Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008337.1 Hibiscus syriacus cultivar Beakdansim tig00111057_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: 840327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:716484 original size:67 final size:67
Alignment explanation
Indices: 716154--716515 Score: 289
Period size: 67 Copynumber: 5.4 Consensus size: 67
716144 CAATCAAGGG
* * * * * *
716154 TTTTGTGTTTCAAGAGGAATTGTCT-ATAGGGAGACAAAATCCAGTTCAAGGGAAACGAT-CTCA
1 TTTTATGTTTCAAGAGAAACTGTCTCA-AGGGAGACAAAATTCATTTAAAGGGAAAC-ATACTCA
716217 AAGA
64 AAGA
* * ** * *
716221 --TCAGTGTTTCAAG-GAAAACTGTCTCAAGAGAGACAAAACACGTTTAAAGGGAAACGA-CCTC
1 TTTTA-TGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTCATTTAAAGGGAAAC-ATACTC
716282 AAAGA
63 AAAGA
* * *
716287 TTTTATGTTTCAAGAGGAATTGTCT-ATAGGGAGACAAAATTCAGTTAAAGGGAAACGAT-CTCA
1 TTTTATGTTTCAAGAGAAACTGTCTCA-AGGGAGACAAAATTCATTTAAAGGGAAAC-ATACTCA
716350 AAGA
64 AAGA
* * * * *
716354 --TCAGTGTTTCAAG-GAAAACTGTCTCAAGAGATACAAAACTCGTTTAAAGGGAAACA-ACCTC
1 TTTTA-TGTTTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTCATTTAAAGGGAAACATA-CTC
716415 AAAGA
63 AAAGA
** * * * *
716420 TTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGAGAAATATATTCAAA
1 TTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTAAAGGGAAACATACTCAAA
716485 GA
66 GA
* * *
716487 TTTTTTTTTTCAAAAGAAACTGTCTCAAG
1 TTTTATGTTTCAAGAGAAACTGTCTCAAG
716516 CTAGATAAAA
Statistics
Matches: 238, Mismatches: 39, Indels: 36
0.76 0.12 0.12
Matches are distributed among these distances:
65 6 0.03
66 98 0.41
67 127 0.53
68 7 0.03
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (67 bp):
TTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTAAAGGGAAACATACTCAAA
GA
Found at i:716880 original size:89 final size:90
Alignment explanation
Indices: 716658--716954 Score: 506
Period size: 90 Copynumber: 3.3 Consensus size: 90
716648 TGAAAATCAT
* * * * *
716658 GCTTAGTTTCTAAAAACTCATTTGAAAATATCCTGCAATGGAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTAATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
716723 CTTACAAATCAAGAAACCCCCGAAG
66 CTTACAAATCAAGAAACCCCCGAAG
*
716748 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTAATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
716813 CTTACAAATCAAGAAA-CCCCGAAG
66 CTTACAAATCAAGAAACCCCCGAAG
* * *
716837 GCTTAGTTTCTAAAATCTAATTTAAAAACATCCTGCACCGAAGGTCTTATGGATGGCCTGAAGGA
1 GCTTAGTTTCTAAAATCTAATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
716902 CTTACAAATCAAGAAACCCCCGAAG
66 CTTACAAATCAAGAAACCCCCGAAG
716927 GCTTAGTTTCTAAAATCTAATTTGAAAA
1 GCTTAGTTTCTAAAATCTAATTTGAAAA
716955 TATCATGTTG
Statistics
Matches: 197, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
89 85 0.43
90 112 0.57
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (90 bp):
GCTTAGTTTCTAAAATCTAATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGA
CTTACAAATCAAGAAACCCCCGAAG
Found at i:718834 original size:4 final size:4
Alignment explanation
Indices: 718827--718937 Score: 70
Period size: 4 Copynumber: 28.0 Consensus size: 4
718817 ATTGATCGAT
* * * * *
718827 TTTC TTTC -TTC TTTC TTTA TTTC TTTA TTTC TCTC TATC TCTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
718874 TTT- TTT- TTTC -TT- TTTC TTTTC TTTT TTTC TTTC TTTTC TTTTT TTTC
1 TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC -TTTC -TTTC TTTC
* *
718921 TATC TTTTT TTTC TTTC
1 TTTC -TTTC TTTC TTTC
718938 CTTTTTTATA
Statistics
Matches: 84, Mismatches: 16, Indels: 14
0.74 0.14 0.12
Matches are distributed among these distances:
3 13 0.15
4 57 0.68
5 14 0.17
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:718900 original size:13 final size:13
Alignment explanation
