Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008117.1 Hibiscus syriacus cultivar Beakdansim tig00110656_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: 1567030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:740124 original size:13 final size:13
Alignment explanation
Indices: 740106--740144 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
740096 ATTTATAATT
740106 TTTTATAATATAA
1 TTTTATAATATAA
* *
740119 TTTTATATTATTA
1 TTTTATAATATAA
740132 TTATTATAATATA
1 TT-TTATAATATA
740145 TAATATTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTATAATATAA
Found at i:740124 original size:27 final size:27
Alignment explanation
Indices: 740077--740144 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
740067 ATAAAAATAT
740077 TAATTATTA-AAT-T-ATATTTAT-TTA
1 TAATTATTATAATATAAT-TTTATATTA
*
740101 TAATTTTTTATAATATAATTTTATATTA
1 TAA-TTATTATAATATAATTTTATATTA
*
740129 TTATTATTATAATATA
1 TAATTATTATAATATA
740145 TAATATTTGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
24 3 0.08
25 5 0.14
26 3 0.08
27 18 0.50
28 7 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TAATTATTATAATATAATTTTATATTA
Found at i:744172 original size:45 final size:46
Alignment explanation
Indices: 744087--744174 Score: 151
Period size: 45 Copynumber: 1.9 Consensus size: 46
744077 AAATAGCTTG
* *
744087 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
744133 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
744175 TTCGATGTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.55
46 18 0.45
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:745353 original size:21 final size:21
Alignment explanation
Indices: 745329--745372 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
745319 GAAAAGGAGG
* *
745329 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
745350 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
745371 AG
1 AG
745373 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:746936 original size:23 final size:22
Alignment explanation
Indices: 746906--746987 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 22
746896 GCATGACCCT
746906 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
746928 CGTGCATCGGTGCATCA-TCAA-G
1 -GTGCATCGATGCA-CATTCAAGG
* *
746950 ATGAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
746973 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
746988 TGTTAAGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
20 2 0.04
21 12 0.25
22 3 0.06
23 17 0.35
24 14 0.29
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:746981 original size:24 final size:23
Alignment explanation
Indices: 746907--746987 Score: 89
Period size: 24 Copynumber: 3.6 Consensus size: 23
746897 CATGACCCTG
746907 TGCATCGATGCACATTCAAGGCG-
1 TGCATCGATGCACATTCAAGG-GA
*
746930 TGCATCGGTGCATCA-TCAA--GA
1 TGCATCGATGCA-CATTCAAGGGA
*
746951 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
746975 TGCATCGATGCAC
1 TGCATCGATGCAC
746988 TGTTAAGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
20 3 0.06
21 12 0.25
22 2 0.04
23 15 0.31
24 16 0.33
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:748277 original size:24 final size:24
Alignment explanation
Indices: 748245--748314 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
748235 ACGAAGATAT
* *
748245 CAGAAATCAAAATAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * *
748269 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAGAACAGAATTCAGAA
*
748293 CAGAAATTAGAACAGAATTCAG
1 CAGAAATCAGAACAGAATTCAG
748315 GTCATGTATC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.51, C:0.16, G:0.16, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:748278 original size:12 final size:11
Alignment explanation
Indices: 748258--748310 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
748248 AAATCAAAAT
748258 AGAATTCAGAAC
1 AGAA-TCAGAAC
748270 AGATATCAGAAC
1 AGA-ATCAGAAC
*
748282 AGAATCCAGATC
1 AGAAT-CAGAAC
*
748294 AGAAATTAGAAC
1 AG-AATCAGAAC
748306 AGAAT
1 AGAAT
748311 TCAGGTCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 5 0.14
12 26 0.74
13 4 0.11
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (11 bp):
AGAATCAGAAC
Found at i:749286 original size:18 final size:19
Alignment explanation
Indices: 749251--749287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
749241 CACAGAATGT
749251 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
749271 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
749288 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:751402 original size:13 final size:13
Alignment explanation
Indices: 751384--751408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
751374 GGTCAACGCC
751384 GGTCAACGGGTCG
1 GGTCAACGGGTCG
751397 GGTCAACGGGTC
1 GGTCAACGGGTC
751409 AGGTTGGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:757630 original size:45 final size:46
Alignment explanation
Indices: 757545--757632 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
757535 AAATAGCCTG
* * *
757545 AGTGCATCGATGCATGGTCTTGTGCATTGATGCATCAAATGCACTA
1 AGTGCACCGATGCATGGTCATGTGCATCGATGCATCAAATGCACTA
*
757591 AGTGCACCGATGCATGGT-ATGTGCATCGATGCATTAAATGCA
1 AGTGCACCGATGCATGGTCATGTGCATCGATGCATCAAATGCA
757633 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (46 bp):
AGTGCACCGATGCATGGTCATGTGCATCGATGCATCAAATGCACTA
Found at i:760025 original size:19 final size:20
Alignment explanation
Indices: 759995--760032 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
759985 AGAAAATATT
759995 TTTTTAACAAATATAATTTA
1 TTTTTAACAAATATAATTTA
*
760015 TTTTTAA-AAATTTAATTT
1 TTTTTAACAAATATAATTT
760033 TTGAAATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTAACAAATATAATTTA
Found at i:763614 original size:65 final size:65
Alignment explanation
Indices: 763509--763694 Score: 300
Period size: 65 Copynumber: 2.9 Consensus size: 65
763499 AAGAGTTAAT
* * * *
763509 AAAATGCTTGGCTAGGTGTGAGAGGCAAACATGGAAGATAGAGCTCATTTTATATTAGAAGTGCC
1 AAAATGCTTGGCTAGCTGTGAGAGGCAAACGTTGACGATAGAGCTCATTTTATATTAGAAGTGCC
* *
763574 AAAATGCTTGGCTAGCTGTGAGAGGCAAACGTTGACGATAGGGCTCATTTTATATTGGAAGTGCC
1 AAAATGCTTGGCTAGCTGTGAGAGGCAAACGTTGACGATAGAGCTCATTTTATATTAGAAGTGCC
* *
763639 AAAATGCTTTGCTAGCTGTGAGAGGCAAACGTTGACGATGGAGCTCATTTTATATT
1 AAAATGCTTGGCTAGCTGTGAGAGGCAAACGTTGACGATAGAGCTCATTTTATATT
763695 GCAAGCGCCA
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 112 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (65 bp):
AAAATGCTTGGCTAGCTGTGAGAGGCAAACGTTGACGATAGAGCTCATTTTATATTAGAAGTGCC
Found at i:764315 original size:25 final size:25
Alignment explanation
Indices: 764250--764325 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 25
764240 TTTAATTTAG
* * *
764250 TAAAATATTAATTAATTTGAGTATT
1 TAAAATATTAATTATTTTTAATATT
*
764275 TAAAATAATTTA-TATTTTTAATATT
1 TAAAAT-ATTAATTATTTTTAATATT
* *
764300 TAATATATTAATTATTTATAAT-TT
1 TAAAATATTAATTATTTTTAATATT
764324 TA
1 TA
764326 TGAGGTAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
24 8 0.19
25 30 0.71
26 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TAAAATATTAATTATTTTTAATATT
Found at i:766073 original size:64 final size:64
Alignment explanation
Indices: 765970--766126 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
765960 GTCAGTGTGT
*
765970 ATCGATGCACAGGAAGTGCATCGATGCA-CCCATTAAAAAT-AGAAACATCGAATGCA-ATTAGT
1 ATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGA-AAACATCGAA-G-AGATTAGT
766032 GC
63 GC
* * *
766034 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTT-AAAATGAAAACATTGAAGATGATTTGTG
1 ATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGA-GATTAGTG
*
766097 T
64 C
* *
766098 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
766127 TTCAAGGGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 68 0.84
65 9 0.11
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (64 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGAGATTAGTGC
Found at i:766509 original size:2 final size:2
Alignment explanation
Indices: 766502--766529 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
766492 GTTGATGTGA
766502 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
766530 GATAAGACAT
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:766988 original size:23 final size:23
Alignment explanation
Indices: 766920--766988 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
766910 CAACCTTATA
*
766920 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGATGCATTTCTACG
* * *
766943 CGGCACTAC-AGTGCAATTCTACG
1 TGGCACTTCGA-TGCATTTCTACG
*
766966 TGGCACTTCGATGCATTTATACG
1 TGGCACTTCGATGCATTTCTACG
766989 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGATGCATTTCTACG
Found at i:770508 original size:64 final size:65
Alignment explanation
Indices: 770405--770561 Score: 185
Period size: 64 Copynumber: 2.4 Consensus size: 65
770395 TTCAGTGTGT
