Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002663.1 Hibiscus syriacus cultivar Beakdansim tig00005465_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: 975815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 4
Found at i:567921 original size:36 final size:38
Alignment explanation
Indices: 567881--567964 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
567871 CTGATTAACC
567881 AAATTTTATTCGGTT-CGATTAATTATTTTTGA-AAAA
1 AAATTTTATTCGGTTACGATTAATTATTTTTGATAAAA
** * * *
567917 AAATTCAATTCGGTTAACGATTCATTTTTTTTGATTAATA
1 AAATTTTATTCGGTT-ACGATTAATTATTTTTGA-TAAAA
567957 AAATTTTA
1 AAATTTTA
567965 AAAGTTTGGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
36 13 0.35
38 15 0.41
40 9 0.24
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (38 bp):
AAATTTTATTCGGTTACGATTAATTATTTTTGATAAAA
Found at i:582310 original size:18 final size:19
Alignment explanation
Indices: 582273--582311 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
582263 TATAGTTATT
* *
582273 AATTTTTTTTCTAAATTAA
1 AATTTATTTTCTAAAATAA
582292 AATTTATTTT-TAAAATAA
1 AATTTATTTTCTAAAATAA
582310 AA
1 AA
582312 ATATATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTATTTTCTAAAATAA
Found at i:582312 original size:19 final size:20
Alignment explanation
Indices: 582285--582323 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
582275 TTTTTTTTCT
* *
582285 AAATTAAAATTTAT-TTTTA
1 AAATAAAAATATATATTTTA
582304 AAATAAAAATATATATTTTA
1 AAATAAAAATATATATTTTA
582324 TACATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATAAAAATATATATTTTA
Found at i:584302 original size:3 final size:3
Alignment explanation
Indices: 584294--584323 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
584284 GCAGTAGCTA
584294 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
584324 TTTCCTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:587054 original size:2 final size:2
Alignment explanation
Indices: 587042--587072 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
587032 TGACACCTTA
*
587042 AT AT CT 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 AT AT A
587073 GGTCAAGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:591366 original size:23 final size:23
Alignment explanation
Indices: 591340--591403 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
591330 CAGCTTGTAT
*
591340 AATTGCACCGAAGTGTCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
591363 AATTTCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
591386 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
591404 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:598594 original size:18 final size:20
Alignment explanation
Indices: 598573--598611 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
598563 TTGGCAACAT
598573 AAAATC-TAT-TAAAAATAA
1 AAAATCATATATAAAAATAA
*
598591 AAAATCATATATCAAAATAA
1 AAAATCATATATAAAAATAA
598611 A
1 A
598612 TACAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATCATATATAAAAATAA
Found at i:599038 original size:50 final size:51
Alignment explanation
Indices: 598976--599075 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 51
598966 TACACTTGTA
* * * *
598976 TATGAATCATATCAATTTAAATTATAA-C-AAATTCAAGAAATATTATTATT
1 TATGAATCATATCAATTCAAACTATAATCAAAATACAA-AAATATAATTATT
*
599026 TATGAATTATATCAATTCAAACTATAATCAAAATACAAAAATATAATTAT
1 TATGAATCATATCAATTCAAACTATAATCAAAATACAAAAATATAATTAT
599076 AATAAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 24 0.56
51 12 0.28
52 7 0.16
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (51 bp):
TATGAATCATATCAATTCAAACTATAATCAAAATACAAAAATATAATTATT
Found at i:599087 original size:50 final size:50
Alignment explanation
Indices: 598984--599087 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 50
598974 TATATGAATC
* * * * * * *
598984 ATATCAATTTAAATTATAACAAATTCAAGAAATATTATTATTTATGAATT
1 ATATCAATTCAAACTATAACAAATACAAGAAATATAATTATTAATAAAAT
599034 ATATCAATTCAAACTATAATCAAAATACAA-AAATATAATTA-TAATAAAAT
1 ATATCAATTCAAACTATAA-C-AAATACAAGAAATATAATTATTAATAAAAT
599084 ATAT
1 ATAT
599088 TTTATATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
50 27 0.60
51 11 0.24
52 7 0.16
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (50 bp):
ATATCAATTCAAACTATAACAAATACAAGAAATATAATTATTAATAAAAT
Found at i:609852 original size:23 final size:23
Alignment explanation
Indices: 609822--609869 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
609812 CCATTGATAG
609822 TCATGAAAACCATCAATCAAAAA
1 TCATGAAAACCATCAATCAAAAA
*
609845 TCATGAAAACCATCTATCAAAAA
1 TCATGAAAACCATCAATCAAAAA
609868 TC
1 TC
609870 TTAGTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.52, C:0.23, G:0.04, T:0.21
Consensus pattern (23 bp):
TCATGAAAACCATCAATCAAAAA
Found at i:624161 original size:76 final size:77
Alignment explanation
Indices: 624002--624210 Score: 264
Period size: 76 Copynumber: 2.8 Consensus size: 77
623992 CAAAGTCAAA
* * * * **
624002 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACAGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
624066 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
* **
624079 ATTTCCAGAATGCTCGGAGGGAACAAATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
624144 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * *
624155 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
624211 TGTACAACGG
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
74 19 0.17
75 8 0.07
76 51 0.44
77 37 0.32
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:630047 original size:21 final size:21
Alignment explanation
Indices: 630021--630060 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
630011 CCCCCTTTGA
*
630021 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
630042 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
630061 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:630448 original size:22 final size:21
Alignment explanation
Indices: 630423--630474 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
630413 AAAACACAAG
*
630423 AATTTTTCAAAAAAAAATTTT
1 AATTTTTCAAAAAAAAATGTT
* *
630444 AAATTTTCGAAAAAAAATGTT
1 AATTTTTCAAAAAAAAATGTT
630465 -ATTTTTCAAA
1 AATTTTTCAAA
630475 TTATTGTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
AATTTTTCAAAAAAAAATGTT
Found at i:632305 original size:30 final size:31
Alignment explanation
Indices: 632269--632335 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 31
632259 AGAATAAGTA
632269 TTAAATGTTTTACATAATAAATTGAAG-GTG
1 TTAAATGTTTTACATAATAAATTGAAGAGTG
632299 TTAAATGTTTTACATAATAAATTGAAGAAGTG
1 TTAAATGTTTTACATAATAAATTGAAG-AGTG
632331 TTAAA
1 TTAAA
632336 GTAAGGGGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 27 0.77
32 8 0.23
ACGTcount: A:0.43, C:0.03, G:0.15, T:0.39
Consensus pattern (31 bp):
TTAAATGTTTTACATAATAAATTGAAGAGTG
Found at i:632803 original size:76 final size:77
Alignment explanation
Indices: 632639--632853 Score: 283
Period size: 76 Copynumber: 2.8 Consensus size: 77
632629 CAATTCAAAG
* * * *
632639 CCAAAAATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTA
**
632703 AATGGTTTTGGCC
65 AACAGTTTTGGCC
* *
632716 CCGAGATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAA
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAA
*
632781 ACAGTTTT-GCT
66 ACAGTTTTGGCC
* * * *
632792 CCAAGAATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
632854 TGTACAACGG
Statistics
Matches: 122, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
75 19 0.16
76 61 0.50
77 42 0.34
ACGTcount: A:0.26, C:0.33, G:0.22, T:0.20
Consensus pattern (77 bp):
CCAAGAATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAA
ACAGTTTTGGCC
Found at i:636080 original size:20 final size:20
Alignment explanation
Indices: 636055--636111 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
636045 TCAATACTTT
636055 TCAAGAGTTTCGAAACTATC
1 TCAAGAGTTTCGAAACTATC
636075 TCAAGAGTTTCGAAACTATC
1 TCAAGAGTTTCGAAACTATC
* *
636095 TTAAGAGTTTCAAAACT
1 TCAAGAGTTTCGAAACT
636112 TTAGGTAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.32
Consensus pattern (20 bp):
TCAAGAGTTTCGAAACTATC
Found at i:640069 original size:24 final size:24
Alignment explanation
Indices: 640042--640089 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
640032 CCTCTAACCC
640042 TTAAACCTTAAATATTAACTTAAG
1 TTAAACCTTAAATATTAACTTAAG
640066 TTAAACCTTAAATATTAACTTAAG
1 TTAAACCTTAAATATTAACTTAAG
640090 ATTTATAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.38
Consensus pattern (24 bp):
