCATGGCGACCTAGTATG
1 TCGCCCGGAAGGCATGGCGACCTAGTATG
825219 TCGCCCGGAAGGCATGGCGAC
1 TCGCCCGGAAGGCATGGCGAC
825240 TTACGACCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.28, G:0.35, T:0.15
Consensus pattern (29 bp):
TCGCCCGGAAGGCATGGCGACCTAGTATG
Found at i:834038 original size:50 final size:51
Alignment explanation
Indices: 833984--834089 Score: 144
Period size: 50 Copynumber: 2.1 Consensus size: 51
833974 TTTTATAATG
* * * *
833984 TTATTGAAATTCGTCATATCGAGAA-GACGAGTTCTAATAAAA-ATTATTTT
1 TTATTGAAATTCGTCATATC-AAAATGACAAATTCTAATAAAATATAATTTT
*
834034 TTATTGAAATTCGTCATCTCAAAATGACAAATTCTAATAAAATATAATTTT
1 TTATTGAAATTCGTCATATCAAAATGACAAATTCTAATAAAATATAATTTT
834085 TTATT
1 TTATT
834090 AACATATATC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 3 0.06
50 34 0.69
51 12 0.24
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (51 bp):
TTATTGAAATTCGTCATATCAAAATGACAAATTCTAATAAAATATAATTTT
Found at i:838500 original size:21 final size:21
Alignment explanation
Indices: 838476--838517 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
838466 ACTAGTATTT
*
838476 AATTT-TTTAATTTATTCATTA
1 AATTTATTT-ATTTATTAATTA
838497 AATTTATTTATTTATTAATTA
1 AATTTATTTATTTATTAATTA
838518 GTTTTGGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTATTTATTTATTAATTA
Found at i:839677 original size:21 final size:21
Alignment explanation
Indices: 839653--839718 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
839643 ATTCACATTA
*
839653 CGAATTAGGAAAATCACAACG
1 CGAATTAGGAAAATCGCAACG
* *
839674 CGAATTAAGAAAATCGTAACG
1 CGAATTAGGAAAATCGCAACG
* *
839695 CGAATTTGGAAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
839716 CGA
1 CGA
839719 TAGTTAGAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.21, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:840515 original size:60 final size:59
Alignment explanation
Indices: 840451--840579 Score: 154
Period size: 59 Copynumber: 2.2 Consensus size: 59
840441 TTTGATGATT
* * ** * *
840451 AATTTAAAATGAGGGCCGTAGTTTGCGAGT-AAATTTAGAATGTTTAAAAGTTTA-AGAACC
1 AATTTAAAATGAGAGCCATAGTTTAAGAATGAAA-TTA-AATATTTAAAAGTTTAGA-AACC
*
840511 AATTTAAAATGAGAGTCATAGTTTAAGAATGAAATTAAATATTTAAAAGTTTAGAAACC
1 AATTTAAAATGAGAGCCATAGTTTAAGAATGAAATTAAATATTTAAAAGTTTAGAAACC
840570 AATTTAAAAT
1 AATTTAAAAT
840580 AAAGATCAAC
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 29 0.48
60 28 0.47
61 3 0.05
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (59 bp):
AATTTAAAATGAGAGCCATAGTTTAAGAATGAAATTAAATATTTAAAAGTTTAGAAACC
Found at i:843744 original size:24 final size:24
Alignment explanation
Indices: 843693--843744 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
843683 TTCAGAGAGG
* * * *
843693 TAAATTATAATTAATCATATAGAG
1 TAAAATATAATTAATCATAGAAAA
*
843717 TAAAATATAATTAATTATAGAAAA
1 TAAAATATAATTAATCATAGAAAA
843741 TAAA
1 TAAA
843745 GAGATAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
TAAAATATAATTAATCATAGAAAA
Found at i:846165 original size:30 final size:31
Alignment explanation
Indices: 846106--846165 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
846096 ACTTATAATT
846106 TTAAAGTTTAATTAAGAATATTCAAAAAAAA
1 TTAAAGTTTAATTAAGAATATTCAAAAAAAA
* *
846137 TTAAAGTTTAA-TATGAAT-TTCTAAAAAAA
1 TTAAAGTTTAATTAAGAATATTCAAAAAAAA
846166 CTAAGGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 6 0.22
31 11 0.41
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (31 bp):
TTAAAGTTTAATTAAGAATATTCAAAAAAAA
Found at i:859283 original size:35 final size:35
Alignment explanation
Indices: 859242--859338 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 35
859232 AACACAATCA
* * *
859242 TCAATTATATTTTAAACCCCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
**
859277 TCAATTACATTCTAAACCTTAAATTCAAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATACT
* * *
859312 TTAATTACATGCTCAACCCCAAATTCA
1 TCAATTACATTCTAAACCCCAAATTCA
859339 TAATCCCATT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATACT
Found at i:874299 original size:20 final size:20
Alignment explanation
Indices: 874261--874299 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
874251 TGTTCCTTAT
*
874261 TAATTTAAAAAATTGAAAAA
1 TAATTTAAAAAATTAAAAAA
874281 TAATTTAAAATAA-TAAAAA
1 TAATTTAAAA-AATTAAAAA
874300 CAGAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
TAATTTAAAAAATTAAAAAA
Found at i:882678 original size:42 final size:42
Alignment explanation
Indices: 882618--882785 Score: 162
Period size: 42 Copynumber: 4.0 Consensus size: 42
882608 ATCTGCACCA
* *
882618 AAAGATGAATTTCAGGGAAATGAT-TCTGATAATGGAAGTAAC
1 AAAGACGAATTTCAGGGAAATGATATC-AATAATGGAAGTAAC
*
882660 AAAGACGAATTTCTGGGAAATGATATCAATAATGGAAGTAAC
1 AAAGACGAATTTCAGGGAAATGATATCAATAATGGAAGTAAC
** * ** * *
882702 AAAGGTGAATTTCCGGTTACTGATATCCAA-AATGGAAGTAGC
1 AAAGACGAATTTCAGGGAAATGATAT-CAATAATGGAAGTAAC
* * * *
882744 AAAGACGAATTTCCGGTAACTGATATCCAA-AATGGAAATAAC
1 AAAGACGAATTTCAGGGAAATGATAT-CAATAATGGAAGTAAC
882786 GATTGTCCTT
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 104 0.95
43 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (42 bp):
AAAGACGAATTTCAGGGAAATGATATCAATAATGGAAGTAAC
Found at i:883614 original size:18 final size:19
Alignment explanation
Indices: 883583--883634 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
883573 AATGCTGAAG
*
883583 AAACCTAAAGGATCAGA-C
1 AAACCTAAAAGATCAGACC
*
883601 AAATCTAAAAGATCA-ACC
1 AAACCTAAAAGATCAGACC
*
883619 AAACCTGAAAGATCAG
1 AAACCTAAAAGATCAG
883635 CTAAACCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.52, C:0.21, G:0.13, T:0.13
Consensus pattern (19 bp):
AAACCTAAAAGATCAGACC
Found at i:886066 original size:115 final size:115
Alignment explanation
Indices: 885864--886089 Score: 443
Period size: 115 Copynumber: 2.0 Consensus size: 115
885854 CAATTGTTGT
885864 TTCATTGTTCCTATTTGCTCAATTTCTTACATATTTAGCTGTTGGGCGAGTTTAATCCGATAAAG
1 TTCATTGTTCCTATTTGCTCAATTTCTTACATATTTAGCTGTTGGGCGAGTTTAATCCGATAAAG
885929 ATGGGAATTTGAATTTTGTAAGAATGTTTGTGAAGTGAAGAAGAAATATG
66 ATGGGAATTTGAATTTTGTAAGAATGTTTGTGAAGTGAAGAAGAAATATG
885979 TTCATTGTTCCTATTTGCTCAATTTCTTACATATTTAGCTGTTGGGCGAGTTTAATCCGATAAAG
1 TTCATTGTTCCTATTTGCTCAATTTCTTACATATTTAGCTGTTGGGCGAGTTTAATCCGATAAAG
*
886044 ATGGGAATTTGAATTTTGTAAGAATGTTTGTGGAGTGAAGAAGAAA
66 ATGGGAATTTGAATTTTGTAAGAATGTTTGTGAAGTGAAGAAGAAA
886090 ACTGTTAAAA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
115 110 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (115 bp):
TTCATTGTTCCTATTTGCTCAATTTCTTACATATTTAGCTGTTGGGCGAGTTTAATCCGATAAAG
ATGGGAATTTGAATTTTGTAAGAATGTTTGTGAAGTGAAGAAGAAATATG
Found at i:895320 original size:40 final size:40
Alignment explanation
Indices: 895265--895355 Score: 146
Period size: 40 Copynumber: 2.3 Consensus size: 40
895255 GAAGTTGTTA
895265 GTATCGATACCCGGCCATCGACATTGCTATCAGATGTACG
1 GTATCGATACCCGGCCATCGACATTGCTATCAGATGTACG
* * *
895305 GTATCGATACCCGGCCATCGATATTGGTATCAGATGTATG
1 GTATCGATACCCGGCCATCGACATTGCTATCAGATGTACG
*
895345 GTACCGATACC
1 GTATCGATACC
895356 ACATGATCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
GTATCGATACCCGGCCATCGACATTGCTATCAGATGTACG
Found at i:897766 original size:16 final size:16
Alignment explanation
Indices: 897745--897782 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
897735 GATGTTGATG
*
897745 CGTCACCATAAGGTAA