* * *
770405 ATCGATGCACAGGAAGTGCATCGATACA-CCCATTAAAAATGAAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
* * ** *
770469 ATCGATGCATAAGG-AGTGTATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATTTGTG
1 ATCGATGCAT-AGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTG
*
770532 T
65 C
* *
770533 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
770562 TTCAAGGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 69 0.87
65 8 0.10
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (65 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCCATTAAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:771381 original size:23 final size:23
Alignment explanation
Indices: 771348--771415 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
771338 AACCTTATAT
771348 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
771371 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
771394 AGCACTTCGGTGTATTTATACG
1 GGCACTTCGGTGCATTTCTACG
771416 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:784775 original size:20 final size:21
Alignment explanation
Indices: 784738--784777 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
784728 TGAAAAAACG
* *
784738 AGTTTTTTAATTATAATTTTA
1 AGTTTTCTAATTAAAATTTTA
784759 AGTTTTCTAA-TAAAATTTT
1 AGTTTTCTAATTAAAATTTT
784778 TAGAATTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (21 bp):
AGTTTTCTAATTAAAATTTTA
Found at i:788282 original size:8 final size:8
Alignment explanation
Indices: 788269--788305 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
788259 GCTGGCACCA
788269 AAGGTTGT
1 AAGGTTGT
788277 AAGGTTGT
1 AAGGTTGT
788285 AAGGTTGT
1 AAGGTTGT
788293 AAGGTT-T
1 AAGGTTGT
788300 AAGGTT
1 AAGGTT
788306 TGTGTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.35, T:0.38
Consensus pattern (8 bp):
AAGGTTGT
Found at i:790544 original size:43 final size:43
Alignment explanation
Indices: 790478--790586 Score: 168
Period size: 43 Copynumber: 2.6 Consensus size: 43
790468 TACAGAAATG
* **
790478 CACTACCGAAAATGTTAACATTTTTTTAACATTTCCGGTAGAA
1 CACTACCTAAAATGTTATTATTTTTTTAACATTTCCGGTAGAA
*
790521 CACTACTTAAAATGTTATTATTTTTTTAACATTTCCGGTAGAA
1 CACTACCTAAAATGTTATTATTTTTTTAACATTTCCGGTAGAA
790564 CACTACCTAAAATGTT-TT-TTTTT
1 CACTACCTAAAATGTTATTATTTTT
790587 CTCCCGAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 5 0.08
42 2 0.03
43 54 0.89
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (43 bp):
CACTACCTAAAATGTTATTATTTTTTTAACATTTCCGGTAGAA
Found at i:797786 original size:111 final size:108
Alignment explanation
Indices: 797589--797799 Score: 271
Period size: 111 Copynumber: 1.9 Consensus size: 108
797579 TCTTCCTCAT
* * * *
797589 TCTCCTCTTTTCAGTTCCACAAAAAACAAGGATTTACAATATGCACTAATATGCTGGAGTTTTAT
1 TCTCCTCTTTTCAGTTCCACAAAAAACAAAGATTTACAATATGCACCAATATACTAGAGTTTTAT
* *
797654 CTATTAGAGATGAAGAGAACTTCTAACTATAGAAATTGGAGCTATA
66 ATATTAGAGATGAAGAAAAC-T-T-ACTATAGAAATTGGAGCTATA
* * * * *
797700 TCTCCTCTTTTCTA-TTCCTCAAAAAATAAAGATTTACAATTTGTACCGATATACTAGAGTTTTA
1 TCTCCTCTTTTC-AGTTCCACAAAAAACAAAGATTTACAATATGCACCAATATACTAGAGTTTTA
*
797764 TATGTTAGAGATGAAGAAAACTTACTATAGAAATTG
65 TATATTAGAGATGAAGAAAACTTACTATAGAAATTG
797800 AAGTTACAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
108 13 0.15
109 1 0.01
110 1 0.01
111 71 0.82
112 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (108 bp):
TCTCCTCTTTTCAGTTCCACAAAAAACAAAGATTTACAATATGCACCAATATACTAGAGTTTTAT
ATATTAGAGATGAAGAAAACTTACTATAGAAATTGGAGCTATA
Found at i:814590 original size:21 final size:21
Alignment explanation
Indices: 814564--814610 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
814554 ATGTGATAAG
*
814564 GTTTAGGATTTAGGGTTTAAA
1 GTTTAGGATTTAGAGTTTAAA
*
814585 GTTTAGGATTTAGAGTTTAGA
1 GTTTAGGATTTAGAGTTTAAA
814606 GTTTA
1 GTTTA
814611 TATAATGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (21 bp):
GTTTAGGATTTAGAGTTTAAA
Found at i:814623 original size:42 final size:41
Alignment explanation
Indices: 814574--814680 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 41
814564 GTTTAGGATT
*
814574 TAGGGTTTAAAGTTTAGGATTT-AGAGTTTAGAGTTTATATAA
1 TAGGGTTTAAAGTTTAGG-TTTAAGA-TTTAGAGTCTATATAA
* * *
814616 TGGGGTTTAAGGTTTAAGGTTTAAGATTTAGAGTCTATATGA
1 TAGGGTTTAAAGTTT-AGGTTTAAGATTTAGAGTCTATATAA
*
814658 TAGGATTTAAAGTTTAGGGTTTA
1 TAGGGTTTAAAGTTTA-GGTTTA
814681 TGTATTATGG
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 1 0.02
42 48 0.87
43 6 0.11
ACGTcount: A:0.31, C:0.01, G:0.26, T:0.42
Consensus pattern (41 bp):
TAGGGTTTAAAGTTTAGGTTTAAGATTTAGAGTCTATATAA
Found at i:815754 original size:20 final size:19
Alignment explanation
Indices: 815731--815772 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
815721 GCTAGAAGTC
815731 TTCTTAATTAATTGTATGTA
1 TTCTTAATTAATTGTAT-TA
* *
815751 TTCTTATTTTATTGTATTA
1 TTCTTAATTAATTGTATTA
815770 TTC
1 TTC
815773 AGTTTAGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (19 bp):
TTCTTAATTAATTGTATTA
Found at i:822399 original size:35 final size:35
Alignment explanation
Indices: 822324--822403 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
822314 TAAATACGAG
* *
822324 ACATGTCACACTACTATGCATTATCTAAATGTGAC
1 ACATGACACACTACTATGCATTATCTAAATGTAAC
* *
822359 CCATGACACACTACTATGCATTATCTAAATGTAAT
1 ACATGACACACTACTATGCATTATCTAAATGTAAC
822394 ACATGACACA
1 ACATGACACA
822404 TTTGTAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.29
Consensus pattern (35 bp):
ACATGACACACTACTATGCATTATCTAAATGTAAC
Found at i:827433 original size:20 final size:20
Alignment explanation
Indices: 827397--827435 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
827387 TACATTTGGC
*
827397 TATGAAAGTAATGTGAAAGT
1 TATGAAAGTAATATGAAAGT
827417 TATGACAAGT-ATATGAAAG
1 TATGA-AAGTAATATGAAAG
827436 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.28
Consensus pattern (20 bp):
TATGAAAGTAATATGAAAGT
Found at i:829347 original size:40 final size:40
Alignment explanation
Indices: 829278--829360 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
829268 CCTGGCCTGA
*
829278 CCTATTTAGTAAAAAGGCCAGGCTCAGGCCT-TTTAAAAG
1 CCTATTTAGTAAAAAGGCCAGGCTCAGGCCTATTAAAAAG
* * * *
829317 CCTATTTAATTAAACAGGCCATGCTTAGGCCTATTAAAAAG
1 CCTATTT-AGTAAAAAGGCCAGGCTCAGGCCTATTAAAAAG
829358 CCT
1 CCT
829361 TATAAGCCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 7 0.19
40 20 0.54
41 10 0.27
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (40 bp):
CCTATTTAGTAAAAAGGCCAGGCTCAGGCCTATTAAAAAG
Found at i:829533 original size:12 final size:12
Alignment explanation
Indices: 829484--829514 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
829474 ATGTTTATTG
829484 TTAAACAGGCTT
1 TTAAACAGGCTT
*
829496 TTAAACATGCTT
1 TTAAACAGGCTT
829508 TTAAACA
1 TTAAACA
829515 AGTCAGGCTT
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:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (12 bp):
TTAAACAGGCTT
Found at i:829538 original size:17 final size:17
Alignment explanation
Indices: 829504--829539 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
829494 TTTTAAACAT
*
829504 GCTTTTAAACAAGTCAG
1 GCTTTTAAACAAGCCAG
*
829521 GCTTTTAAACAGGCCAG
1 GCTTTTAAACAAGCCAG
829538 GC
1 GC
829540 CAGGCCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (17 bp):
GCTTTTAAACAAGCCAG
Found at i:830182 original size:15 final size:15
Alignment explanation
Indices: 830157--830196 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
830147 GTTAAACAGA
830157 AAATGAG-AAGAAGG
1 AAATGAGAAAGAAGG
*
830171 AAATGAGAAAGAATG
1 AAATGAGAAAGAAGG
830186 AAATGAAGAAA
1 AAATG-AGAAA
830197 TAAAGACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 11 0.48
16 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (15 bp):
AAATGAGAAAGAAGG
Found at i:832835 original size:2 final size:2
Alignment explanation
Indices: 832828--832864 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
832818 TAAAAATAAT
832828 TA TA TA TA TA 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 TA TA TA TA TA T
832865 TTTTGTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:835141 original size:22 final size:22
Alignment explanation
Indices: 835092--835134 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
835082 ATATTTATAA
* *
835092 TAAAAAATAAAAAGATATTCAT
1 TAAAAAATAAAAAGAAATTAAT
835114 TAAAAAATAAAAA-AAATTAAT
1 TAAAAAATAAAAAGAAATTAAT
835135 CTCAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TAAAAAATAAAAAGAAATTAAT
Found at i:837280 original size:46 final size:46
Alignment explanation
Indices: 837213--837332 Score: 159
Period size: 46 Copynumber: 2.6 Consensus size: 46
837203 TATCGATTAG
* * * *
837213 TTTCGATTCGGGTGAAGCTTTAGATTTTTGGGTCAATTTGGGTTGA
1 TTTCGATTCGGATCAAACTTTAGATTTTTGGGTCAATTCGGGTTGA
* * * *
837259 TTTCGGTTCGGATCAAACTTTAAAATTTTGGGTCAATTCGGGTTGG
1 TTTCGATTCGGATCAAACTTTAGATTTTTGGGTCAATTCGGGTTGA
*
837305 TTTCGATTCGGATCAACCTTTAGATTTT