TTAAACCTTAAATATTAACTTAAG
Found at i:642348 original size:39 final size:38
Alignment explanation
Indices: 642286--642369 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 38
642276 AAATCATAAT
* *
642286 TTTATTGGAGTTTTTTAGGAATAAATAATTATAATTCA
1 TTTATTGGAGTTTTTTAGAAATAAATAATTACAATTCA
* *
642324 TTTATTGTGGGTTTTTTAGAAATAAATAATTACAATTTA
1 TTTATTG-GAGTTTTTTAGAAATAAATAATTACAATTCA
642363 TTTATTG
1 TTTATTG
642370 AGATAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 7 0.17
39 34 0.83
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (38 bp):
TTTATTGGAGTTTTTTAGAAATAAATAATTACAATTCA
Found at i:645238 original size:97 final size:94
Alignment explanation
Indices: 644963--645243 Score: 426
Period size: 94 Copynumber: 3.0 Consensus size: 94
644953 AACAAAAAAC
644963 TGAACATATCAATAGTCAACCACATGT----AACTTTGTAAGTTTATTGAGTCTAGTAATCTTTA
1 TGAACATATCAATAGTCAACCACATGTGAGCAACTTTGTAAGTTTATTGAGTCTAGTAATCTTTA
*
645024 ATTATTAACCTATTTGCAAAGAAAATATG
66 ATTATTAACCTATTTGCAAAGAAAATAGG
* **
645053 TGAACATATCAATAGTCAACCACATGTGAGTAACTTTGTAAGTTTATCCAGTCTAGTAATCTTTA
1 TGAACATATCAATAGTCAACCACATGTGAGCAACTTTGTAAGTTTATTGAGTCTAGTAATCTTTA
645118 ATTATTAACCTATTTGCAAAGAAAATAGG
66 ATTATTAACCTATTTGCAAAGAAAATAGG
* * *
645147 TGAACATATCAAATAGTCAACCACGTGTGTGAGCAACTTTGTATGTTTATTGAGCCTAGTAATCT
1 TGAACATATC-AATAGTCAACCAC--ATGTGAGCAACTTTGTAAGTTTATTGAGTCTAGTAATCT
**
645212 TTAATTAAGAACCTATTTGCAAAGAAAATAGG
63 TTAATTATTAACCTATTTGCAAAGAAAATAGG
645244 CGAGTATGAA
Statistics
Matches: 173, Mismatches: 11, Indels: 7
0.91 0.06 0.04
Matches are distributed among these distances:
90 27 0.16
94 70 0.40
95 13 0.08
97 63 0.36
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (94 bp):
TGAACATATCAATAGTCAACCACATGTGAGCAACTTTGTAAGTTTATTGAGTCTAGTAATCTTTA
ATTATTAACCTATTTGCAAAGAAAATAGG
Found at i:645375 original size:29 final size:29
Alignment explanation
Indices: 645333--645390 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
645323 GAAACAAAAA
645333 ATACAAATTAGAAGTAACAAATAATTCCC
1 ATACAAATTAGAAGTAACAAATAATTCCC
645362 ATACAAATTAGAAGTAACAAATAATTCCC
1 ATACAAATTAGAAGTAACAAATAATTCCC
645391 TCTTTAACTC
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:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (29 bp):
ATACAAATTAGAAGTAACAAATAATTCCC
Found at i:648412 original size:363 final size:363
Alignment explanation
Indices: 647741--648472 Score: 1419
Period size: 363 Copynumber: 2.0 Consensus size: 363
647731 CCGAGTGAGC
*
647741 ATGCTTCACATCATGAAAGACGATTGGAATCAAACGCTGTCGTTTTGACCTCTTAAATAACCCCC
1 ATGCTCCACATCATGAAAGACGATTGGAATCAAACGCTGTCGTTTTGACCTCTTAAATAACCCCC
647806 AATCGCAATCGTAACTCTGCTTTGTTTTCTATATAGTTGACAACCTTCCAACTGTCAGTTCCGCA
66 AATCGCAATCGTAACTCTGCTTTGTTTTCTATATAGTTGACAACCTTCCAACTGTCAGTTCCGCA
647871 ATTGCCACGTCAATAGTTTCCATGCCATCCATGACGTGGCGAGACTCTATCGAGTCTTTAAATGA
131 ATTGCCACGTCAATAGTTTCCATGCCATCCATGACGTGGCGAGACTCTATCGAGTCTTTAAATGA
*
647936 AGGGTGAGGGGTGTAAACGAGCCGAGTCGAGTTTGAGTATTGCTGAGCTCGATTTGACTCGAAAA
196 AGGGTGAGGGGTGTAAACGAGCCGAGTCGAGATTGAGTATTGCTGAGCTCGATTTGACTCGAAAA
*
648001 TTTTGAAATAGAGCTTGACTCGATTCAAAAACTCACGAGCTTAAAATTTTTAAGTTCGACTCAAA
261 TTTTGAAATAGAGCTTGACTCGACTCAAAAACTCACGAGCTTAAAATTTTTAAGTTCGACTCAAA
648066 CTCGAAATCCTAAACTGAAACTCGTGAGTAACTCGAAA
326 CTCGAAATCCTAAACTGAAACTCGTGAGTAACTCGAAA
648104 ATGCTCCACATCATGAAAGACGATTGGAATCAAACGCTGTCGTTTTGACCTCTTAAATAACCCCC
1 ATGCTCCACATCATGAAAGACGATTGGAATCAAACGCTGTCGTTTTGACCTCTTAAATAACCCCC
648169 AATCGCAATCGTAACTCTGCTTTGTTTTCTATATAGTTGACAACCTTCCAACTGTCAGTTCCGCA
66 AATCGCAATCGTAACTCTGCTTTGTTTTCTATATAGTTGACAACCTTCCAACTGTCAGTTCCGCA
648234 ATTGCCACGTCAATAGTTTCCATGCCATCCATGACGTGGCGAGACTCTATCGAGTCTTTAAATGA
131 ATTGCCACGTCAATAGTTTCCATGCCATCCATGACGTGGCGAGACTCTATCGAGTCTTTAAATGA
*
648299 ATGGTGAGGGGTGTAAACGAGCCGAGTCGAGATTGAGTATTGCTGAGCTCGATTTGACTCGAAAA
196 AGGGTGAGGGGTGTAAACGAGCCGAGTCGAGATTGAGTATTGCTGAGCTCGATTTGACTCGAAAA
648364 TTTTGAAATAGAGCTTGACTCGACTCAAAAACTCACGAGCTTAAAATTTTTAAGTTCGACTCAAA
261 TTTTGAAATAGAGCTTGACTCGACTCAAAAACTCACGAGCTTAAAATTTTTAAGTTCGACTCAAA
*
648429 CTCGAAATCCTGAACTGAAACTCGTGAGTAACTCGAAA
326 CTCGAAATCCTAAACTGAAACTCGTGAGTAACTCGAAA
648467 ATGCTC
1 ATGCTC
648473 GAAATGAAAA
Statistics
Matches: 364, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
363 364 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (363 bp):
ATGCTCCACATCATGAAAGACGATTGGAATCAAACGCTGTCGTTTTGACCTCTTAAATAACCCCC
AATCGCAATCGTAACTCTGCTTTGTTTTCTATATAGTTGACAACCTTCCAACTGTCAGTTCCGCA
ATTGCCACGTCAATAGTTTCCATGCCATCCATGACGTGGCGAGACTCTATCGAGTCTTTAAATGA
AGGGTGAGGGGTGTAAACGAGCCGAGTCGAGATTGAGTATTGCTGAGCTCGATTTGACTCGAAAA
TTTTGAAATAGAGCTTGACTCGACTCAAAAACTCACGAGCTTAAAATTTTTAAGTTCGACTCAAA
CTCGAAATCCTAAACTGAAACTCGTGAGTAACTCGAAA
Found at i:649887 original size:24 final size:24
Alignment explanation
Indices: 649860--649953 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 24
649850 AGAAAGGGAT
**
649860 CGTTCGTTCATTTATGTTCGTGAA
1 CGTTCGTTCATTTATGTTCGTTTA
* * * *
649884 CGTTTGGT-A-ATACGTTCGTTTA
1 CGTTCGTTCATTTATGTTCGTTTA
* *
649906 TGTTTGTTCATTTATGTTCGTTTA
1 CGTTCGTTCATTTATGTTCGTTTA
* *
649930 CATTCGTTCTTTTATGTTCGTTTA
1 CGTTCGTTCATTTATGTTCGTTTA
649954 TATTCAACCC
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
22 15 0.28
23 2 0.04
24 37 0.69
ACGTcount: A:0.15, C:0.14, G:0.18, T:0.53
Consensus pattern (24 bp):
CGTTCGTTCATTTATGTTCGTTTA
Found at i:649958 original size:24 final size:24
Alignment explanation
Indices: 649897--649958 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
649887 TTGGTAATAC
* *
649897 GTTCGTTTATGTTTGTTCATTTAT
1 GTTCGTTTATATTCGTTCATTTAT
* *
649921 GTTCGTTTACATTCGTTCTTTTAT
1 GTTCGTTTATATTCGTTCATTTAT
649945 GTTCGTTTATATTC
1 GTTCGTTTATATTC
649959 AACCCAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.60
Consensus pattern (24 bp):
GTTCGTTTATATTCGTTCATTTAT
Found at i:650110 original size:38 final size:38
Alignment explanation
Indices: 650067--650145 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
650057 AAAAGTACTT
650067 AAATCAATTAAAAGAATATAAATTCTAAAATTATTTGA
1 AAATCAATTAAAAGAATATAAATTCTAAAATTATTTGA
650105 AAATCAATTAAAAGAATATAAATTCTAAAATTATTTGA
1 AAATCAATTAAAAGAATATAAATTCTAAAATTATTTGA
650143 AAA
1 AAA
650146 GAAAAACACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (38 bp):
AAATCAATTAAAAGAATATAAATTCTAAAATTATTTGA
Found at i:650271 original size:29 final size:31
Alignment explanation
Indices: 650199--650271 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
650189 TTTGTGTTTG
650199 TTTA-TCATTTTAACGAATAATCATAAACAAGT
1 TTTATTCA-TTTAACGAATAA-CATAAACAAGT
*
650231 TTTATT-TTTTAACGAATAA-ATAAGA-AA-T
1 TTTATTCATTTAACGAATAACATAA-ACAAGT
650259 TTTATTCATTTAA
1 TTTATTCATTTAA
650272 TTGTTTATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
28 7 0.19
29 11 0.31
30 1 0.03
31 12 0.33
32 4 0.11
33 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (31 bp):
TTTATTCATTTAACGAATAACATAAACAAGT
Found at i:650307 original size:6 final size:6
Alignment explanation
Indices: 650296--650320 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
650286 TCGCTTCTTC
650296 AATTAA AATTAA AATTAA AATTAA A
1 AATTAA AATTAA AATTAA AATTAA A
650321 TAAATAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTAA
Found at i:653948 original size:24 final size:24
Alignment explanation
Indices: 653921--653967 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
653911 CAAGCATCGA
*
653921 TTCGAGAAACACC-GACATCTTCAG
1 TTCGAGAAAC-CCTGACACCTTCAG
*
653945 TTCGGGAAACCCTGACACCTTCA
1 TTCGAGAAACCCTGACACCTTCA
653968 ATCAGGTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (24 bp):
TTCGAGAAACCCTGACACCTTCAG
Found at i:655398 original size:11 final size:11
Alignment explanation
Indices: 655382--655406 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
655372 AGGAAAGGCT
655382 GGTTAATATAC
1 GGTTAATATAC
655393 GGTTAATATAC
1 GGTTAATATAC
655404 GGT
1 GGT
655407 AGTATCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:656073 original size:229 final size:230
Alignment explanation
Indices: 655653--656145 Score: 875
Period size: 230 Copynumber: 2.1 Consensus size: 230
655643 GTTATATTGT
* * *
655653 AAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTA
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
655718 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
66 TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
655783 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACACTATT-
131 TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACACTATTA
655847 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
655882 AAAGTATATATCATTTTTAAAAAAGTGTCCATACTTATTTCACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGT-GAAAACATATTTATTATT
*
655947 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAATAATCAA
65 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
* *
656011 ATAATTTTTTTGTGTAAATGAAATTATTAAATTAATA-TTGTTGGTGGAAAACATGAAACACTAT
130 ATAA-TTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACACTAT
656075 TAAAAAAAATTGAAACATAAATTACATAACTTTAAAA
194 TAAAAAAAATTGAAACATAAATTACATAACTTTAAAA
*
656112 AAAGTATATGTCATTTTTATAAAAGTGTCCATAC
1 AAAGTATATATCATTTTTATAAAAGTGTCCATAC
656146 ATATAAAAGT
Statistics
Matches: 252, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
229 83 0.33
230 169 0.67
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (230 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA
TCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAA
TAATTTTGTGTGTAAATGAAATTATTAAATTAATATTTGTAGGTGGAAAACATGAAACACTATTA
AAAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:656217 original size:20 final size:19
Alignment explanation
Indices: 656194--656240 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
656184 CGATATACCA
656194 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
656214 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
656234 GGTAAAA
1 GGTAAAA
656241 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:656394 original size:20 final size:20
Alignment explanation
Indices: 656366--656418 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
656356 GATCCACAAC
* *
656366 GATATAACATGTA-AAAATAT
1 GATAAAACAGGTATAAAA-AT
*
656386 GATAAAACAGGTATCAAAAT
1 GATAAAACAGGTATAAAAAT
*
656406 GATAAAACCGGTA
1 GATAAAACAGGTA
656419 AAATGATACC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.53, C:0.09, G:0.15, T:0.23
Consensus pattern (20 bp):
GATAAAACAGGTATAAAAAT
Found at i:658663 original size:21 final size:21
Alignment explanation
Indices: 658639--658682 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
658629 AAGACAATCA
658639 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
658660 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
658681 AG
1 AG
658683 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:658758 original size:33 final size:33
Alignment explanation
Indices: 658716--658781 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
658706 AAATAGATGG
*
658716 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
658749 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
658782 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:660596 original size:19 final size:19
Alignment explanation
Indices: 660572--660620 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
660562 AATGTAGGGT
660572 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
660591 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
660610 TATTTTTGTAT
1 TAATTTTGTAT
660621 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:661080 original size:199 final size:199
Alignment explanation
Indices: 660739--662031 Score: 2471
Period size: 199 Copynumber: 6.5 Consensus size: 199
660729 CAATATGGCC
* * * *
660739 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAAATATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
660804 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
660869 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
660934 TGGAA
195 TGGAA
*
660939 AACAGGGTGCACCCATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
661004 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
661069 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
661134 GGAA
196 GGAA
*
661138 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
661203 CAAAAATATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
661268 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
661333 GGAA
196 GGAA
*
661337 AACAGGGTGCACCCATAAAGTGTCGATCCGTATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
661402 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
661467 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
661532 GGAA
196 GGAA
*
661536 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
661601 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
661666 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCATAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
661731 GGAA
196 GGAA
661735 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
661800 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
661865 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTGTT-TTCCAGAATGAA
131 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTT-TTGTTCCAGAATGAA
661929 TGGAA
195 TGGAA
661934 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
661999 CAAAAGTATAATGTAATATGTAATTTTTCAATC
66 CAAAAGTATAATGTAATATGTAATTTTTCAATC
662032 GATCCATATA
Statistics
Matches: 1076, Mismatches: 16, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
199 1017 0.95
200 59 0.05
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
GGAA
Found at i:662330 original size:18 final size:18
Alignment explanation
Indices: 662309--662345 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
662299 GTAATTGGAG
662309 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
662327 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
662345 T
1 T
662346 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:662353 original size:24 final size:24
Alignment explanation
Indices: 662301--662347 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
662291 TTTCATATGT
* *
662301 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
662325 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
662348 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:662647 original size:39 final size:39
Alignment explanation
Indices: 662604--662690 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
662594 TCCGATGCTC
*
662604 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
662643 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
662682 ATCAAAATC
1 ATCAAAATC
662691 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:663125 original size:23 final size:23
Alignment explanation
Indices: 663094--663166 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
663084 ATAGGTAAAC
*
663094 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
663117 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
663140 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
663163 ATAT
1 ATAT
663167 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:666583 original size:16 final size:16
Alignment explanation
Indices: 666562--666602 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
666552 AATAAATAAT
666562 TAAAATATATAATTTA-
1 TAAAATATAT-ATTTAG
*
666578 TAAAATAGATATTTAG
1 TAAAATATATATTTAG
666594 TAAAA-ATAT
1 TAAAATATAT
666603 CAGAAAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (16 bp):
TAAAATATATATTTAG
Found at i:666755 original size:3 final size:3
Alignment explanation
Indices: 666749--666848 Score: 116
Period size: 3 Copynumber: 33.0 Consensus size: 3
666739 ATATATATAT
*
666749 ATA ATAA ATA ATAA ATA ATA ATA ATA ATA ATG A-A ATA ATA ATTA A-A
1 ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
**
666795 GCA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
666841 A-A ATA ATA
1 ATA ATA ATA
666849 TTACAAATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
2 4 0.05
3 69 0.81
4 12 0.14
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:666856 original size:12 final size:11
Alignment explanation
Indices: 666807--666870 Score: 65
Period size: 12 Copynumber: 5.5 Consensus size: 11
666797 AATAAATAAT
*
666807 AATAATAATAA
1 AATAATATTAA
*
666818 TAATAATAATAA
1 -AATAATATTAA
*
666830 TAATAATAATAA
1 -AATAATATTAA
666842 AATAATATTACA
1 AATAATATTA-A
666854 AATAATGATTAA
1 AATAAT-ATTAA
666866 AATAA
1 AATAA
666871 AAGGAATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
11 9 0.18
12 36 0.73
13 4 0.08
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAATATTAA
Found at i:668226 original size:3 final size:3
Alignment explanation
Indices: 668218--668261 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
668208 ATTAATTATT
*
668218 TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
668262 ATAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:668239 original size:16 final size:15