Indices: 718870--718944 Score: 59
Period size: 13 Copynumber: 5.8 Consensus size: 13
718860 TCTATCTCTC
718870 TTTCTTTTTTT-T
1 TTTCTTTTTTTCT
718882 TCTT-TTTCTTTTCT
1 T-TTCTTT-TTTTCT
*
718896 TTT-TTTCTTTCT
1 TTTCTTTTTTTCT
718908 TTTCTTTTTTT-T
1 TTTCTTTTTTTCT
*
718920 CTATCTTTTTTTTCT
1 -TTTC-TTTTTTTCT
*
718935 TTCCTTTTTT
1 TTTCTTTTTT
718945 ATATATTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 13 0.25
13 26 0.51
14 11 0.22
15 1 0.02
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:720179 original size:20 final size:20
Alignment explanation
Indices: 720150--720187 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
720140 GATACAAAAA
720150 ATGCACATGCAAATGCAAAG
1 ATGCACATGCAAATGCAAAG
*
720170 ATGCATATGCAAATGCAA
1 ATGCACATGCAAATGCAA
720188 CCCGATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
ATGCACATGCAAATGCAAAG
Found at i:723068 original size:14 final size:15
Alignment explanation
Indices: 723049--723086 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
723039 AAAGTGCTAG
*
723049 AAAATAAATAAAA-T
1 AAAATAAATAAAACA
*
723063 AAAATAAAAAAAACA
1 AAAATAAATAAAACA
723078 AAAATAAAT
1 AAAATAAAT
723087 TGCATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAATAAAACA
Found at i:723331 original size:4 final size:4
Alignment explanation
Indices: 723322--723347 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
723312 TGAATATTAG
723322 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
723348 CAATGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:723680 original size:19 final size:20
Alignment explanation
Indices: 723651--723690 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
723641 AAATTAGGGT
723651 ATTACATTTTACATTTTAAA
1 ATTACATTTTACATTTTAAA
723671 ATTA-ATTTTACATTTTAAA
1 ATTACATTTTACATTTTAAA
723690 A
1 A
723691 ACCAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTACATTTTACATTTTAAA
Found at i:728237 original size:20 final size:20
Alignment explanation
Indices: 728196--728265 Score: 53
Period size: 20 Copynumber: 3.8 Consensus size: 20
728186 GTCACACAAT
* *
728196 TAAAATAACATAAATTTTAA
1 TAAAATAACATAAATATAAA
728216 TAAAATAACATAACA-ATAAA
1 TAAAATAACATAA-ATATAAA
* *
728236 TATAATATCA-AAA-AT---
1 TAAAATAACATAAATATAAA
728251 TAAAATAACATAAAT
1 TAAAATAACATAAAT
728266 TTCAATATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
15 8 0.20
16 3 0.07
18 3 0.07
19 2 0.05
20 24 0.59
21 1 0.02
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAATAACATAAATATAAA
Found at i:729829 original size:22 final size:23
Alignment explanation
Indices: 729778--729829 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
729768 ATAATACCAT
*
729778 AAATTAAAAATAACATAAATTTC
1 AAATTAAAAATAACATAAATTAC
729801 AATATTAAAAA-AACA-AAATTAC
1 AA-ATTAAAAATAACATAAATTAC
729823 ATAATTA
1 A-AATTA
729830 TGGTACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 11 0.42
23 7 0.27
24 8 0.31
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATTAAAAATAACATAAATTAC
Found at i:732904 original size:18 final size:18
Alignment explanation
Indices: 732883--732946 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
732873 CAAATCACTG
732883 TAAAATAAAAAATTATCA
1 TAAAATAAAAAATTATCA
*
732901 TAAATTATAAAAATTATCA
1 TAAAATA-AAAAATTATCA
* ** *
732920 GAAAAATTTAAAA-TAACA
1 -TAAAATAAAAAATTATCA
732938 TAAAATAAA
1 TAAAATAAA
732947 TAAAAATTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
17 6 0.17
18 10 0.29
19 15 0.43
20 4 0.11
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAATAAAAAATTATCA
Found at i:732985 original size:20 final size:21
Alignment explanation
Indices: 732940--732986 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
732930 AAATAACATA
*
732940 AAATAAATAAAAATTCAATAT