1 TTTCGATTCGGATCAAACTTTAGATTTT
837333 CGACTTAATT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (46 bp):
TTTCGATTCGGATCAAACTTTAGATTTTTGGGTCAATTCGGGTTGA
Found at i:837564 original size:16 final size:16
Alignment explanation
Indices: 837485--837567 Score: 57
Period size: 16 Copynumber: 5.1 Consensus size: 16
837475 GGTAAATTAA
* *
837485 TTCGAGTTGCTTTCAG
1 TTCGAGTTGATTTCGG
*
837501 TTTGAGTT-ATTTTCGG
1 TTCGAGTTGA-TTTCGG
837517 TTC-AGGTT-ATTTTCGG
1 TTCGA-GTTGA-TTTCGG
*
837533 TTTG-GTTTGAATTTCGG
1 TTCGAG-TTG-ATTTCGG
837550 TTCGAGTTGATTTCGG
1 TTCGAGTTGATTTCGG
837566 TT
1 TT
837568 ATGGTTGGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.04
16 38 0.70
17 12 0.22
18 2 0.04
ACGTcount: A:0.12, C:0.11, G:0.27, T:0.51
Consensus pattern (16 bp):
TTCGAGTTGATTTCGG
Found at i:837574 original size:16 final size:16
Alignment explanation
Indices: 837527--837574 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
837517 TTCAGGTTAT
837527 TTTCGGTTTGGTTTGAA
1 TTTCGGTTTGG-TTGAA
*
837544 TTTCGGTTCGAGTTG-A
1 TTTCGGTTTG-GTTGAA
837560 TTTCGGTTATGGTTG
1 TTTCGGTT-TGGTTG
837575 GTTTTTTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 13 0.48
17 13 0.48
18 1 0.04
ACGTcount: A:0.10, C:0.08, G:0.31, T:0.50
Consensus pattern (16 bp):
TTTCGGTTTGGTTGAA
Found at i:838073 original size:3 final size:3
Alignment explanation
Indices: 838067--838096 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
838057 CTTGATGATG
838067 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
838097 TACAAAGAGT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:838489 original size:18 final size:19
Alignment explanation
Indices: 838461--838497 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
838451 GCAAACCAAA
838461 CAGGCTAATACAACATTCC
1 CAGGCTAATACAACATTCC
838480 CAGG-TAATACAACATTCC
1 CAGGCTAATACAACATTCC
838498 TAGAGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.22
Consensus pattern (19 bp):
CAGGCTAATACAACATTCC
Found at i:839702 original size:22 final size:21
Alignment explanation
Indices: 839659--839711 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
839649 TGTATGAACA
839659 GTATCGATACCATAAGGAAGGG
1 GTATCGATACCATAAGGAA-GG
* *
839681 GTATCGATACC-TATGTGTAGG
1 GTATCGATACCATAAG-GAAGG
839702 GTATCGATAC
1 GTATCGATAC
839712 TAGGGAACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (21 bp):
GTATCGATACCATAAGGAAGG
Found at i:841395 original size:16 final size:16
Alignment explanation
Indices: 841374--841404 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
841364 ATTACATTTC
841374 TTTTATTAGTTAATTA
1 TTTTATTAGTTAATTA
*
841390 TTTTATTATTTAATT
1 TTTTATTAGTTAATT
841405 TATACTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTATTAGTTAATTA
Found at i:841848 original size:50 final size:50
Alignment explanation
Indices: 841789--841913 Score: 171
Period size: 49 Copynumber: 2.5 Consensus size: 50
841779 GTAGCAGTAA
* * *
841789 AGCGCGCCCCCTGAACCGCGTTATACGCTGATTTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCACCACGTGGGTAT
** *
841839 AGCGCG-CCCCTGCCCCGCGATATACGGTGATCTGGCACCACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCACCACGTGGGTAT
* *
841888 AGCGCGCCCCCTGATCCGCGCTATAC
1 AGCGCGCCCCCTGAACCGCGATATAC
841914 ATGGGTATCT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 43 0.66
50 22 0.34
ACGTcount: A:0.16, C:0.36, G:0.29, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCACCACGTGGGTAT
Found at i:842040 original size:10 final size:10
Alignment explanation
Indices: 842025--842064 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
842015 TTTATCACAC
842025 CAAATTCTCT
1 CAAATTCTCT
842035 CAAATTCTCT
1 CAAATTCTCT
842045 -AAATTTCTCT
1 CAAA-TTCTCT
*
842055 CAAATACTCT
1 CAAATTCTCT
842065 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:842394 original size:105 final size:108
Alignment explanation
Indices: 842187--842509 Score: 532
Period size: 105 Copynumber: 3.0 Consensus size: 108
842177 GATGGAAATC
*
842187 ATATCTCTACACTTT-CTGATACGGTAACA-TTAACGTTTTAATTTAATTTAAATTATTAGTAAT
1 ATATCTCGACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAA-
842250 ATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 A-TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
842295 ATATCTCGACACTTTGCTGATACGGTAACATTTAAC-ATTTAA-TTAATTTAAATTATTAGTAAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAAA
842358 TTA-TTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
842400 ATATCTCGACACTTTG-TGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACA-TTTAACGTTTTAATTTAATTTAAATTATTAGT-A
*
842464 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
64 -AATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
842510 TTTTTGTAAT
Statistics
Matches: 203, Mismatches: 4, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
104 13 0.06
105 61 0.30
106 8 0.04
107 19 0.09
108 35 0.17
109 24 0.12
110 43 0.21
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.44
Consensus pattern (108 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTAACGTTTTAATTTAATTTAAATTATTAGTAAA
TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:844364 original size:6 final size:6
Alignment explanation
Indices: 844347--844403 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
844337 TGCTCAGGAC
* * * * * *
844347 GACGAC GACGAT GACGAT GATGAT GATGGT GACGAT GACGAC AACGAT
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
*
844395 GATGAT GAC
1 GACGAT GAC
844404 AGCGAGGAGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.33, T:0.18
Consensus pattern (6 bp):
GACGAT
Found at i:844395 original size:24 final size:24
Alignment explanation
Indices: 844353--844403 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
844343 GGACGACGAC
** * *
844353 GACGATGACGATGATGATGATGGT
1 GACGATGACGACAACGATGATGAT
844377 GACGATGACGACAACGATGATGAT
1 GACGATGACGACAACGATGATGAT
844401 GAC
1 GAC
844404 AGCGAGGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (24 bp):
GACGATGACGACAACGATGATGAT
Found at i:848379 original size:50 final size:50
Alignment explanation
Indices: 848298--848425 Score: 141
Period size: 50 Copynumber: 2.6 Consensus size: 50
848288 CCCCTACGTG
* * * * *
848298 GCGTATAGCGC-GGATCAGGGGGCGCATTATACCCACGTGGCGTCAGATCA
1 GCGTATAGCGCGGGA-CAGGGGGCACACTATACCCACGTAGCGCCAAATCA
* * *
848348 TCGTATATCGCGGGACAGGGGGCACGCTATACCCACGTAGCGCCAAATCA
1 GCGTATAGCGCGGGACAGGGGGCACACTATACCCACGTAGCGCCAAATCA
** *
848398 GCGTATAGCGCGGTTCAGGGGGCGCACT
1 GCGTATAGCGCGGGACAGGGGGCACACT
848426 TTACTGCTAC
Statistics
Matches: 63, Mismatches: 14, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
50 60 0.95
51 3 0.05
ACGTcount: A:0.22, C:0.27, G:0.34, T:0.17
Consensus pattern (50 bp):
GCGTATAGCGCGGGACAGGGGGCACACTATACCCACGTAGCGCCAAATCA
Found at i:853817 original size:40 final size:39
Alignment explanation
Indices: 853773--853909 Score: 126
Period size: 38 Copynumber: 3.6 Consensus size: 39
853763 TTATTTTATT
853773 ATATAAATATATATTATATAG-TTTGCAAATGATTTTTGAA
1 ATAT-AATATATATTATATAGTTTTG-AAATGATTTTTGAA
*
853813 ATAT-ATATATAATATATAGTTTTGAAAATGATTTTT-AA
1 ATATAATATATATTATATAGTTTTG-AAATGATTTTTGAA
* * * *
853851 AAAT-GTGTATATTATATAGTTTTGAAATCA-TTTTGAA
1 ATATAATATATATTATATAGTTTTGAAATGATTTTTGAA
** *
853888 A-A-CCTATATAATATATAGTTTT
1 ATATAATATATATTATATAGTTTT
853910 TTTAAAAAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
36 21 0.25
37 8 0.10
38 36 0.43
39 15 0.18
40 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (39 bp):
ATATAATATATATTATATAGTTTTGAAATGATTTTTGAA
Found at i:853830 original size:38 final size:37
Alignment explanation
Indices: 853779--854166 Score: 226
Period size: 36 Copynumber: 10.4 Consensus size: 37
853769 TATTATATAA
*
853779 ATATATATTATATAG-TTTGCAAATGATTTTTGAAATAT
1 ATATATAATATATAGTTTTG-AAATGATTTTTGAAA-AT
*
853817 ATATATAATATATAGTTTTGAAAATGATTTTTAAAAAT
1 ATATATAATATATAGTTTTG-AAATGATTTTTGAAAAT
* * * * *
853855 GTGTATATTATATAGTTTTGAAATCA-TTTTGAAAAC
1 ATATATAATATATAGTTTTGAAATGATTTTTGAAAAT
* * ** *
853891 CTATATAATATATAGTTTTTTTAAAAAAAAAGTTTTGAAAAT
1 ATATATAATATATAG---TTTT--GAAATGATTTTTGAAAAT
* **
853933 ATATATAATATATAGTTTTTAAAACA-TTTTGAAAACT
1 ATATATAATATATAGTTTTGAAATGATTTTTGAAAA-T
* * * *
853970 -TATATAATATATGGGTTTTTAAA-AACATTTTGAAAAT
1 ATATATAATATAT-AGTTTTGAAATGA-TTTTTGAAAAT
* **
854007 ATATATAATATATAGTTTTTTAAAACA-TTTTGAAAACT
1 ATATATAATATATAG-TTTTGAAATGATTTTTGAAAA-T
* ** *
854045 -TATATAATATATAG-TTTAAAAAAACTTTTTAAAAAT
1 ATATATAATATATAGTTTTGAAATGA-TTTTTGAAAAT
* * * * **
854081 ATATATATTATATAATTTTTAAA-AACAATTTGAAAA-
1 ATATATAATATATAGTTTTGAAATGA-TTTTTGAAAAT
*
854117 CTATATAATATATAGTTTTGAAA--ACTTTTT-AAAATT
1 ATATATAATATATAGTTTTGAAATGA-TTTTTGAAAA-T
*
854153 TTATATAATATATA
1 ATATATAATATATA
854167 TGTAGACACC
Statistics
Matches: 290, Mismatches: 39, Indels: 44
0.78 0.10 0.12
Matches are distributed among these distances:
34 4 0.01
35 13 0.04
36 75 0.26
37 75 0.26
38 69 0.24
39 27 0.09
41 4 0.01
42 23 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAATGATTTTTGAAAAT
Found at i:854068 original size:74 final size:73
Alignment explanation
Indices: 853818--854166 Score: 378
Period size: 74 Copynumber: 4.7 Consensus size: 73
853808 TTGAAATATA
** ** * * * * *
853818 TATATAATATATAGTTTTGAAAATGATTTTTAAAAATGTGTATATTATATAGTTTTGAAATCATT
1 TATATAATATATAGTTTAAAAAAACA-TTTTAAAAATATATATAATATATAGTTTTTAAAACATT
*
853883 TTGAAAACC
65 TTGAAAACT
* *
853892 TATATAATATATAGTTTTTTTAAAAAAAAAGTTTTGAAAATATATATAATATATAGTTTTTAAAA
1 TATATAATATATAG----TTTAAAAAAACA-TTTTAAAAATATATATAATATATAGTTTTTAAAA
853957 CATTTTGAAAACT
61 CATTTTGAAAACT
* ** *
853970 TATATAATATATGGGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTTTAAAACAT
1 TATATAATATAT-AGTTTAAAAAAACATTTTAAAAATATATATAATATATAG-TTTTTAAAACAT
854035 TTTGAAAACT
64 TTTGAAAACT
* * * *
854045 TATATAATATATAGTTTAAAAAAACTTTTTAAAAATATATATATTATATAATTTTTAAAAACAAT
1 TATATAATATATAGTTTAAAAAAACATTTTAAAAATATATATAATATATAGTTTTT-AAAACATT
854110 TTGAAAAC-
65 TTGAAAACT
** * * *
854118 TATATAATATATAGTTT-TGAAAACTTTTTAAAATTTTATATAATATATA
1 TATATAATATATAGTTTAAAAAAACATTTTAAAAATATATATAATATATA
854167 TGTAGACACC
Statistics
Matches: 239, Mismatches: 29, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
72 27 0.11
73 22 0.09
74 86 0.36
75 43 0.18
78 60 0.25
79 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (73 bp):
TATATAATATATAGTTTAAAAAAACATTTTAAAAATATATATAATATATAGTTTTTAAAACATTT
TGAAAACT
Found at i:854215 original size:14 final size:13
Alignment explanation
Indices: 854198--854246 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 13
854188 TGGTTATAAA
854198 TATTATATTATAGT
1 TATTATATTATA-T
854212 TATTACTATTATAT
1 TATTA-TATTATAT
854226 TATTATATTATTAT
1 TATTATATTA-TAT
854240 TATTATA
1 TATTATA
854247 ACAATTATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.15
14 21 0.64
15 7 0.21
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATATTATAT
Found at i:854231 original size:3 final size:3
Alignment explanation
Indices: 854198--854277 Score: 53
Period size: 3 Copynumber: 27.7 Consensus size: 3
854188 TGGTTATAAA
*
854198 TAT TA- TAT TA- TAGT TAT TAC TAT TA- TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
854240 TAT TAT AAC AAT TA- TAT TAAT AAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TA
854278 ATATCAGGTA
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
2 10 0.17
3 46 0.77
4 4 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:861416 original size:3 final size:3
Alignment explanation
Indices: 861408--861445 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
861398 CTTTAGTATT
*
861408 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GATA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA G
861446 GCCTTGGTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:862583 original size:9 final size:9
Alignment explanation
Indices: 862562--862643 Score: 57
Period size: 8 Copynumber: 8.8 Consensus size: 9
862552 CTTAAAGATA
862562 AAAAAAATG
1 AAAAAAATG
862571 --AAAAATG
1 AAAAAAATG
862578 AAAAAAAAATG
1 --AAAAAAATG
862589 AAAAAAATG
1 AAAAAAATG
862598 -AAAAAATG
1 AAAAAAATG
862606 AAATAGAAAAAT-
1 --A-A-AAAAATG
862618 AGAAAAAATGG
1 A-AAAAAAT-G
862629 AAAAAAAT-
1 AAAAAAATG
862637 AAAAAAA
1 AAAAAAA
862644 AAAGAAGAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 23
0.72 0.01 0.27
Matches are distributed among these distances:
7 7 0.11
8 15 0.25
9 15 0.25
10 9 0.15
11 8 0.13
12 1 0.02
13 6 0.10
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAAATG
Found at i:862644 original size:9 final size:9
Alignment explanation
Indices: 862559--862684 Score: 62
Period size: 9 Copynumber: 13.7 Consensus size: 9
862549 TTGCTTAAAG
862559 ATAAAAAAA
1 ATAAAAAAA
**
862568 ATGAAAAATG
1 AT-AAAAAAA
862578 A-AAAAAAA
1 ATAAAAAAA
*
862586 ATGAAAAAA
1 ATAAAAAAA
862595 ATGAAAAAATGA
1 AT-AAAAAA--A
*
862607 A-ATAGAAAA
1 ATA-AAAAAA
*
862616 ATAGAAAAA
1 ATAAAAAAA
*
862625 ATGGAAAAAA
1 AT-AAAAAAA
862635 ATAAAAAAA
1 ATAAAAAAA
*
862644 A-AAGAAGAA
1 ATAA-AAAAA
*
862653 A-AAAAGAA
1 ATAAAAAAA
**
862661 GGAAAAAAA
1 ATAAAAAAA
*
862670 ACAAAAAAA
1 ATAAAAAAA
862679 ATAAAA
1 ATAAAA
862685 GGGGGTTCAA
Statistics
Matches: 89, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
8 13 0.15
9 50 0.56
10 20 0.22
11 4 0.04
12 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.11, T:0.09
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:862653 original size:39 final size:39
Alignment explanation
Indices: 862582--862660 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
862572 AAAATGAAAA
* * *
862582 AAAAATGAAAAAAATGAAAAAATGAAATAGAAAAATAGA
1 AAAAATGAAAAAAATGAAAAAATAAAAAAGAAAAAAAGA
862621 AAAAATGGAAAAAAAT-AAAAAA-AAAAGAAGAAAAAAAGA
1 AAAAAT-GAAAAAAATGAAAAAATAAAA-AAGAAAAAAAGA
862660 A
1 A
862661 GGAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 3 0.09
39 23 0.66
40 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (39 bp):
AAAAATGAAAAAAATGAAAAAATAAAAAAGAAAAAAAGA
Found at i:862686 original size:24 final size:24
Alignment explanation
Indices: 862639--862686 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
862629 AAAAAAATAA
* *
862639 AAAAAAAAGAAGAAAAAAAGAAGG
1 AAAAAAAACAAGAAAAAAAAAAGG
862663 AAAAAAAACAA-AAAAAATAAAAGG
1 AAAAAAAACAAGAAAAAA-AAAAGG
862687 GGGTTCAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAAAACAAGAAAAAAAAAAGG
Found at i:863921 original size:55 final size:55
Alignment explanation
Indices: 863837--864227 Score: 610
Period size: 55 Copynumber: 7.2 Consensus size: 55
863827 TGAAGCAAAA
* *
863837 GAAGATTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
863892 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
863947 GAAGATT-GTGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
864000 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGAT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
864055 GAAGATT-GTGGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
864108 GAAGATTGTTCGAGTCTTATACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
864163 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
864218 GGAGATTATT
1 GAAGATTATT
864228 GTTCGAGTTC
Statistics
Matches: 306, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
53 91 0.30
54 12 0.04
55 203 0.66
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (55 bp):
GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:864040 original size:108 final size:108
Alignment explanation
Indices: 863851--864227 Score: 682
Period size: 108 Copynumber: 3.5 Consensus size: 108
863841 ATTGTTCAAG
863851 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
1 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
863916 TCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGA
66 TCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGA
863959 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
1 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
*
864024 TCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATTGTGGA
66 TCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGA
*
864067 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTATACTC
1 TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
* * *
864132 TCTGAATAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTCGA
66 TCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTG-TGGA
*
864176 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTATT
1 -TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
864228 GTTCGAGTTC
Statistics
Matches: 259, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
108 207 0.80
109 3 0.01
110 49 0.19
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATTCGAGTCTTATACTC
TCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGA
Found at i:864128 original size:163 final size:163
Alignment explanation
Indices: 863837--864225 Score: 620
Period size: 163 Copynumber: 2.4 Consensus size: 163
863827 TGAAGCAAAA
* * *
863837 GAAGATTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTAGT
* *
863902 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGATGAAGATTGTGGATCTTATAC
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTCGATCTTATAC
863967 TCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
131 TCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
864000 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACACGATTGATGAAGATT-GT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTAGT
* *
864064 GGA-TCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGAAGATTGTTCGAGTCTTAT
66 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTG-TCGA-TCTTAT
* *
864128 ACTCTCTGAATAAATAGGGGGCAGACGCGATTGTT
129 ACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
864163 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTTGGAGATTA
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTA
864226 TTGTTCGAGT
Statistics
Matches: 206, Mismatches: 17, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
161 47 0.23
162 6 0.03
163 153 0.74
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (163 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTAGT
CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGATGAAGATTGTCGATCTTATAC
TCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:864280 original size:52 final size:52
Alignment explanation
Indices: 864220--864824 Score: 1021
Period size: 52 Copynumber: 11.6 Consensus size: 52
864210 CGATCGTTGG
864220 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
** *
864272 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCATTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
864324 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
864376 AAATTATTGTTCGAGTTCTAGTCCTTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
864428 AGATTATTTTTCGAGTTCTAGTCCCTGAAGAAAATTAGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
864480 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
864532 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
*
864584 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAAGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
864636 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
864688 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* * *
864740 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGCAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
* *
864792 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
864825 TAGAGAGCGA
Statistics
Matches: 524, Mismatches: 29, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 524 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
Found at i:864354 original size:28 final size:28
Alignment explanation
Indices: 864270--864354 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
864260 AGACCCGTAG
864270 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
** ** * **
864298 GAAGAAAATTGGGC-A-TTCTCGT--AG
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
864322 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGATTATTGTTCGAGTTCTAGTCCCT
864350 GAAGA
1 GAAGA
864355 AAATTGGGCA
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
24 10 0.26
25 1 0.03
26 12 0.31
27 1 0.03
28 15 0.38
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (28 bp):
GAAGATTATTGTTCGAGTTCTAGTCCCT
Found at i:864360 original size:28 final size:28
Alignment explanation
Indices: 864225--864360 Score: 78
Period size: 28 Copynumber: 5.1 Consensus size: 28
864215 GTTGGAGATT
864225 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
* **
864253 ATTG---G-G--C-AGACCCGTAGGAAGATT
1 ATTGTTCGAGTTCTAGTCCC-T--GAAGAAA
864277 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
** * ** **
864305 ATTGGGC-A-TTCTCGT--AGGAAGATT
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
864329 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
1 ATTGTTCGAGTTCTAGTCCCTGAAGAAA
864357 ATTG
1 ATTG
864361 GGCAGACCCG
Statistics
Matches: 74, Mismatches: 20, Indels: 28
0.61 0.16 0.23
Matches are distributed among these distances:
21 5 0.07
22 2 0.03
24 20 0.27
25 2 0.03
26 12 0.16
27 2 0.03
28 24 0.32
30 2 0.03
31 5 0.07
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (28 bp):
ATTGTTCGAGTTCTAGTCCCTGAAGAAA
Found at i:865142 original size:5 final size:5
Alignment explanation
Indices: 865081--865123 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
865071 CTGGTTATAA
*
865081 ATATT ATATT ATAGT -TATT ACTATT ATATT ATATT ATTATT AT
1 ATATT ATATT ATATT ATATT A-TATT ATATT ATATT A-TATT AT
865124 TATAAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 20 0.61
6 10 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
ATATT
Found at i:867606 original size:9 final size:10
Alignment explanation
Indices: 867561--867608 Score: 59
Period size: 9 Copynumber: 5.1 Consensus size: 10
867551 AGTTTTAAAA
867561 TATT-TTTAT
1 TATTATTTAT
867570 TATTA-TTAT
1 TATTATTTAT
867579 TATTATTTAT
1 TATTATTTAT
867589 T-TTATTTTAT
1 TATTA-TTTAT
867599 T-TTATTTAT
1 TATTATTTAT
867608 T
1 T
867609 GTGGTCCAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 22 0.61
10 14 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TATTATTTAT
Found at i:868795 original size:11 final size:11
Alignment explanation
Indices: 868779--868816 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
868769 TTTCCCTTTG
868779 ATTTATTTATT
1 ATTTATTTATT
868790 ATTTATTTATTT
1 ATTTATTTA-TT
868802 ATTGTATTT-TT
1 ATT-TATTTATT
868813 ATTT
1 ATTT
868817 TCTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 14 0.56
12 5 0.20
13 5 0.20
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:868867 original size:63 final size:62
Alignment explanation
Indices: 868730--868874 Score: 154
Period size: 62 Copynumber: 2.3 Consensus size: 62
868720 TATTTCATGT
* * * * *
868730 TTTTTC-TTTGATTTATTTTTTTTTTTTTTTTATATTTTGTTTCCCTTTGATTTATTTATTA
1 TTTTTCATTTTATTTATTTTTTTTTCTTTTTTATACTTTGTTTCCATTTGATTTATTTAATA
* *
868791 TTTATTTA-TTTATTGTATTTTTATTTTCTTTTTTCTACTTT-TTT-CATTTGATTTATTTAATA
1 TTT-TTCATTTTATT-TATTTTT-TTTTCTTTTTTATACTTTGTTTCCATTTGATTTATTTAATA
868853 TGTTTTCATTTTATTTTATTTT
1 T-TTTTCATTTTA-TTTATTTT
868875 CTTTCCCTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
61 3 0.04
62 27 0.39
63 22 0.32
64 17 0.25
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.74
Consensus pattern (62 bp):
TTTTTCATTTTATTTATTTTTTTTTCTTTTTTATACTTTGTTTCCATTTGATTTATTTAATA
Found at i:868898 original size:33 final size:36
Alignment explanation
Indices: 868861--868943 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
868851 TATGTTTTCA
868861 TTTTATTTTATTT-TCTTT-CCCTTTGATTTATT-T
1 TTTTATTTTATTTATCTTTGCCCTTTGATTTATTAT
* * *
868894 TTTTAATTTATTTTATTTTTGCCTTTTGATTTATTAT
1 TTTTATTTTA-TTTATCTTTGCCCTTTGATTTATTAT
*
868931 TATTATTATTATT
1 TTTTATT-TTATT
868944 ATTTATTCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 9 0.22
34 3 0.08
35 4 0.10
36 13 0.32
37 8 0.20
38 3 0.08
ACGTcount: A:0.18, C:0.07, G:0.04, T:0.71
Consensus pattern (36 bp):
TTTTATTTTATTTATCTTTGCCCTTTGATTTATTAT
Found at i:869008 original size:18 final size:17
Alignment explanation
Indices: 868969--869001 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
868959 TTTAATCTTT
868969 TTTTCTTATTGTTTTTA
1 TTTTCTTATTGTTTTTA
868986 TTTTCTTATTGTTTTT
1 TTTTCTTATTGTTTTT
869002 TCCTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTCTTATTGTTTTTA
Found at i:870675 original size:38 final size:41
Alignment explanation
Indices: 870591--870675 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 41
870581 ACTTACAACT
* * *
870591 ATTTATTTATTTTTATTTAAAATATAAGTATTAATATTGTTT
1 ATTTATTTATTTTTATCTAAAATATAAGTA-TAATATTGCTA
870633 ATTTATTTATTTTATATCTAAAA-ATAAG-A-AATA-TGCTA
1 ATTTATTTATTTT-TATCTAAAATATAAGTATAATATTGCTA
870671 ATTTA
1 ATTTA
870676 CTATTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
38 8 0.21
39 4 0.10
41 1 0.03
42 18 0.46
43 8 0.21
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (41 bp):
ATTTATTTATTTTTATCTAAAATATAAGTATAATATTGCTA
Found at i:872245 original size:15 final size:15
Alignment explanation
Indices: 872219--872270 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
872209 TAGTTAAAAT
872219 TATTTT-ATATTTTA
1 TATTTTAATATTTTA
*
872233 TATTTTAATATTTAA
1 TATTTTAATATTTTA
*
872248 TATATTAATCATTTTA
1 TATTTTAAT-ATTTTA
*
872264 TAATTTA
1 TATTTTA
872271 TGAGATGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:872269 original size:8 final size:7
Alignment explanation
Indices: 872219--872271 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
872209 TAGTTAAAAT
872219 TATTTTA
1 TATTTTA
872226 TATTTTA
1 TATTTTA
872233 TATTTTAA
1 TATTTT-A
*
872241 TATTTAA
1 TATTTTA
*
872248 TATATTAA
1 TAT-TTTA
872256 TCATTTTA
1 T-ATTTTA
*
872264 TAATTTA
1 TATTTTA
872271 T
1 T
872272 GAGATGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
7 23 0.57
8 15 0.38
9 2 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (7 bp):
TATTTTA
Found at i:873801 original size:2 final size:2
Alignment explanation
Indices: 873794--873841 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
873784 TTTCATTCGC
873794 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
873836 AT AT AT
1 AT AT AT
873842 CATGCTAAAT
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):
AT
Found at i:875982 original size:73 final size:73
Alignment explanation
Indices: 875884--876021 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 73
875874 AAGTGTGCAT
*
875884 AAATAAATTTTTAGGGTAGAAACCAT-TAATAAAT-CGATCACTAATCGAAGAAAATTCAGATTT
1 AAATAAATTTTTAGGGTAGAAACCATCT-ATAAATACG-TCACTAATCAAAGAAAATTCAGATTT
875947 CAAGGTGGAC
64 CAAGGTGGAC