Alignment explanation
Indices: 668218--668264 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
668208 ATTAATTATT
668218 TAATAATAATATAATA
1 TAATAATAATA-AATA
* *
668234 TAATAATAAAACAAAA
1 TAATAATAATA-AATA
668250 TAATAATAATAAATA
1 TAATAATAATAAATA
668265 AAACAAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TAATAATAATAAATA
Found at i:668251 original size:23 final size:23
Alignment explanation
Indices: 668228--668271 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
668218 TAATAATAAT
668228 ATAAT-ATAAT-AATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
668249 ATAATAATAATAAATAAAACAAA
1 ATAATAATAATAAATAAAACAAA
668272 TGAAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 11 0.52
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
ATAATAATAATAAATAAAACAAA
Found at i:672491 original size:16 final size:18
Alignment explanation
Indices: 672458--672493 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
672448 AACTACCAAC
672458 TTTAATTTATTCATAATA
1 TTTAATTTATTCATAATA
672476 TTTAA-TTATT-ATAATA
1 TTTAATTTATTCATAATA
672492 TT
1 TT
672494 ATTTTTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 5 0.28
18 5 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAATTTATTCATAATA
Found at i:672573 original size:10 final size:11
Alignment explanation
Indices: 672546--672570 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
672536 ATCAAAATAA
672546 AAAATATTTAT
1 AAAATATTTAT
672557 AAAATATTTAT
1 AAAATATTTAT
672568 AAA
1 AAA
672571 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAAATATTTAT
Found at i:672650 original size:5 final size:5
Alignment explanation
Indices: 672613--672665 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
672603 TTTATCTTAC
* * * * *
672613 AATTT AATAT ATTTT AATCT ACTTT AATCT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT
672663 AAT
1 AAT
672666 CATTAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:672787 original size:20 final size:20
Alignment explanation
Indices: 672762--672812 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
672752 TTATCTATTT
672762 TATAATTTAATCTACTTCAA
1 TATAATTTAATCTACTTCAA
*
672782 TATAATTTAATCTACTTTAA
1 TATAATTTAATCTACTTCAA
*
672802 TCTAATTTAAT
1 TATAATTTAAT
672813 TATTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATTTAATCTACTTCAA
Found at i:672802 original size:10 final size:10
Alignment explanation
Indices: 672764--672812 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
672754 ATCTATTTTA
672764 TAATTTAATC
1 TAATTTAATC
* * *
672774 TACTTCAATA
1 TAATTTAATC
672784 TAATTTAATC
1 TAATTTAATC
*
672794 TACTTTAATC
1 TAATTTAATC
672804 TAATTTAAT
1 TAATTTAAT
672813 TATTAAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (10 bp):
TAATTTAATC
Found at i:673078 original size:20 final size:19
Alignment explanation
Indices: 673055--673101 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
673045 AAAAATATTT
* *
673055 TTTTATAATAAAAAAGTTAA
1 TTTTAT-ATAAAAAAATGAA
673075 TTTTAT-TAAAAAAATGAA
1 TTTTATATAAAAAAATGAA
673093 TTTTATATA
1 TTTTATATA
673102 TTAATATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 16 0.67
19 2 0.08
20 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (19 bp):
TTTTATATAAAAAAATGAA
Found at i:676246 original size:300 final size:299
Alignment explanation
Indices: 675704--676300 Score: 1149
Period size: 300 Copynumber: 2.0 Consensus size: 299
675694 TTCCTTATCA
675704 GATACAAGTTCTTTTGATTGTCCCATTAGTTCTATTAATTTTTAAATATAATTGAGTATCAATCA
1 GATACAAGTTCTTTTGATTGTCCCATTAGTTCTATTAATTTTTAAATATAATTGAGTATCAATCA
675769 TTCATATGAATGCTGCATAATATTATCATCTTCCACTTTATCCCATGTTTCTACTTAACCATATT
66 TTCATATGAATGCTGCATAATATTATCATCTTCCACTTTATCCCATGTTTCTACTTAACCATATT
675834 TCTATGATTGCTGAATGCTGATAAAGCTGTTCAAATCTAGGTATTCTATGCAGGTGAGGCTGCAA
131 TCTATGATTGCTGAATGCTGATAAAGCTGTTCAAATCTAGGTATTCTATGCAGGTGAGGCTGCAA
*
675899 ATGGGTATAAAAGTTGGATATTTTAGATCCCTATATATTGAATTGTTCCCACTGTCCATAATGTA
196 ATGGGTATAAAAGTTGGATAGTTTAGATCCCTATATATTGAATTGTTCCCACTGTCCATAATGTA
*
675964 TTGCAAAGAATAATGCTTCTGATGGTGCTATTTCTTATGG
261 TTGCAAACAATAATGCTTCTGATGGTGCTA-TTCTTATGG
*
676004 GATACAAGTTCTTTTGATTGTCCCATTAGTTCTATTAATTTTTAAATATTATTGAGTATCAATCA
1 GATACAAGTTCTTTTGATTGTCCCATTAGTTCTATTAATTTTTAAATATAATTGAGTATCAATCA
676069 TTCATATGAATGCTGCATAATATTATCATCTTCCACTTTATCCCATGTTTCTACTTAACCATATT
66 TTCATATGAATGCTGCATAATATTATCATCTTCCACTTTATCCCATGTTTCTACTTAACCATATT
676134 TCTATGATTGCTGAATGCTGATAAAGCTGTTCAAATCTAGGTATTCTATGCAGGTGAGGCTGCAA
131 TCTATGATTGCTGAATGCTGATAAAGCTGTTCAAATCTAGGTATTCTATGCAGGTGAGGCTGCAA
*
676199 ATGGGTATAAAAGTTGGATAGTTTAGATCCCTATATATTGAATTGTTCCTACTGTCCATAATGTA
196 ATGGGTATAAAAGTTGGATAGTTTAGATCCCTATATATTGAATTGTTCCCACTGTCCATAATGTA
676264 TTGCAAACAATAATGCTTCTGATGGTGCTATTCTTAT
261 TTGCAAACAATAATGCTTCTGATGGTGCTATTCTTAT
676301 TGGTGGTTTG
Statistics
Matches: 293, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
299 7 0.02
300 286 0.98
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (299 bp):
GATACAAGTTCTTTTGATTGTCCCATTAGTTCTATTAATTTTTAAATATAATTGAGTATCAATCA
TTCATATGAATGCTGCATAATATTATCATCTTCCACTTTATCCCATGTTTCTACTTAACCATATT
TCTATGATTGCTGAATGCTGATAAAGCTGTTCAAATCTAGGTATTCTATGCAGGTGAGGCTGCAA
ATGGGTATAAAAGTTGGATAGTTTAGATCCCTATATATTGAATTGTTCCCACTGTCCATAATGTA
TTGCAAACAATAATGCTTCTGATGGTGCTATTCTTATGG
Found at i:697331 original size:2 final size:2
Alignment explanation
Indices: 697324--697348 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
697314 CGTGTAATGA
697324 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
697349 GAGAGAGAGA
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:699399 original size:29 final size:29
Alignment explanation
Indices: 699365--699423 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
699355 CCTAAATTAA
699365 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
699394 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
699423 T
1 T
699424 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:704084 original size:29 final size:29
Alignment explanation
Indices: 704050--704108 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
704040 CCTAAATTAA
704050 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
704079 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
704108 T
1 T
704109 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:707040 original size:14 final size:14
Alignment explanation
Indices: 707021--707049 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
707011 TATATTTAAG
707021 AATTAGAAATTTGA
1 AATTAGAAATTTGA
707035 AATTAGAAATTTGA
1 AATTAGAAATTTGA
707049 A
1 A
707050 GTTTGAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
AATTAGAAATTTGA
Found at i:707893 original size:12 final size:12
Alignment explanation
Indices: 707876--707900 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
707866 TAGAGTTGAT
707876 AAGTTGAATTTG
1 AAGTTGAATTTG
707888 AAGTTGAATTTG
1 AAGTTGAATTTG
707900 A
1 A
707901 CTTGTCATCT
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:708618 original size:17 final size:16
Alignment explanation
Indices: 708596--708634 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
708586 TTATATAAAC
*
708596 TGATATGTGTTTATATG
1 TGATATGTGATT-TATG
708613 TGATATGTGATTTATG
1 TGATATGTGATTTATG
708629 TGATAT
1 TGATAT
708635 ACCATATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (16 bp):
TGATATGTGATTTATG
Found at i:712772 original size:21 final size:19
Alignment explanation
Indices: 712713--712800 Score: 79
Period size: 21 Copynumber: 4.4 Consensus size: 19
712703 AGAATTATTG
*
712713 TTAAATTATATTAAAATATGA
1 TTAAATTAT-TTAAAAT-TTA
*
712734 TAAAATTA-TTAAAATTTA
1 TTAAATTATTTAAAATTTA
*
712752 TTAAATAATATTTAAATTTTA
1 TTAAAT--TATTTAAAATTTA
*
712773 TTGAATTATTATAAAATTTA
1 TTAAATTATT-TAAAATTTA
712793 TTGAAATT
1 TT-AAATT
712801 GTACAATTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.13
19 11 0.20
20 12 0.22
21 25 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (19 bp):
TTAAATTATTTAAAATTTA
Found at i:712787 original size:20 final size:19
Alignment explanation
Indices: 712737--712797 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
712727 AATATGATAA
*
712737 AATTATTA-AAATTTATTA
1 AATTATTATAAATTTATTG
712755 AATAATATT-TAAATTTTATTG
1 AAT--TATTATAAA-TTTATTG
712776 AATTATTATAAAATTTATTG
1 AATTATTAT-AAATTTATTG
712796 AA
1 AA
712798 ATTGTACAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 17 0.47
21 12 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTATTATAAATTTATTG
Found at i:722397 original size:14 final size:14
Alignment explanation
Indices: 722378--722407 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
722368 GGTAATAATA
722378 TTAAATTATGTTAT
1 TTAAATTATGTTAT
*
722392 TTAAATTATTTTAT
1 TTAAATTATGTTAT
722406 TT
1 TT
722408 TTTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (14 bp):
TTAAATTATGTTAT
Found at i:726930 original size:23 final size:23
Alignment explanation
Indices: 726885--726932 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
726875 TGCAGTTTTA
* *
726885 TTTATTCTTTTAATTACTTTATT
1 TTTATTCATTTAAATACTTTATT
726908 TTTATTCATTTAAATA-TTATATT
1 TTTATTCATTTAAATACTT-TATT
726931 TT
1 TT
726933 AATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTATTCATTTAAATACTTTATT
Found at i:727104 original size:19 final size:20
Alignment explanation
Indices: 727080--727121 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
727070 ATGTTTCTAT
*
727080 TTTTTATTTATTT-ATTTTC
1 TTTTTATTTATTTCATTTCC
*
727099 TTTTTATTTCTTTCATTTCC
1 TTTTTATTTATTTCATTTCC
727119 TTT
1 TTT
727122 ACGTTTATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATTTATTTCATTTCC
Found at i:727259 original size:21 final size:20
Alignment explanation
Indices: 727235--727287 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
727225 CATATTTTCA
*
727235 TTTTATTTATTGTCTCTTATT
1 TTTTATTTATT-TATCTTATT
* *
727256 TTTTTTTTCATTTATCTTTTT
1 TTTTATTT-ATTTATCTTATT
727277 TTTTACTTTAT
1 TTTTA-TTTAT
727288 CCTTTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTATTTATTTATCTTATT
Found at i:727275 original size:16 final size:17
Alignment explanation
Indices: 727251--727294 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
727241 TTATTGTCTC
*
727251 TTATTTTTTTTTTCA-T
1 TTATCTTTTTTTTCACT
*
727267 TTATCTTTTTTTTTACT
1 TTATCTTTTTTTTCACT
727284 TTATCCTTTTT
1 TTAT-CTTTTT
727295 ATTTACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
17 5 0.21
18 6 0.25
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATCTTTTTTTTCACT
Found at i:727277 original size:17 final size:17
Alignment explanation
Indices: 727251--727301 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
727241 TTATTGTCTC
727251 TTAT-TTTTTTTTT-CAT
1 TTATCTTTTTTTTTAC-T
727267 TTATCTTTTTTTTTACT
1 TTATCTTTTTTTTTACT
*
727284 TTATCCTTTTTATTTACT
1 TTAT-CTTTTTTTTTACT
727302 ATTTTACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 4 0.13
17 14 0.45
18 13 0.42
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATCTTTTTTTTTACT
Found at i:727277 original size:18 final size:18
Alignment explanation
Indices: 727254--727301 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
727244 TTGTCTCTTA
*
727254 TTTTTTTTTTCATTTAT-C
1 TTTTTTTTTAC-TTTATCC
727272 TTTTTTTTTACTTTATCC
1 TTTTTTTTTACTTTATCC
*
727290 TTTTTATTTACT
1 TTTTTTTTTACT
727302 ATTTTACTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTTTTACTTTATCC
Found at i:731364 original size:95 final size:95
Alignment explanation
Indices: 731251--731513 Score: 323
Period size: 95 Copynumber: 2.7 Consensus size: 95
731241 AAATTATAAT
* * * * *
731251 ATTATATATATACGATAAAGCTTGAGCTGTCACTCTAAAGCAATTGGTTAAATGTCCCGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGACCCGGCTTTA
731316 TGGATAAGATTCAGCTAGCATGATAAAGGTA
65 TGGATAAGATTCAGCTAGCATGATAAAGGTA
* *
731347 ATTATAATATACAATAAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAA-CACCCTGGCTTTA
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGACCC-GGCTTTA
* * *
731411 TGGATAATATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCATGATAAAGGTA
* * * * *
731442 ATTATAATAT-CTATACAATGATATTAAGTTGTCCCTCTAGAGCAATTAGTTAAATGCCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGACCCGGCT
731506 TTATGGAT
62 TTATGGAT
731514 TCAACTAGCC
Statistics
Matches: 144, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
94 7 0.05
95 87 0.60
96 6 0.04
98 41 0.28
99 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAATGACCCGGCTTTAT
GGATAAGATTCAGCTAGCATGATAAAGGTA
Found at i:732857 original size:120 final size:121
Alignment explanation
Indices: 732606--732977 Score: 550
Period size: 121 Copynumber: 3.1 Consensus size: 121
732596 ATACAACTCA
* * * *
732606 AAGCATCAATGCAACCCTTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTT
1 AAGCATCAATACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTT
* * *
732671 CATGACAAAGGGGTCATCCACGATTTTAACTCCACGACAGAGGATATCGTGCCCAC
66 CATGACGAAGGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
* * *
732727 AAGCAGCAATACAAACCTTAGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCAT-AACT
1 AAGCATCAATACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGC-TCAACT
* * * * * **
732791 TCACGATGAA-GGGCCATCCATGATTTCAACTCCACGATGGAGGATATCGTGCCTGC
65 TCATGACGAAGGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
*
732847 AAGCATCAATACAACCCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCGAGGCTCAACTT
1 AAGCATCAATACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTT
732912 CATGACGAAGGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
66 CATGACGAAGGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
*
732968 AAGCAACAAT
1 AAGCATCAAT
732978 GTCATCCACA
Statistics
Matches: 219, Mismatches: 29, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
119 1 0.00
120 105 0.48
121 112 0.51
122 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (121 bp):
AAGCATCAATACAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTT
CATGACGAAGGGGTCATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
Found at i:732992 original size:120 final size:118
Alignment explanation
Indices: 732627--733013 Score: 481
Period size: 120 Copynumber: 3.2 Consensus size: 118
732617 CAACCCTTGG
* * * *
732627 ATTTTAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCATGACAAAGGGGTCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGTCATCCAC
* * * *
732692 GATTTTAACTCCACGACAGAGGATATCGTGCCCACAAGCAGCAATACAAACCTTA
66 GATTTCAACTCCACGACGGAGGATATCGTGCCCACAAGCAACAATAC-AACC-CA
* * *
732747 GATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCAT-AACTTCACGATGAA-GGGCCATCC
1 -ATTTCAACTTCACGACGAAGGATATCCAATTCGAGGC-TCAACTTCATGACGAAGGGGTCATCC
* * ** * *
732810 ATGATTTCAACTCCACGATGGAGGATATCGTGCCTGCAAGCATCAATACAACCCTTGG
64 ACGATTTCAACTCCACGACGGAGGATATCGTGCCCACAAGCAACAATACAACCC---A
*
732868 ATTTCAACTTCACGACAAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGTCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGTCATCCAC
* *
732933 GATTTCAACTCCACGACGGAGGATATCGTGCCCACAAGCAACAATGTCATCCACA
66 GATTTCAACTCCACGACGGAGGATATCGTGCCCACAAGCAACAAT-ACAACC-CA
* *
732988 ATTTCAATTTCTCGACGAAGGATATC
1 ATTTCAACTTCACGACGAAGGATATC
733014 GTGTTCATTT
Statistics
Matches: 227, Mismatches: 31, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
119 5 0.02
120 121 0.53
121 95 0.42
122 5 0.02
123 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (118 bp):
ATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATGACGAAGGGGTCATCCAC
GATTTCAACTCCACGACGGAGGATATCGTGCCCACAAGCAACAATACAACCCA
Found at i:733160 original size:84 final size:84
Alignment explanation
Indices: 733018--733415 Score: 374
Period size: 84 Copynumber: 4.7 Consensus size: 84
733008 GATATCGTGT
* * ** * * *
733018 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATATGCCAATAAAAGATCTTCGAGTTCGACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGAATTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
733083 CGCTCAGCTCCAAGGAACA
66 CGCTCAGCTCCAAGGAACA
* * * * * *
733102 TCATTTGCAACATAGCTGAAAGCAAGAAGAACTATTTGCCAACAAAAGACATTTGAGTTCAACTA
1 TCATTTGCAACATAGCTCAAGGCAAGAAGAATTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
733167 CGCTCAGCTCCAAGGCAGA
66 CGCTCAGCTCCAAGGAACA
* * *
733186 TCATTTGCAACATAGCTCAAGGCAAGAAGGAA-TATTTTCCAGCAAAAGACCTTCGAGTTCGATT
1 TCATTTGCAACATAGCTCAAGGCAAGAA-GAATTATTTGCCAACAAAAGACCTTCGAGTTCGACT
* * *
733250 ACGCTCAACT-CAAAGACATA
65 ACGCTCAGCTCCAAGGA-ACA
* * * * ** * *
733270 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT-ACAAGCCAAAA-ACCTTCGAGTTCGAC
1 TCATTTGCAACATAGCTCAAGGCAAGAAGAATTATTTGCCAA--CAAAAGACCTTCGAGTTCGAC
* * *
733333 TACGCTTAGCTCTAAGGCACA
64 TACGCTCAGCTCCAAGGAACA
** * * * *
733354 TCATTTGCAACATAGCTCAAGGCGAA-AAGGGTTATCTGTCGACAAAATACCTTCGAGTTCGA
1 TCATTTGCAACATAGCTCAAGGC-AAGAAGAATTATTTGCCAACAAAAGACCTTCGAGTTCGA
733416 TTTCATTCAG
Statistics
Matches: 256, Mismatches: 49, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
83 12 0.05
84 230 0.90
85 14 0.05
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (84 bp):