1 AAATAAATAAAAATTCAAAAT
*
732961 -TATAAATAAAAA-TCAAAAT
1 AAATAAATAAAAATTCAAAAT
732980 AAATAAA
1 AAATAAA
732987 CGTAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAAATAAAAATTCAAAAT
Found at i:733460 original size:21 final size:22
Alignment explanation
Indices: 733431--733487 Score: 98
Period size: 21 Copynumber: 2.6 Consensus size: 22
733421 CCCTTCAAAT
*
733431 AATATATAAATAAATTATTC-A
1 AATAAATAAATAAATTATTCAA
733452 AATAAATAAATAAATTATTCAA
1 AATAAATAAATAAATTATTCAA
733474 AATAAATAAATAAA
1 AATAAATAAATAAA
733488 AATCGCCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.56
22 15 0.44
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (22 bp):
AATAAATAAATAAATTATTCAA
Found at i:733612 original size:69 final size:68
Alignment explanation
Indices: 733533--733662 Score: 224
Period size: 69 Copynumber: 1.9 Consensus size: 68
733523 TATGCCTTCA
* *
733533 ATAAAGCTTCAGTAATCCCTTCATAATAATCGAATAATGGAATAAATAAGAGAGAAAAATGAGCA
1 ATAAAGCTTCAGTAATCCCTCCATAATAATCGAATAATGGAATAAATAACAGA-AAAAATGAGCA
733598 TTCG
65 TTCG
*
733602 ATAAAGCTTCAGTAATCCCTCCATAATAATCGAATAATGGAATAGATAACAGAAAAAATGA
1 ATAAAGCTTCAGTAATCCCTCCATAATAATCGAATAATGGAATAAATAACAGAAAAAATGA
733663 AAGAGAGAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 8 0.14
69 50 0.86
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.24
Consensus pattern (68 bp):
ATAAAGCTTCAGTAATCCCTCCATAATAATCGAATAATGGAATAAATAACAGAAAAAATGAGCAT
TCG
Found at i:736969 original size:16 final size:16
Alignment explanation
Indices: 736948--736994 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
736938 TTACCCGACC
*
736948 TGTTTTCAACCTGACA
1 TGTTTTTAACCTGACA
736964 TGTTTTTAGA-CTGACA
1 TGTTTTTA-ACCTGACA
736980 TGTTTTTAACCTGAC
1 TGTTTTTAACCTGAC
736995 CTGTAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (16 bp):
TGTTTTTAACCTGACA
Found at i:737287 original size:14 final size:14
Alignment explanation
Indices: 737265--737311 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
737255 TGAAAAGGAA
*
737265 AATTAATATAGTTT
1 AATTTATATAGTTT
737279 AATTTATATA----
1 AATTTATATAGTTT
737289 AA-TTATATAGTTT
1 AATTTATATAGTTT
737302 AATTTATATA
1 AATTTATATA
737312 AAAAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:737298 original size:23 final size:24
Alignment explanation
Indices: 737264--737313 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
737254 ATGAAAAGGA
737264 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
737288 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
737311 AAA
1 AAA
737314 AAATAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:738042 original size:21 final size:21
Alignment explanation
Indices: 738004--738043 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
737994 TGGTTTAGTG
* *
738004 TTTAGTGTTTACGGTTTAAAA
1 TTTAGGGTTTACGATTTAAAA
*
738025 TTTAGGGTTTATGATTTAA
1 TTTAGGGTTTACGATTTAA
738044 GGTTTAAGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTACGATTTAAAA
Found at i:738145 original size:2 final size:2
Alignment explanation
Indices: 738140--738187 Score: 69
Period size: 2 Copynumber: 23.0 Consensus size: 2
738130 TTATATAAAC
*
738140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
738183 CTA TA
1 -TA TA
738188 CTTGGTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:738161 original size:27 final size:28
Alignment explanation
Indices: 738106--738187 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
738096 ATAGTATTTC
* *
738106 TATAAACTATATA-AGTA-ATTTACTTTA
1 TATAAACTATATATA-TATATATACTATA
738133 TATAAACTATATATATATATATA-TATA
1 TATAAACTATATATATATATATACTATA
* *
738160 TATATA-TATATAGTTTATATATACTATA
1 TATAAACTATATA-TATATATATACTATA
738188 CTTGGTTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 6 0.13