* * * *
875957 AAATGAAA-TTTTAGGGTGGACACCATCTATAAATATGTGACTAATCAAAGAAAATTCAGATTTC
1 AAAT-AAATTTTTAGGGTAGAAACCATCTATAAATACGTCACTAATCAAAGAAAATTCAGATTTC
876021 A
65 A
876022 GGTTTTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
73 52 0.91
74 5 0.09
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (73 bp):
AAATAAATTTTTAGGGTAGAAACCATCTATAAATACGTCACTAATCAAAGAAAATTCAGATTTCA
AGGTGGAC
Found at i:877384 original size:105 final size:104
Alignment explanation
Indices: 877242--877649 Score: 656
Period size: 105 Copynumber: 3.9 Consensus size: 104
877232 AAAATTGAGT
* * *
877242 AAGTTCTTCTCATTATGAACTTCCTCCTCTAACG-TGAGTTCTTCTCATTATGAACTCTTCTGGA
1 AAGTTCTTCTCATTATGAACTTTCTCCTTTAA-GACGAGTTCTTCTCATTATGAACTCTTCTGGA
877306 AATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAAGAAAC
65 AATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAAG-AAC
**
877347 AAGTTCTTCTCATTATGAACTTTCTCCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
1 AAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
* *
877412 ATGTTGGTTCACCTGCTTATGTGGTGGATTTGAAAGAAC
66 ATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAAGAAC
*
877451 AAGTTCTTATCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
1 AAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
* * * *
877516 ATGTTAGTTCACTTCCTTCTACGGTGGATTTGAAAGGAAC
66 ATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAA-GAAC
*
877556 ATGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
1 AAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
*
877621 ATGTTGGTTCACCTCCTTCTGCGGTGGAT
66 ATGTTGGTTCACCTCCTTATGCGGTGGAT
877650 CATAGTTGTT
Statistics
Matches: 283, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
104 95 0.34
105 188 0.66
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (104 bp):
AAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAA
ATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAAGAAC
Found at i:877602 original size:209 final size:209
Alignment explanation
Indices: 877242--877649 Score: 665
Period size: 209 Copynumber: 2.0 Consensus size: 209
877232 AAAATTGAGT
* *
877242 AAGTTCTTCTCATTATGAACTTCCTCCTCTAACGTGAGTTCTTCTCATTATGAACTCTTCTGGAA
1 AAGTTCTTATCATTATGAACTTCCTCCTCTAACGCGAGTTCTTCTCATTATGAACTCTTCTGGAA
* *
877307 ATGTTGGTTCACCTCCTTATGCGGTGGATTTGAAAGAAACAAGTTCTTCTCATTATGAACTTTCT
66 ATGTTAGTTCACCTCCTTATACGGTGGATTTGAAAGAAACAAGTTCTTCTCATTATGAACTTTCT
** * *
877372 CCTTTAAGGTGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTGCTTATGTGGT
131 CCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTATGCGGT
877437 GGATTTGAAAGAAC
196 GGATTTGAAAGAAC
* *
877451 AAGTTCTTATCATTATGAACTTTCTCCTTTAA-GACGAGTTCTTCTCATTATGAACTCTTCTGGA
1 AAGTTCTTATCATTATGAACTTCCTCCTCTAACG-CGAGTTCTTCTCATTATGAACTCTTCTGGA
* * * *
877515 AATGTTAGTTCACTTCCTTCTACGGTGGATTTGAAAGGAACATGTTCTTCTCATTATGAACTTTC
65 AATGTTAGTTCACCTCCTTATACGGTGGATTTGAAAGAAACAAGTTCTTCTCATTATGAACTTTC
*
877580 TCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGG
130 TCCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTATGCGG
877645 TGGAT
195 TGGAT
877650 CATAGTTGTT
Statistics
Matches: 183, Mismatches: 15, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
208 1 0.01
209 182 0.99
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (209 bp):
AAGTTCTTATCATTATGAACTTCCTCCTCTAACGCGAGTTCTTCTCATTATGAACTCTTCTGGAA
ATGTTAGTTCACCTCCTTATACGGTGGATTTGAAAGAAACAAGTTCTTCTCATTATGAACTTTCT
CCTTTAAGACGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTATGCGGT
GGATTTGAAAGAAC
Found at i:878609 original size:7 final size:7
Alignment explanation
Indices: 878573--878709 Score: 121
Period size: 7 Copynumber: 19.7 Consensus size: 7
878563 TCTCGAACCC
878573 TCATTTT
1 TCATTTT
878580 TC--TTT
1 TCATTTT
878585 TC-TTTT
1 TCATTTT
878591 TCA--TT
1 TCATTTT
*
878596 TCTTTTT
1 TCATTTT
878603 TCATTTTTT
1 TCA--TTTT
878612 TCATTTT
1 TCATTTT
878619 TCATTTT
1 TCATTTT
878626 TCATTTT
1 TCATTTT
878633 TCATTTT
1 TCATTTT
878640 TCATTTT
1 TCATTTT
878647 TCATTTTT
1 TCA-TTTT
878655 TCATCTTTT
1 TCA--TTTT
878664 TCATCTTT
1 TCAT-TTT
878672 T--TTCTT
1 TCATT-TT
*
878678 T-TTTTT
1 TCATTTT
878684 TC-TTTT
1 TCATTTT
878690 TCACTTTT
1 TCA-TTTT
878698 TCATTTT
1 TCATTTT
878705 TCATT
1 TCATT
878710 CATTGATTCT
Statistics
Matches: 113, Mismatches: 3, Indels: 28
0.78 0.02 0.19
Matches are distributed among these distances:
5 10 0.09
6 18 0.16
7 53 0.47
8 18 0.16
9 14 0.12
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (7 bp):
TCATTTT
Found at i:882116 original size:40 final size:40
Alignment explanation
Indices: 882061--882142 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
882051 TCACATTCTA
*
882061 CCTCATCCTGACACTCATTGATTTCTTCAAGACATATGGG
1 CCTCATCCTAACACTCATTGATTTCTTCAAGACATATGGG
882101 CCTCATCCTAACACTCATTGATTTCTTCAAGACATATGGG
1 CCTCATCCTAACACTCATTGATTTCTTCAAGACATATGGG
882141 CC
1 CC
882143 GCTCCAAGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (40 bp):
CCTCATCCTAACACTCATTGATTTCTTCAAGACATATGGG
Found at i:890624 original size:2 final size:2
Alignment explanation
Indices: 890617--890649 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
890607 CATTTAGAGA
890617 AT AT AT 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 AT AT AT A
890650 AATGCACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:893630 original size:31 final size:30
Alignment explanation
Indices: 893577--893634 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
893567 TTTTTTTTAC
* *
893577 CTATTAGGACATTAGGGTTTTTTTATTTAGT
1 CTATTAGGACATTAGAG-ATTTTTATTTAGT
*
893608 CTATTAGGACATTCGAGATTTTTATTT
1 CTATTAGGACATTAGAGATTTTTATTT
893635 TGGAAAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (30 bp):
CTATTAGGACATTAGAGATTTTTATTTAGT
Found at i:893950 original size:29 final size:30
Alignment explanation
Indices: 893890--893955 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
893880 CTGGCATAGG
* * *
893890 TTTT-TTTAGCCTATTAGGGTATTCGGTTT
1 TTTTATTTAGCCCATTAGGGTATCCGGATT
*
893919 TTTTATTTAGCCCATTAGGGTA-CCTGATT
1 TTTTATTTAGCCCATTAGGGTATCCGGATT
893948 TTTTATTT
1 TTTTATTT
893956 TGGAGAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.55
Consensus pattern (30 bp):
TTTTATTTAGCCCATTAGGGTATCCGGATT
Found at i:905951 original size:16 final size:17
Alignment explanation
Indices: 905925--905956 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
905915 ACTCCGATTT
905925 TTTTAATTAATTATATA
1 TTTTAATTAATTATATA
905942 TTTT-ATTAATTATAT
1 TTTTAATTAATTATAT
905957 TCATCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATTATATA
Found at i:906360 original size:2 final size:2
Alignment explanation
Indices: 906353--906385 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
906343 CTAGAAGAAA
906353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
906386 ATTCAACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:906522 original size:13 final size:13
Alignment explanation
Indices: 906504--906528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
906494 AAGTTGATGT
906504 ATGGACAAAAATC
1 ATGGACAAAAATC
906517 ATGGACAAAAAT
1 ATGGACAAAAAT
906529 ATTATTTCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.16, T:0.16
Consensus pattern (13 bp):
ATGGACAAAAATC
Found at i:915264 original size:2 final size:2
Alignment explanation
Indices: 915259--915289 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
915249 TATATTTAAT
915259 TA TA 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 TA TA T
915290 TTATGTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:917242 original size:25 final size:25
Alignment explanation
Indices: 917208--917259 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
917198 AATCAAACTC
917208 ATCAAGCTATCTCGGTGTTTAAAGA
1 ATCAAGCTATCTCGGTGTTTAAAGA
917233 ATCAAGCTATCTCGGTGTTTAAAGA
1 ATCAAGCTATCTCGGTGTTTAAAGA
917258 AT
1 AT
917260 GTGTTATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
ATCAAGCTATCTCGGTGTTTAAAGA
Found at i:920279 original size:30 final size:29
Alignment explanation
Indices: 920248--920328 Score: 128
Period size: 30 Copynumber: 2.8 Consensus size: 29
920238 ACTAGTAAAT
*
920248 TTTTAGTTTT-TATCAATTATAACATTGAA
1 TTTTAATTTTATATCAATTATAACATT-AA
920277 TTTTAATTTTATATCAATTATAACATTAAA
1 TTTTAATTTTATATCAATTATAACATT-AA
920307 TTTTAATTTTATATCAATTATA
1 TTTTAATTTTATATCAATTATA
920329 TACTATATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 9 0.18
30 40 0.82
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (29 bp):
TTTTAATTTTATATCAATTATAACATTAA
Found at i:921425 original size:14 final size:14
Alignment explanation
Indices: 921384--921427 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
921374 TCTATATTAT
*
921384 TTATAATCATTATA
1 TTATAATCATTAAA
* *
921398 TTACAAT-TTTAAA
1 TTATAATCATTAAA
921411 TTATAATCATTAAA
1 TTATAATCATTAAA
921425 TTA
1 TTA
921428 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATCATTAAA
Found at i:922243 original size:30 final size:30
Alignment explanation
Indices: 922212--922292 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
922202 ACTAGTAAAT
*
922212 TTTTAGTTTT-TATCAATTATAACATTGAA
1 TTTTAATTTTATATCAATTATAACATTGAA
922241 TTTTAATTTTATATCAATTATAACATTGAA
1 TTTTAATTTTATATCAATTATAACATTGAA
922271 TTTTAATTTTATATCAATTATA
1 TTTTAATTTTATATCAATTATA
922293 TACTATATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 9 0.18
30 41 0.82
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTAATTTTATATCAATTATAACATTGAA
Found at i:923124 original size:16 final size:16
Alignment explanation
Indices: 923103--923133 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
923093 TTACAAGACA
923103 TGTTATCAACTTGACC
1 TGTTATCAACTTGACC
*
923119 TGTTATGAACTTGAC
1 TGTTATCAACTTGAC
923134 TTGTAATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
TGTTATCAACTTGACC
Found at i:923391 original size:14 final size:14
Alignment explanation
Indices: 923350--923393 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
923340 TCTATATTAT
*
923350 TTATAATCATTATA
1 TTATAATCATTAAA
* *
923364 TTACAAT-TTTAAA
1 TTATAATCATTAAA
923377 TTATAATCATTAAA
1 TTATAATCATTAAA
923391 TTA
1 TTA
923394 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATCATTAAA
Found at i:924072 original size:15 final size:15
Alignment explanation
Indices: 924054--924084 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
924044 AAATTCTAAA
924054 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
924069 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
924084 T
1 T
924085 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:924190 original size:11 final size:11
Alignment explanation
Indices: 924174--924198 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
924164 TAATTTATCG
924174 TAAAAATATAT
1 TAAAAATATAT
924185 TAAAAATATAT
1 TAAAAATATAT
924196 TAA
1 TAA
924199 TGTTTACATT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:948542 original size:18 final size:19
Alignment explanation
Indices: 948499--948534 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
948489 TAGAACGACT
948499 ATTTTATATTTTTATATAA
1 ATTTTATATTTTTATATAA
*
948518 AATTTATA-TTTTATATA
1 ATTTTATATTTTTATATA
948535 GCTTTTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATTTTTATATAA
Found at i:951116 original size:31 final size:31
Alignment explanation
Indices: 951072--951180 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
951062 TCCATAGATT
951072 CGAAGAATC-TAGGTAAACAGTCCATATGTCC
1 CGAAGAA-CATAGGTAAACAGTCCATATGTCC
951103 CGAAGAACATAGGTAAACAGTCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
*
951134 CGAAGAACATAGGTAAACAATCCATATGTCC
1 CGAAGAACATAGGTAAACAGTCCATATGTCC
951165 CGAAGAACATAGGTAA
1 CGAAGAACATAGGTAA
951181 GCCCTCGACC
Statistics
Matches: 76, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
30 1 0.01
31 75 0.99
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (31 bp):
CGAAGAACATAGGTAAACAGTCCATATGTCC
Found at i:954946 original size:23 final size:24
Alignment explanation
Indices: 954895--954947 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
954885 CCTAGGGATT
**
954895 TGATTTGGATTTATTTCATTTTTA
1 TGATTTGGATTTATTTCATTGATA
954919 T-ATTTGGATTT-TTT-ATCTGATA
1 TGATTTGGATTTATTTCAT-TGATA
954941 TGATTTG
1 TGATTTG
954948 CGGTCACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
23 15 0.60
24 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.15, T:0.60
Consensus pattern (24 bp):
TGATTTGGATTTATTTCATTGATA
Found at i:955268 original size:3 final size:3
Alignment explanation
Indices: 955262--955318 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
955252 CAAAAAAAGT
*
955262 TAA TAA TAT TGAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
955307 TAA TTAA TAA TA
1 TAA -TAA TAA TA
955319 TTTTTAAGAC
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.88
4 4 0.08
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:955641 original size:80 final size:80
Alignment explanation
Indices: 955502--955650 Score: 201
Period size: 80 Copynumber: 1.9 Consensus size: 80
955492 GTTCTAGTCG
* * *
955502 TCTAAGGGTGACACGACTGCTACGTGACGAGGATATCTGGTCGGTGGATGACACAGTTCCTACGT
1 TCTAAGGGTGACACGACTCCTACGTGACGAGAAGATCTGGTCGGTGGATGACACAGTTCCTACGT
955567 GATGGCACGGTGATA
66 GATGGCACGGTGATA
* * * * * *
955582 TCTAGGGGTGACGCGGCTCCTACGTGATGAGAAGATCTGGTCAGG-GGATGGCACGGTTCCTACG
1 TCTAAGGGTGACACGACTCCTACGTGACGAGAAGATCTGGTC-GGTGGATGACACAGTTCCTACG
955646 TGATG
65 TGATG
955651 AGGATGGTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
80 57 0.97
81 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.35, T:0.23
Consensus pattern (80 bp):
TCTAAGGGTGACACGACTCCTACGTGACGAGAAGATCTGGTCGGTGGATGACACAGTTCCTACGT
GATGGCACGGTGATA
Found at i:955919 original size:65 final size:65
Alignment explanation
Indices: 955810--956093 Score: 372
Period size: 65 Copynumber: 4.4 Consensus size: 65
955800 TAGGGATAAT
* *
955810 GTTTCAAGGGAAACAAACTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAATTC
1 GTTTCAAGGGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
* * *
955875 GTTTCAAGGTAAACAAGCTCAAAGATAATTGTTTCAAGAG-AACTGTCTCAAGAGAGACAAAATT
1 GTTTCAAGGGAAACAATCTCAAAGATGA-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
955939 T
65 C
* *** * * *
955940 GTTTTAAGGGAAATGTTCTCAAAGATGAGGTTTCAAGAGAAACGGTCTCAAGAGAGATAAAATTC
1 GTTTCAAGGGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
* * * * * *
956005 GTTTCAAGTGAAACGATATCAAAGATCATGTTTAAAGAGAAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGGGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
*
956070 GTTTCAAGAGAAACAATCTCAAAG
1 GTTTCAAGGGAAACAATCTCAAAG
956094 GTTTATTAAT
Statistics
Matches: 187, Mismatches: 30, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
64 10 0.05
65 166 0.89
66 11 0.06
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (65 bp):
GTTTCAAGGGAAACAATCTCAAAGATGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
Found at i:956330 original size:37 final size:36
Alignment explanation
Indices: 956240--956365 Score: 139
Period size: 36 Copynumber: 3.4 Consensus size: 36
956230 TCGTAAAGGG
* *
956240 AAAA-TGTCTCAAGCGAGACTAAATTTATTTTGAGA
1 AAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
* *
956275 AAAATTGTCTCAAGCGAGACAAAACTTATTTTTA-A
1 AAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
*
956310 AGAAAGCTGTCTCAAGCGAGACAAAATTTGTTTTTTTAGA
1 A-AAA-CTGTCTCAAGCGAGACAAAA-TT-TATTTTTAGA
* *
956350 AAAACTGACTCTAGCG
1 AAAACTGTCTCAAGCG
956366 GGATGACGCT
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
35 6 0.08
36 29 0.38
37 19 0.25
38 11 0.14
39 10 0.13
40 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (36 bp):
AAAACTGTCTCAAGCGAGACAAAATTTATTTTTAGA
Found at i:962783 original size:3 final size:3
Alignment explanation
Indices: 962775--962817 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
962765 TATAATATTG
* * *
962775 ATA ATA ATA GTA TTA AAA ATA ATA ATA ATA ATTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
962818 TTTTTTTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:963470 original size:2 final size:2
Alignment explanation
Indices: 963463--963495 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
963453 AGCTAAAATA
963463 AT AT AT 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 AT AT AT A
963496 ATTTAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:969140 original size:33 final size:33
Alignment explanation
Indices: 969103--969166 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
969093 GCTTCCACAG
969103 GTTTAGAATGAATAAACTGATTTGAAATATGAA
1 GTTTAGAATGAATAAACTGATTTGAAATATGAA
*
969136 GTTTAGAATGAATAAACTGATTTGGAATATG
1 GTTTAGAATGAATAAACTGATTTGAAATATG
969167 TGTAACCTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.34
Consensus pattern (33 bp):
GTTTAGAATGAATAAACTGATTTGAAATATGAA
Found at i:969163 original size:19 final size:19
Alignment explanation
Indices: 969108--969163 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
969098 CACAGGTTTA
969108 GAATGAATAAACTGATTTG
1 GAATGAATAAACTGATTTG
* * *
969127 AAAT--ATGAA--G-TTTA
1 GAATGAATAAACTGATTTG
969141 GAATGAATAAACTGATTTG
1 GAATGAATAAACTGATTTG
969160 GAAT
1 GAAT
969164 ATGTGTAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 10
0.62 0.14 0.24
Matches are distributed among these distances:
14 6 0.23
15 1 0.04
16 4 0.15
17 4 0.15
18 1 0.04
19 10 0.38
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.32
Consensus pattern (19 bp):
GAATGAATAAACTGATTTG
Found at i:969703 original size:30 final size:30
Alignment explanation
Indices: 969667--969723 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
969657 GCTGGTGGTG
969667 GAGGAGACAATGGAGGAGATAGTGATGATA
1 GAGGAGACAATGGAGGAGATAGTGATGATA
** * *
969697 GAGGAGACGGTGGAGGAGGTTGTGATG