1 CGTCACCATAAGATAA
897761 CGTCACCATAAGATAA
1 CGTCACCATAAGATAA
897777 CGTCAC
1 CGTCAC
897783 ATCATCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (16 bp):
CGTCACCATAAGATAA
Found at i:900351 original size:2 final size:2
Alignment explanation
Indices: 900344--900370 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
900334 AATATTTATG
900344 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
900371 TTAGACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:901164 original size:21 final size:21
Alignment explanation
Indices: 901138--901200 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
901128 CTTGCATACC
*
901138 ATCTAAATTTTAAATCTTAAA
1 ATCTAAATTTTAAATCATAAA
* * *
901159 ATCTAAACTCT-AATCATAACG
1 ATCTAAATTTTAAATCATAA-A
* *
901180 ATCTAAATCTTAAATCCTAAA
1 ATCTAAATTTTAAATCATAAA
901201 CTTTAATAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.46, C:0.17, G:0.02, T:0.35
Consensus pattern (21 bp):
ATCTAAATTTTAAATCATAAA
Found at i:901200 original size:35 final size:34
Alignment explanation
Indices: 901148--901218 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 34
901138 ATCTAAATTT
*
901148 TAAATCTTAAAATCTAAACTCTAATCATAACGATC
1 TAAATCTTAAAATCTAAACTCTAATAATAAC-ATC
*
901183 TAAATCTT-AAATCCTAAACTTTAATAATAACATC
1 TAAATCTTAAAAT-CTAAACTCTAATAATAACATC
901217 TA
1 TA
901219 TACCTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 9 0.27
35 24 0.73
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.34
Consensus pattern (34 bp):
TAAATCTTAAAATCTAAACTCTAATAATAACATC
Found at i:901235 original size:34 final size:35
Alignment explanation
Indices: 901148--901240 Score: 91
Period size: 34 Copynumber: 2.7 Consensus size: 35
901138 ATCTAAATTT
* *
901148 TAAATCTTAAAAT-CTAAACTCTAATCATAACGATC
1 TAAACCTT-AAATCCTAAACTCTAATAATAACGATC
* *
901183 TAAATCTTAAATCCTAAACTTTAATAATAAC-ATC
1 TAAACCTTAAATCCTAAACTCTAATAATAACGATC
* * * *
901217 TATACCTTATATCTTAAACCCTAA
1 TAAACCTTAAATCCTAAACTCTAA
901241 ACCCTAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 25 0.51
35 24 0.49
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.34
Consensus pattern (35 bp):
TAAACCTTAAATCCTAAACTCTAATAATAACGATC
Found at i:901748 original size:2 final size:2
Alignment explanation
Indices: 901741--901788 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
901731 ACCTTAAATT
901741 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
901783 TA TA TA
1 TA TA TA
901789 AAACTCAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:903641 original size:2 final size:2
Alignment explanation
Indices: 903634--903660 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
903624 AATAAAAAGA
903634 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
903661 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:905022 original size:5 final size:5
Alignment explanation
Indices: 905012--905065 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
905002 AACAAACAAT
*
905012 AATAA AAT-A AAT-A AAT-A AATAAA TAATGA AATAA AATAA AATAA AAT-A
1 AATAA AATAA AATAA AATAA AAT-AA -AATAA AATAA AATAA AATAA AATAA
905060 AATAA A
1 AATAA A
905066 TAGATAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
4 16 0.37
5 22 0.51
6 2 0.05
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AATAA
Found at i:905023 original size:4 final size:4
Alignment explanation
Indices: 905016--905078 Score: 74
Period size: 4 Copynumber: 15.0 Consensus size: 4
905006 AACAATAATA
905016 AAAT AAAT AAAT AAAT AAAT -AAT GAAAT AAAAT AAAAT AAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT -AAAT -AAAT AAAT
*
905063 AAAT AGAT AAAT AAAT
1 AAAT AAAT AAAT AAAT