TCATTTGCAACATAGCTCAAGGCAAGAAGAATTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGAACA
Found at i:735694 original size:15 final size:15
Alignment explanation
Indices: 735676--735705 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
735666 ATTATTTCAT
*
735676 TTTTTCTTTATTTTA
1 TTTTTCCTTATTTTA
735691 TTTTTCCTTATTTTA
1 TTTTTCCTTATTTTA
735706 GTTATTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCCTTATTTTA
Found at i:736117 original size:25 final size:25
Alignment explanation
Indices: 736087--736210 Score: 97
Period size: 24 Copynumber: 5.3 Consensus size: 25
736077 ACAACTAAAC
*
736087 AATAAAAACATTAAGAAACAAAATA
1 AATAAAAACATTAAGTAACAAAATA
* ***
736112 AATAAAAA-ATTTA-TATTTAAAT-
1 AATAAAAACATTAAGTAACAAAATA
736134 AATAAAAACATTAAGTAACAAAATA
1 AATAAAAACATTAAGTAACAAAATA
* *
736159 AAT-AAAA-A--AA-T-CCATAATGA
1 AATAAAAACATTAAGTAACAAAAT-A
*
736179 AATAAAAACATTAAG-AAAAAAATA
1 AATAAAAACATTAAGTAACAAAATA
736203 AATAAAAA
1 AATAAAAA
736211 GTCAACAATT
Statistics
Matches: 75, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
19 5 0.07
20 5 0.07
21 6 0.08
22 9 0.12
23 10 0.13
24 25 0.33
25 15 0.20
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (25 bp):
AATAAAAACATTAAGTAACAAAATA
Found at i:736138 original size:47 final size:45
Alignment explanation
Indices: 736082--736210 Score: 163
Period size: 47 Copynumber: 2.8 Consensus size: 45
736072 TTCAAACAAC
** *
736082 TAAACAATAAAAACATTAAGAAACAAAATAAATAAAAAATTTATATT
1 TAAA-AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATA-A
*
736129 TAAATAATAAAAACATTAAGTAACAAAATAAATAAAAAAATCCATAA
1 TAAA-AATAAAAACATTAAGAAACAAAATAAAT-AAAAAATCCATAA
*
736176 T-GAAATAAAAACATTAAGAAA-AAAATAAATAAAAA
1 TAAAAATAAAAACATTAAGAAACAAAATAAATAAAAA
736211 GTCAACAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
43 5 0.07
44 9 0.12
45 17 0.23
46 1 0.01
47 32 0.43
48 10 0.14
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (45 bp):
TAAAAATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAA
Found at i:737136 original size:44 final size:44
Alignment explanation
Indices: 737070--737170 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
737060 TGCACAGGGA
* **
737070 GTGCATCGATGCACCCATTAAAATGGAAACATCGAATGCGATTG
1 GTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTG
* * * *
737114 GTGCATCGATGCGTCCC-CTAAAATACAAACATTGAATGGGATTT
1 GTGCATCGATGC-ACCCACTAAAATACAAACATCGAATGCGATTG
* *
737158 ATGCATAGATGCA
1 GTGCATCGATGCA
737171 TAGATAGTGC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (44 bp):
GTGCATCGATGCACCCACTAAAATACAAACATCGAATGCGATTG
Found at i:738016 original size:31 final size:31
Alignment explanation
Indices: 737927--738054 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
737917 AGAGTCGAGG
* *
737927 GTTTATCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * *
737958 GTTTTACCTATG-TCTTTCGAGATATATGGACA
1 G-TTTACCTATGTTCTATGGA-ACATATGGACA
* *
737990 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
* * * *
738021 GTTTACCTAGGTTCTTTGGGACCTATGGACA
1 GTTTACCTATGTTCTATGGAACATATGGACA
738052 GTT
1 GTT
738055 GCCGAGGTTC
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
31 53 0.68
32 25 0.32
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTATGGAACATATGGACA
Found at i:738074 original size:30 final size:31
Alignment explanation
Indices: 737982--738079 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
737972 TTTCGAGATA
* * * * *
737982 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGTTTACCGAGGTTCTTTAGG-ACC
* *
738013 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
738044 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
738074 TCTGGA
1 TATGGA
738080 TAGGTCATTC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
30 22 0.39
31 31 0.55
32 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:739213 original size:21 final size:21
Alignment explanation
Indices: 739169--739225 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
739159 CCTTACGGTG
* **
739169 GTGGCATCTGAAATGGTTGTA
1 GTGGCATCTGAAATAGTTACA
739190 GTGGCATCTGAAATAGTTACA
1 GTGGCATCTGAAATAGTTACA
* *
739211 GTGACATCAGAAATA
1 GTGGCATCTGAAATA
739226 AATGCGTTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
GTGGCATCTGAAATAGTTACA
Found at i:747909 original size:34 final size:34
Alignment explanation
Indices: 747866--747938 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
747856 AACATTGAAA
*
747866 AAATGGATCTATACTTGGTGACTGTGTCTACTAG
1 AAATGGATCTATACTTAGTGACTGTGTCTACTAG
* **
747900 AAATGGATCTTTACTTAGTGTTTGTGTCTACTAG
1 AAATGGATCTATACTTAGTGACTGTGTCTACTAG
747934 AAATG
1 AAATG
747939 CCATTGAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.38
Consensus pattern (34 bp):
AAATGGATCTATACTTAGTGACTGTGTCTACTAG
Found at i:749099 original size:38 final size:40
Alignment explanation
Indices: 749047--749122 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
749037 CGATTAGGTA
*
749047 CCTTGGTGCTGATAAAAGCC-GT-GTTTAGTATTACTTAT
1 CCTTGGTGCAGATAAAAGCCAGTCGTTTAGTATTACTTAT
*
749085 CCTTGGTGCAGATAATAGCCATGTCGTTTAGTATTACT
1 CCTTGGTGCAGATAAAAGCCA-GTCGTTTAGTATTACT
749123 CTAAGTCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
38 18 0.55
40 2 0.06
41 13 0.39
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (40 bp):
CCTTGGTGCAGATAAAAGCCAGTCGTTTAGTATTACTTAT
Found at i:753589 original size:38 final size:38
Alignment explanation
Indices: 753539--753615 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
753529 ACAACCTGGT
753539 TTTTGCAGCTTTTCTGATGATTTCACCACATATTGATG
1 TTTTGCAGCTTTTCTGATGATTTCACCACATATTGATG
*
753577 TTTTGCAGCTTTTCTGATGATTTCACTACATATTGATG
1 TTTTGCAGCTTTTCTGATGATTTCACCACATATTGATG
753615 T
1 T
753616 ATTTTATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.47
Consensus pattern (38 bp):
TTTTGCAGCTTTTCTGATGATTTCACCACATATTGATG
Found at i:753613 original size:19 final size:19
Alignment explanation
Indices: 753553--753619 Score: 50
Period size: 19 Copynumber: 3.5 Consensus size: 19
753543 GCAGCTTTTC
*
753553 TGATGATTTCACCACATAT
1 TGATGATTTCACTACATAT
* *
753572 TGATGTTTTGCAGCT---TTT
1 TGATGATTT-CA-CTACATAT
753590 CTGATGATTTCACTACATAT
1 -TGATGATTTCACTACATAT
753610 TGATGTATTT
1 TGATG-ATTT
753620 TATTTTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 13
0.67 0.09 0.24
Matches are distributed among these distances:
17 2 0.06
18 4 0.11
19 21 0.58
20 8 0.22
21 1 0.03
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (19 bp):
TGATGATTTCACTACATAT
Found at i:759564 original size:18 final size:18
Alignment explanation
Indices: 759505--759569 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
759495 GAATAACAAT
759505 TCAATTTTTAAGAATTTA
1 TCAATTTTTAAGAATTTA
* * *
759523 T-AATATCTATAA-TATTAAA
1 TCAAT-T-TTTAAGAATT-TA
759542 TCAATTTTTAAGAATTTA
1 TCAATTTTTAAGAATTTA
759560 TCAATTTTTA
1 TCAATTTTTA
759570 TCAATTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
17 3 0.08
18 20 0.56
19 10 0.28
20 3 0.08
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
TCAATTTTTAAGAATTTA
Found at i:759575 original size:18 final size:18
Alignment explanation
Indices: 759541--759576 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
759531 ATAATATTAA
*
759541 ATCAATTTTTAAGAATTT
1 ATCAATTTTTAACAATTT
*
759559 ATCAATTTTTATCAATTT
1 ATCAATTTTTAACAATTT
759577 TAAGTGTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (18 bp):
ATCAATTTTTAACAATTT
Found at i:760718 original size:19 final size:19
Alignment explanation
Indices: 760694--760733 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
760684 TGAAGAAAGA
760694 TTAGGAGTTTCGACCATGG
1 TTAGGAGTTTCGACCATGG
760713 TTAGGAGTTTCGACCATGG
1 TTAGGAGTTTCGACCATGG
760732 TT
1 TT
760734 TGATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (19 bp):
TTAGGAGTTTCGACCATGG
Found at i:765601 original size:24 final size:24
Alignment explanation
Indices: 765569--765616 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
765559 TGGCCGGAGG
765569 CAAATCAATAGAGATGTAAGAACA
1 CAAATCAATAGAGATGTAAGAACA
*
765593 CAAATCAATGGAGATGTAAGAACA
1 CAAATCAATAGAGATGTAAGAACA
765617 AATTACATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (24 bp):
CAAATCAATAGAGATGTAAGAACA
Found at i:770898 original size:23 final size:24
Alignment explanation
Indices: 770867--770911 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
770857 GTACTTATGA
*
770867 CACG-CTTTTCTCTGTTCTTGTAG
1 CACGTCTTTTCTCTGCTCTTGTAG
*
770890 CACGTTTTTTCTCTGCTCTTGT
1 CACGTCTTTTCTCTGCTCTTGT