1 GAGGAGACAATGGAGGAGATAGTGATG
969724 GTGGTGGTGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.47, T:0.18
Consensus pattern (30 bp):
GAGGAGACAATGGAGGAGATAGTGATGATA
Found at i:969731 original size:66 final size:66
Alignment explanation
Indices: 969659--969804 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 66
969649 AATGTGGTGC
* * * * *
969659 TGGTGGTGGAGGAGACAATGGAGGAGATAGTGATGATAGAGGAGACGGTGGAGGAGGTTGTGATG
1 TGGTGGTGGAGGAGACAACGGAAGAGATAGTGATGATAGAGGAGACGATGGAGGAGATTGTGATA
969724 G
66 G
* * *
969725 TGGTGGTGGAGGAGACAACGGAAGAGGTAGTGGTGATGGAGGAGACGATGGAGGAGATTGTGATA
1 TGGTGGTGGAGGAGACAACGGAAGAGATAGTGATGATAGAGGAGACGATGGAGGAGATTGTGATA
969790 G
66 G
* *
969791 TGGCGGTGGTGGAG
1 TGGTGGTGGAGGAG
969805 GTTGTGATAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 70 1.00
ACGTcount: A:0.26, C:0.04, G:0.51, T:0.19
Consensus pattern (66 bp):
TGGTGGTGGAGGAGACAACGGAAGAGATAGTGATGATAGAGGAGACGATGGAGGAGATTGTGATA
G
Found at i:969809 original size:24 final size:24
Alignment explanation
Indices: 969777--969825 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
969767 AGACGATGGA
*
969777 GGAGATTGTGATAGTGGCGGTGGT
1 GGAGATTGTGATAGTGGCGCTGGT
*
969801 GGAGGTTGTGATAGTGGCGCTGGT
1 GGAGATTGTGATAGTGGCGCTGGT
969825 G
1 G
969826 CTATTTATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.06, G:0.51, T:0.29
Consensus pattern (24 bp):
GGAGATTGTGATAGTGGCGCTGGT
Found at i:971596 original size:102 final size:102
Alignment explanation
Indices: 971409--971610 Score: 388
Period size: 101 Copynumber: 2.0 Consensus size: 102
971399 TTCAAATTAT
971409 ACGCGAGATTAGTCAATGTGGGTAACAATTTTTTTCATTTTAATATTTAAAATTATATTTTATTA
1 ACGCGAGATTAGTCAATGTGGGTAACAATTTTTTTCATTTTAATATTTAAAATTATATTTTATTA
*
971474 TGTAACTAAAATATATTTTTTTGGTCAGGATTTTGCG
66 TGTAACCAAAATATATTTTTTTGGTCAGGATTTTGCG
971511 ACGCGAGATTAGTCAATGTGGGTAACAA-TTTTTTCATTTTAATATTTAAAATTATATTTTATTA
1 ACGCGAGATTAGTCAATGTGGGTAACAATTTTTTTCATTTTAATATTTAAAATTATATTTTATTA
971575 TGTAACCAAAATATATTTTTTTGGTCAGGATTTTGC
66 TGTAACCAAAATATATTTTTTTGGTCAGGATTTTGC
971611 TTTTATTTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
101 71 0.72
102 28 0.28
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (102 bp):
ACGCGAGATTAGTCAATGTGGGTAACAATTTTTTTCATTTTAATATTTAAAATTATATTTTATTA
TGTAACCAAAATATATTTTTTTGGTCAGGATTTTGCG
Found at i:983284 original size:21 final size:21
Alignment explanation
Indices: 983259--983303 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
983249 AAATAAATAC
*
983259 CATAGTTTTAATTATCATAAA
1 CATAGTTTTAATTACCATAAA
* *
983280 CATAGTTTTGATTGCCATAAA
1 CATAGTTTTAATTACCATAAA
983301 CAT
1 CAT
983304 GGGCACAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (21 bp):
CATAGTTTTAATTACCATAAA
Found at i:989251 original size:31 final size:31
Alignment explanation
Indices: 989213--989371 Score: 275
Period size: 31 Copynumber: 5.2 Consensus size: 31
989203 GGTCACAATA
989213 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
989244 TAGACTGTT-ATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
989274 TAAACTGTTCATATGTGCCTTTAAAAATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
989305 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
989336 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
989367 TAAAC
1 TAAAC
989372 CCTCGACTCT
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
30 28 0.23
31 92 0.77
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:989988 original size:64 final size:65
Alignment explanation
Indices: 989880--990103 Score: 222
Period size: 64 Copynumber: 3.5 Consensus size: 65
989870 TAATGAAGGT
* * * * ** *
989880 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTAGT-AATATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGAG
* ** * *
989944 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAATGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGAG
* * ** * *
990008 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCAATGTA-TTTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGAG
** *
990071 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
990104 CATTCAAACA
Statistics
Matches: 133, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
63 4 0.03
64 129 0.97
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTAGTCAATATTAATGAG
Found at i:1000051 original size:50 final size:50
Alignment explanation
Indices: 999957--1000053 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
999947 TATATTTCTC
* * * *
999957 TTAGGGTGAAAACCCGAAAGGGCGCCTTAAGTTGAAGAGTAAAAAAACTT
1 TTAGAGTGAAAACCCGAAAGGGCACCTTAAGTTGAAAAATAAAAAAACTT
*
1000007 TTAGAGTGAAAACCCGACAGGGCA-CTCTAA-TTGAAAAATAAAAAAAC
1 TTAGAGTGAAAACCCGAAAGGGCACCT-TAAGTTGAAAAATAAAAAAAC
1000054 AAAGAAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 17 0.41
50 24 0.59
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (50 bp):
TTAGAGTGAAAACCCGAAAGGGCACCTTAAGTTGAAAAATAAAAAAACTT
Found at i:1001800 original size:22 final size:22
Alignment explanation
Indices: 1001761--1001809 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 22
1001751 ATAATTTCAA
1001761 AAAATATATATATATAGTTTTT
1 AAAATATATATATATAGTTTTT
1001783 GAAAATATATA-ATATAGTTTTT
1 -AAAATATATATATATAGTTTTT
1001805 AAAAT
1 AAAAT
1001810 GATTTTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 5 0.19
22 11 0.42
23 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
AAAATATATATATATAGTTTTT
Found at i:1001855 original size:22 final size:22
Alignment explanation
Indices: 1001813--1001861 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1001803 TTAAAATGAT
1001813 TTTTTGAAACATGTATCATATAG
1 TTTTTGAAACA-GTATCATATAG
*
1001836 TTTTTGAAAACA-TATTATATAG
1 TTTTTG-AAACAGTATCATATAG
1001858 TTTT
1 TTTT
1001862 AAAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 6 0.25
24 5 0.21
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (22 bp):
TTTTTGAAACAGTATCATATAG
Found at i:1001874 original size:19 final size:19
Alignment explanation
Indices: 1001830--1001894 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1001820 AACATGTATC
*
1001830 ATATAGTTTTTGAAAACATATT
1 ATATAG-TTTT-AAAA-ATATA
1001852 ATATAGTTTTAAAAATATA
1 ATATAGTTTTAAAAATATA
* *
1001871 ATATATGTTATATAAATA-A
1 ATATA-GTTTTAAAAATATA
1001890 ATATA
1 ATATA
1001895 ACGTACGTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 15 0.38
20 14 0.36
21 4 0.10
22 6 0.15
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (19 bp):
ATATAGTTTTAAAAATATA
Found at i:1001922 original size:3 final size:3
Alignment explanation
Indices: 1001914--1001980 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
1001904 TCATTTAATA
1001914 TAT TAT TATT TAT TAT TA- TAT ATAT TA- TAT TA- TAT TA- TAT TA-
1 TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
*
1001956 TAT TA- TAT TAT TAA TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1001981 ATTTATTTAG
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
2 14 0.26
3 33 0.62
4 6 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1001944 original size:5 final size:5
Alignment explanation
Indices: 1001917--1001987 Score: 87
Period size: 5 Copynumber: 14.8 Consensus size: 5
1001907 TTTAATATAT
1001917 TATTA T-TTA TTATTA TA-TA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
* *
1001966 T-TAA TATTA TTTTA TATT- TATT
1 TATTA TATTA TATTA TATTA TATT
1001988 TAGGTCCAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
4 14 0.24
5 41 0.71
6 3 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:1001959 original size:29 final size:29
Alignment explanation
Indices: 1001908--1001987 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
1001898 TACGTGTCAT
1001908 TTAATA-TATTATTAT-TTATTATTATATATA
1 TTAATATTA-TATTATATTA-TATTATAT-TA
1001938 TT-ATATTATATTATATTATATTATATTA
1 TTAATATTATATTATATTATATTATATTA
*
1001966 TTAATATTATTTTATATT-TATT
1 TTAATATTATATTATATTATATT
1001988 TAGGTCCAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
28 8 0.17
29 31 0.67
30 7 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TTAATATTATATTATATTATATTATATTA
Found at i:1003025 original size:13 final size:13
Alignment explanation
Indices: 1003009--1003038 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1002999 TAGATCGAAT
1003009 ATTTAAATTTTAA
1 ATTTAAATTTTAA
*
1003022 ATTTAACTTTTAA
1 ATTTAAATTTTAA
1003035 ATTT
1 ATTT
1003039 CTTAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTAAATTTTAA
Found at i:1003242 original size:26 final size:26
Alignment explanation
Indices: 1003213--1003265 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1003203 TGGCGATTCA
1003213 AACACATCAAATCAAGTCGTAACCCG
1 AACACATCAAATCAAGTCGTAACCCG
1003239 AACACATCAAATCAAGTCGTAACCCG
1 AACACATCAAATCAAGTCGTAACCCG
1003265 A
1 A
1003266 TTCCAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.11, T:0.15
Consensus pattern (26 bp):
AACACATCAAATCAAGTCGTAACCCG
Done.