905079 TAAAAACATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
3 3 0.06
4 34 0.63
5 17 0.31
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:905157 original size:38 final size:38
Alignment explanation
Indices: 905088--905431 Score: 191
Period size: 37 Copynumber: 8.9 Consensus size: 38
905078 TTAAAAACAT
* * *
905088 TTTTTAAAACTATA-CA-ATATATGTTTTAAAAAATAA
1 TTTTAAAAACTATATAATATATATATTTTAAAAAATAA
* *
905124 TTTTAAAAACCATATCATATATAT-TTTTAAAAAATAA
1 TTTTAAAAACTATATAATATATATATTTTAAAAAATAA
* *
905161 TTTTCAAAACTATATAATATATATATTTTTAAAAACTAA
1 TTTTAAAAACTATATAATATATATA-TTTTAAAAAATAA
*
905200 TTTT-AAAACTATATAATATATATA--TTAAAAACTAA
1 TTTTAAAAACTATATAATATATATATTTTAAAAAATAA
* *
905235 TTTTCAAAAAAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAATAT
1 TTTT---AAAAACT-A---T----A-TA-AT-ATATATA---TTTTAAAAAATAA
* *
905290 TTTTAAAAACTATATATTATATATATATATT-AAAAA-AG
1 TTTTAAAAACTATATA--ATATATATATTTTAAAAAATAA
* * *
905328 TTTTCAAAACAATAT-A-ATATATATTTTCAAAAAT-A
1 TTTTAAAAACTATATAATATATATATTTTAAAAAATAA
* *
905363 TTTTCAAAAACTATAT-AT-TATTTATTTT-CAAAAT-A
1 TTTT-AAAAACTATATAATATATATATTTTAAAAAATAA
* *
905398 -TTTAAAAACCTCATATATTATATA-ATTTTTAAAA
1 TTTTAAAAA-CT-ATATAATATATATATTTTAAAAA
905432 TGATTTCATA
Statistics
Matches: 252, Mismatches: 22, Indels: 67
0.74 0.06 0.20
Matches are distributed among these distances:
33 5 0.02
34 15 0.06
35 35 0.14
36 37 0.15
37 42 0.17
38 40 0.16
39 27 0.11
40 4 0.02
43 10 0.04
44 4 0.02
47 1 0.00
48 3 0.01
49 2 0.01
50 7 0.03
51 1 0.00
52 7 0.03
55 12 0.05
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (38 bp):
TTTTAAAAACTATATAATATATATATTTTAAAAAATAA
Found at i:905259 original size:15 final size:16
Alignment explanation
Indices: 905226--905259 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
905216 TATATATATT
905226 AAAAACTAATTTTCAA
1 AAAAACTAATTTTCAA
905242 AAAAACTAATTTTCAA
1 AAAAACTAATTTTCAA
905258 AA
1 AA
905260 TTATATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAACTAATTTTCAA
Found at i:905265 original size:90 final size:90
Alignment explanation
Indices: 905152--905315 Score: 260
Period size: 90 Copynumber: 1.8 Consensus size: 90
905142 ATATATTTTT
905152 AAAAAATAATTTTCAAAACTATATAATATATATATTTTT-AAAAACTAATTTT-AAAACTATATA
1 AAAAAATAATTTTCAAAACTATATAATATATATATTTTTCAAAAA-TAATTTTAAAAACTATATA
905215 ATATATATATTAAAAACTAATTTTCA
65 ATATATATATTAAAAACTAATTTTCA
* * *
905241 AAAAAACTAATTTTCAAAATTATATAATATATATGTTTTTCAAAAATATTTTTAAAAACTATATA
1 AAAAAA-TAATTTTCAAAACTATATAATATATATATTTTTCAAAAATAATTTTAAAAACTATATA
*
905306 TTATATATAT
65 ATATATATAT
905316 ATATTAAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
89 6 0.09
90 37 0.54
91 25 0.37
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (90 bp):
AAAAAATAATTTTCAAAACTATATAATATATATATTTTTCAAAAATAATTTTAAAAACTATATAA
TATATATATTAAAAACTAATTTTCA
Found at i:905286 original size:41 final size:40
Alignment explanation
Indices: 905235--905379 Score: 110
Period size: 39 Copynumber: 3.8 Consensus size: 40
905225 TAAAAACTAA
* *
905235 TTTTCAAAAAAACTAATTTTCAAAATTATATAATATATATGT
1 TTTTC-AAAAAA-TAATTTTAAAAACTATATAATATATATGT
* * *
905277 TTTTC-AAAAATATTTTTAAAAACTATATATTATATATAT
1 TTTTCAAAAAATAATTTTAAAAACTATATAATATATATGT
* * * *
905316 ATATT--AAAAA-AGTTTTCAAAACAATATAATATATA---
1 -TTTTCAAAAAATAATTTTAAAAACTATATAATATATATGT
905351 TTTTC-AAAAAT-ATTTTCAAAAACTATATA
1 TTTTCAAAAAATAATTTT-AAAAACTATATA
905380 TTATTTATTT
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
34 3 0.04
35 9 0.11
36 10 0.12
38 21 0.25
39 29 0.34
40 8 0.09
42 5 0.06
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (40 bp):
TTTTCAAAAAATAATTTTAAAAACTATATAATATATATGT
Done.