770912 GGTACATTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.07, C:0.27, G:0.16, T:0.51
Consensus pattern (24 bp):
CACGTCTTTTCTCTGCTCTTGTAG
Found at i:771205 original size:205 final size:205
Alignment explanation
Indices: 770842--771256 Score: 677
Period size: 205 Copynumber: 2.0 Consensus size: 205
770832 TTTTCACTTT
* *
770842 TAAATTAGAATATATGTACTTATGACACGCTTTTCTCTGTTCTTGTAGCACGTTTTTTCTCTGCT
1 TAAATAAGAATATATGTACTTATGACACGCTTTTCTCTGTTCTTGTAGCACGCTTTTTCTCTGCT
770907 CTTGTGGTACATTCCTTATAGTTTTCGGTAAGTTTTTCACATACTTCTGAGGTTGTGTTGGTGTT
66 CTTGTGGTACATTCCTTATAGTTTTCGGTAAGTTTTTCACATACTTCTGAGGTTGTGTTGGTGTT
* *
770972 TCCACAAAGATCCTCATGGCATTTGTTTCATGATTGGCTTTTCAGTGGTCACGTTTTGTTAGATC
131 TCCACAAAGATCCTCATGGCACTTGTTTCATGATTGGCTTTTCAGTGGTCACGTTTTGTCAGATC
*
771037 CCCTCTTTTG
196 CCCTATTTTG
* * * * *
771047 TAAATAAGAATATATGTATTTGTGATATGCTTTTCTCTTTTCTTGTAGCACGCTTTTTCTCTGCT
1 TAAATAAGAATATATGTACTTATGACACGCTTTTCTCTGTTCTTGTAGCACGCTTTTTCTCTGCT
* * * * *
771112 CTTGTGGTACGTTTCTTATGGTTTTCGGTAAGTTTTTCGCATACTTTTGAGGTTGTGTTGGTGTT
66 CTTGTGGTACATTCCTTATAGTTTTCGGTAAGTTTTTCACATACTTCTGAGGTTGTGTTGGTGTT
*
771177 TCCACAAAGATCCTCATGGCACTTGTTTCATGATTGGCTTTTTAGTGGTCACGTTTTGTCAGATC
131 TCCACAAAGATCCTCATGGCACTTGTTTCATGATTGGCTTTTCAGTGGTCACGTTTTGTCAGATC
*
771242 CCTTATTTTG
196 CCCTATTTTG
771252 TAAAT
1 TAAAT
771257 GGTCGACTGC
Statistics
Matches: 193, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
205 193 1.00
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.46
Consensus pattern (205 bp):
TAAATAAGAATATATGTACTTATGACACGCTTTTCTCTGTTCTTGTAGCACGCTTTTTCTCTGCT
CTTGTGGTACATTCCTTATAGTTTTCGGTAAGTTTTTCACATACTTCTGAGGTTGTGTTGGTGTT
TCCACAAAGATCCTCATGGCACTTGTTTCATGATTGGCTTTTCAGTGGTCACGTTTTGTCAGATC
CCCTATTTTG
Found at i:777143 original size:21 final size:18
Alignment explanation
Indices: 777117--777166 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
777107 ATTAATTAAG
*
777117 AACATTTAATAAATTTTCAT
1 AACATTTAATAAA-ATTC-T
777137 ATACATTTAACTAAAATTCT
1 A-ACATTTAA-TAAAATTCT
777157 AACATTTAAT
1 AACATTTAAT
777167 GTAATATGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 1 0.04
19 8 0.30
20 3 0.11
21 11 0.41
22 4 0.15
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
AACATTTAATAAAATTCT
Found at i:778955 original size:2 final size:2
Alignment explanation
Indices: 778950--778974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
778940 CTTTTGTGTG
778950 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
778975 CATCCTTTCT
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:779857 original size:31 final size:30
Alignment explanation
Indices: 779810--779879 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
779800 TTCATTTAAG
*
779810 TACCTAAAG-TACTTTTTGGTAAAAATAAA
1 TACCTAAAGTTACTTTTTAGTAAAAATAAA
* * *
779839 TACTTAAAGTTATCTTTTTAGTCAAAATAGA
1 TACCTAAAGTTA-CTTTTTAGTAAAAATAAA
779870 TACCTAAAGT
1 TACCTAAAGT
779880 ATTTTATATC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 8 0.24
30 2 0.06
31 24 0.71
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (30 bp):
TACCTAAAGTTACTTTTTAGTAAAAATAAA
Found at i:779893 original size:28 final size:29
Alignment explanation
Indices: 779810--779910 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 29
779800 TTCATTTAAG
* * *
779810 TACCTAAAGTACTTTT-TGGTAAAAATAAA
1 TACCTAAAGTA-TTTTATAGTCAAAATAGA
* *
779839 TACTTAAAGTTATCTTTTTAGTCAAAATAGA
1 TACCTAAAG-TAT-TTTATAGTCAAAATAGA
*
779870 TACCTAAAGTATTTTATA-TCAAAATAGG
1 TACCTAAAGTATTTTATAGTCAAAATAGA
*
779898 TACCTAAACTATT
1 TACCTAAAGTATT
779911 CAAACTTTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
28 21 0.34
29 14 0.23
30 8 0.13
31 18 0.30
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
TACCTAAAGTATTTTATAGTCAAAATAGA
Found at i:780029 original size:20 final size:20
Alignment explanation
Indices: 780001--780040 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
779991 TTGAATACTT
780001 TAGGCACCTATTTTAACCAA
1 TAGGCACCTATTTTAACCAA
* *
780021 TAGGTACCTATTTTGACCAA
1 TAGGCACCTATTTTAACCAA
780041 AACAATAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (20 bp):
TAGGCACCTATTTTAACCAA
Found at i:780064 original size:31 final size:28
Alignment explanation
Indices: 780021--780089 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
780011 TTTTAACCAA
* *
780021 TAGGTACCTATTTTGACCAAAACAATAACTT
1 TAGGTACTTATTTAGA-CAAAA-AAT-ACTT
780052 TAGGTACTTATTTAGACAAAAAATACTT
1 TAGGTACTTATTTAGACAAAAAATACTT
*
780080 TAGCTACTTA
1 TAGGTACTTA
780090 AATGAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 13 0.37
29 3 0.09
30 5 0.14
31 14 0.40
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (28 bp):
TAGGTACTTATTTAGACAAAAAATACTT
Found at i:780088 original size:28 final size:31
Alignment explanation
Indices: 780029--780089 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 31
780019 AATAGGTACC
* *
780029 TATTTTGACCAAAACAATAACTTTAGGTACT
1 TATTTAGACCAAAACAATAACTTTAGCTACT
780060 TATTTAGA-CAAAA-AAT-ACTTTAGCTACT
1 TATTTAGACCAAAACAATAACTTTAGCTACT
780088 TA
1 TA
780090 AATGAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 13 0.46
29 3 0.11
30 5 0.18
31 7 0.25
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (31 bp):
TATTTAGACCAAAACAATAACTTTAGCTACT
Found at i:780797 original size:16 final size:17
Alignment explanation
Indices: 780759--780797 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
780749 TAGTTAACCC
780759 TAATT-TTTAATATATA
1 TAATTATTTAATATATA
780775 TAA--ATTTAA-ATATA
1 TAATTATTTAATATATA
780789 TAATTATTT
1 TAATTATTT
780798 TAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 8 0.40
15 5 0.25
16 7 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTATTTAATATATA
Found at i:785134 original size:6 final size:6
Alignment explanation
Indices: 785123--785159 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
785113 GACACGTATT
785123 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
785160 GTCGAGCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:785170 original size:5 final size:5
Alignment explanation
Indices: 785157--785235 Score: 86
Period size: 5 Copynumber: 15.8 Consensus size: 5
785147 ACCACGACCA
* * * * * * *
785157 CGAGT CGAGC CGAGC CGAGC CGAGC CGAGT CGTGC TGTGC CGTGC CGTGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
785207 CGAGC CGAGC CGAGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
785236 ACGGACGGAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 66 1.00
ACGTcount: A:0.16, C:0.34, G:0.41, T:0.09
Consensus pattern (5 bp):
CGAGC
Found at i:791108 original size:6 final size:6
Alignment explanation
Indices: 791097--791122 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
791087 GACACGTATT
791097 ACCACG ACCACG ACCACG ACCACG AC
1 ACCACG ACCACG ACCACG ACCACG AC
791123 AAGGAAGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.50, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:794166 original size:17 final size:18
Alignment explanation
Indices: 794144--794185 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
794134 CCCAAAAATA
*
794144 TTTTCTTCTTTC-TCTTC
1 TTTTCTCCTTTCTTCTTC
794161 TTTTCTCCTTTCTTCTTC
1 TTTTCTCCTTTCTTCTTC
794179 -TTTCTCC
1 TTTTCTCC
794186 AGAATAAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCTCCTTTCTTCTTC
Found at i:794167 original size:10 final size:9
Alignment explanation
Indices: 794147--794184 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
794137 AAAAATATTT
794147 TCTTCTTTC
1 TCTTCTTTC
794156 TCTTCTTT-
1 TCTTCTTTC
*
794164 TCTCCTTTC
1 TCTTCTTTC
794173 TTCTTCTTTC
1 -TCTTCTTTC
794183 TC
1 TC
794185 CAGAATAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 10 0.40
10 8 0.32
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (9 bp):
TCTTCTTTC
Found at i:800726 original size:35 final size:35
Alignment explanation
Indices: 800680--800751 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
800670 GGTATCTGAG
800680 AAAGGTTGTAATCTACGAGG-TTCTACCTAGGATGT
1 AAAGGTTGTAATCTAC-AGGTTTCTACCTAGGATGT
800715 AAAGGTTGTAATCTACAGGTTTCTACCTAGGATGT
1 AAAGGTTGTAATCTACAGGTTTCTACCTAGGATGT
800750 AA
1 AA
800752 TCTATGTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 3 0.08
35 33 0.92
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (35 bp):
AAAGGTTGTAATCTACAGGTTTCTACCTAGGATGT
Found at i:804212 original size:15 final size:15
Alignment explanation
Indices: 804194--804231 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
804184 ACCATCTTCG
*
804194 TCGTCTTCTTCATCA
1 TCGTCGTCTTCATCA
*
804209 TCGTCGTCTTCATCT
1 TCGTCGTCTTCATCA
804224 TCGTCGTC
1 TCGTCGTC
804232 GGTTTGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.34, G:0.13, T:0.45
Consensus pattern (15 bp):
TCGTCGTCTTCATCA
Found at i:804230 original size:18 final size:18
Alignment explanation
Indices: 804186--804232 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
804176 AGGACGTCAC
* *
804186 CATCTTCGTCGTCTTCTT
1 CATCATCGTCGTCTTCAT
804204 CATCATCGTCGTCTTCAT
1 CATCATCGTCGTCTTCAT
* *
804222 CTTCGTCGTCG
1 CATCATCGTCG
804233 GTTTGGAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.34, G:0.15, T:0.43
Consensus pattern (18 bp):
CATCATCGTCGTCTTCAT
Found at i:805292 original size:31 final size:31
Alignment explanation
Indices: 805220--805349 Score: 140
Period size: 31 Copynumber: 4.2 Consensus size: 31
805210 TTCGTTAACT
* * * *
805220 TATTATAAAATTATCACTAAATTTTATTAAAT
1 TATTATAAAATAATCATTAAA-TTTATCAAAC
* * *
805252 TATTA-AAAATGATCCTTAAATTTATCAAAT
1 TATTATAAAATAATCATTAAATTTATCAAAC
*
805282 TA-TAGTAAAATAATCATTATATTTATCAAAC
1 TATTA-TAAAATAATCATTAAATTTATCAAAC
*
805313 TATTATAAAATAATCATGAAATTTATCAAAC
1 TATTATAAAATAATCATTAAATTTATCAAAC
805344 T-TTATA
1 TATTATA
805350 TTCGTGAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
29 2 0.02
30 16 0.19
31 60 0.71
32 7 0.08
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (31 bp):
TATTATAAAATAATCATTAAATTTATCAAAC
Found at i:812648 original size:60 final size:59
Alignment explanation
Indices: 812546--812663 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
812536 ATATCATAAT
* * **
812546 GTTCTAAACTTTTGAATATTTTAATTTTATCATCAAACTATGATATTTATTTTAAATTA
1 GTTCTAAACTTTTGAATATTTTAATTTCATCATCAAAATATGATATGCATTTTAAATTA
* * * *
812605 GTTCTTAAATTTTTGAGTATTTTAATTTCATCCTCAAAATATGATCTGCATTTTAAATT
1 GTTC-TAAACTTTTGAATATTTTAATTTCATCATCAAAATATGATATGCATTTTAAATT
812664 GATCCCCAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 4 0.08
60 46 0.92
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (59 bp):
GTTCTAAACTTTTGAATATTTTAATTTCATCATCAAAATATGATATGCATTTTAAATTA
Found at i:817175 original size:17 final size:17
Alignment explanation
Indices: 817153--817189 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
817143 GTTCGGAGTA
*
817153 GTGACCACTGACGAACG
1 GTGACCACTGACAAACG
*
817170 GTGACCATTGACAAACG
1 GTGACCACTGACAAACG
817187 GTG
1 GTG
817190 GCCGGCGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.16
Consensus pattern (17 bp):
GTGACCACTGACAAACG
Found at i:824677 original size:20 final size:19
Alignment explanation
Indices: 824654--824788 Score: 90
Period size: 20 Copynumber: 6.7 Consensus size: 19
824644 GAATAAGTAA
824654 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
*
824674 ATCGCAATGAGATACTTACT
1 ATCGCAATGCGATAC-TACT
* *
824694 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
824715 ATCGCAACGAGATACTAACT
1 ATCGCAATGCGATACT-ACT
* * *
824735 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACT-ACT
* * * *
824755 TTCGCAACGAGATAATACAT
1 ATCGCAATGCGATACTAC-T
824775 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
824789 TTTCAAAGCA
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
19 5 0.05
20 60 0.66
21 24 0.26
22 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:824729 original size:61 final size:61
Alignment explanation
Indices: 824652--824782 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
824642 GCGAATAAGT
* * * * * * *
824652 AAATCGCAATGCGATACTGACTATCGCAATGAGATACTTACTATCGCAATGCGATAATACA
1 AAATCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGAGATAATACA
* * * *
824713 AAATCGCAACGAGATACTAACTTTCGCAACGCGATTCTGACTTTCGCAACGAGATAATACA
1 AAATCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGAGATAATACA
*
824774 TAATCGCAA
1 AAATCGCAA
824783 TGCGATTTTC
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (61 bp):
AAATCGCAACGAGATACTAACTATCGCAACGAGATACTGACTATCGCAACGAGATAATACA
Found at i:824984 original size:22 final size:22
Alignment explanation
Indices: 824956--824999 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
824946 CACTCTCTCA
824956 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
824978 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
825000 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:825511 original size:25 final size:24
Alignment explanation
Indices: 825457--825511 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
825447 TGTTTATTAT
* *
825457 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
825481 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
825507 TGTTT
1 TGTTT
825512 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:826644 original size:18 final size:18
Alignment explanation
Indices: 826623--826667 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
826613 TCCACTTCGG
*
826623 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
826641 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
826659 GAGCCATCA
1 GAGCCATCA
826668 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:827081 original size:12 final size:13
Alignment explanation
Indices: 827064--827092 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
827054 TTTGTTAGTA
827064 TTTGTTTTTGT-T
1 TTTGTTTTTGTCT
827076 TTTGTTTTTGTCT
1 TTTGTTTTTGTCT
827089 TTTG
1 TTTG
827093 GTTGAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.79
Consensus pattern (13 bp):
TTTGTTTTTGTCT
Found at i:827174 original size:20 final size:20
Alignment explanation
Indices: 827149--827194 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
827139 TAGTTTACTT
*
827149 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
827169 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
827189 TCGCAA
1 TCGCAA
827195 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:827203 original size:19 final size:20
Alignment explanation
Indices: 827160--827215 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
827150 CGCAACATGA
827160 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
827180 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
827199 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
827216 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:827246 original size:19 final size:18
Alignment explanation
Indices: 827188--827251 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
827178 GGAAATGGCT
827188 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAT-AAA
*
827207 ATCGCAA--CG--ACAAA
1 ATCGCAATGCGAAATAAA
827221 ATCGCAATGCGAAATAAA
1 ATCGCAATGCGAAATAAA
827239 AGTCGCAATGCGA
1 A-TCGCAATGCGA
827252 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 5 0.13
19 18 0.47
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATAAA
Found at i:827325 original size:20 final size:19
Alignment explanation
Indices: 827288--827343 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
827278 GTTGCGATTT
* *
827288 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCAATAGC
*
827307 CATTTCCGCGTTGCAATAGT
1 CATTT-CGCGTTGCAATAGC
827327 CATTTTCGCGTTGCAAT
1 CA-TTTCGCGTTGCAAT
827344 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCAATAGC
Found at i:829456 original size:19 final size:19
Alignment explanation
Indices: 829382--829449 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
829372 ATCGCAACGA
829382 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
829401 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
829420 GAAAATCGCAATTCGAAAT
1 GAAAATCGCAATGCGAAAT
829439 GAAAATCGCAA
1 GAAAATCGCAA
829450 CGAGAAAATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.49, C:0.16, G:0.19, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:829509 original size:20 final size:20
Alignment explanation
Indices: 829484--829558 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
829474 TCGCATTGCG
*
829484 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* ***
829504 ATTTTCGCGTTGCGATTTTTC
1 ATTTTCGAGTTGCGA-TAGCC
* *
829525 A-TTTCGAATCGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
829544 ATTTTCTAGTTGCGA
1 ATTTTCGAGTTGCGA
829559 AAGTCAGAAT
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
19 3 0.08
20 33 0.85
21 3 0.08
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:830681 original size:3 final size:3
Alignment explanation
Indices: 830673--830708 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
830663 ATATAATCCT
* *
830673 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
830709 AAAGTCCCCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Done.