27 32 0.68
28 9 0.19
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (28 bp):
TATAAACTATATATATATATATACTATA
Found at i:738568 original size:21 final size:21
Alignment explanation
Indices: 738544--738595 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
738534 TATATTTATA
*
738544 TTAGGATTTAA-GGTTTAGAGT
1 TTAGG-TTTAATGGTTTAAAGT
738565 TTA-GTGTTAATGGTTTAAAGT
1 TTAGGT-TTAATGGTTTAAAGT
738586 TTAGGGTTTA
1 TTA-GGTTTA
738596 GAATTTCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 1 0.04
20 5 0.19
21 15 0.58
22 3 0.12
23 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
TTAGGTTTAATGGTTTAAAGT
Found at i:738674 original size:546 final size:552
Alignment explanation
Indices: 737673--738750 Score: 1612
Period size: 565 Copynumber: 1.9 Consensus size: 552
737663 ATAAAATTAT
737673 TTAATAAAATTATTAAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTAT
1 TTAATAAAATTATTAAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTAT
* *
737738 GTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAAT
66 GTCACATTGCATATTATATGGCTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAAT
*
737803 TAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGACCATTTATTTTGTTGTTATGAATA
131 TAATATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGACCATTTATTTTGTTGTTATGAATA
*
737868 AGTAATAATAAAACCAAAAAATAAGTCATAGTGCTAGTCCATTTACATTAGTTTATATAAGCCCA
196 AGTAATAATAAAACC--AAAATAA--CATA--G--AGTCCATTTACATTAGTTTACATAAGCCCA
* * * *
737933 ATACATAAGCCCACTCTTTTATTACAAATATATATGCATTTGTGCTAGTCTGTTTATATTATGGT
253 ATACATAAGCCCACTATTTTATTACAAATATATATGCATTAGTGCTAGTATATTTATATTATGGT
* * * *
737998 TTAGTGTTTAGTGTTTACGGTTTAAAATTTAGGGTTTATGATTTAAGGTTTAAGGTTTTTATAAA
318 TTAGTGTTTAGAGTTTACGGTTT-AAA-TTA-GGTTTAAGATTTAAGGTTTAAGATTTCTATAAA
738063 ACTATATACTTTATTACTTTATATAGTCTATGCATAGTATTTCTATAAACTATATAAGTAATTTA
380 ACTATATACTTTATTACTTTATATAGTCTATGCATAGTATTTCTATAAACTATATAAGTAATTTA
* *
738128 CTTTATATA-AACTATATATATATATA-TATATATATA-TATATATAGTTTATATATACTATACT
445 CTTTATATAGAA-T-TATATATATATACT-T-TATATAGTATATATA-TATATATATACTATACA
738190 TGGTTTATACATACATACATACATATTATATAAAATTATTTAATAAAA
505 TGGTTTATACATACATACATACATATTATATAAAATTATTTAATAAAA
* *
738238 TTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTATGTGTTAAATAATTAGTAT
1 TTAATAAAATTATTAAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTAT
738303 GTCACATTGCATATTATATGGCTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAAT
66 GTCACATTGCATATTATATGGCTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAAT
*
738368 TAATATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCATTTATTTTGTTGTTATGAATA
131 TAATATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGACCATTTATTTTGTTGTTATGAATA
* * * *
738433 AGTAATAATAAAACC-CAA-AA-ATA-AGTCCATTTACATTAGTTTACATAGGCTCAATATATAA
196 AGTAATAATAAAACCAAAATAACATAGAGTCCATTTACATTAGTTTACATAAGCCCAATACATAA
*
738494 GCCCAGTATTTTATTACAAATATATATGCATTAGTGCTAGTATATTTATATTA-GGATTTAAG-G
261 GCCCACTATTTTATTACAAATATATATGCATTAGTGCTAGTATATTTATATTATGG-TTT-AGTG
* *
738557 TTTAGAGTTTA--GTGTT-AA-T-GGTTTAA-AGTTTAGGGTTT-AGAATTTCTATAAAATTATA
324 TTTAGAGTTTACGGT-TTAAATTAGGTTTAAGA-TTTAAGGTTTAAG-ATTTCTATAAAACTATA
*
738615 TACTTTATTACTTTATATAGTTTATGCATAGTATTTCTATAAACTATATAAGTAATTTACTTTAT
386 TACTTTATTACTTTATATAGTCTATGCATAGTATTTCTATAAACTATATAAGTAATTTACTTTAT
*
738680 ATAGTAATTATATATATATACTTTATATAGTTTATATATATATATATACTATACATGGTTTATAC
451 ATAG-AATTATATATATATACTTTATATAGTATATATATATATATATACTATACATGGTTTATAC
738745 ATACAT
515 ATACAT
738751 GTACTATAAG
Statistics
Matches: 478, Mismatches: 26, Indels: 38
0.88 0.05 0.07
Matches are distributed among these distances:
545 40 0.08
546 116 0.24
547 2 0.00
548 3 0.01
550 2 0.00
551 2 0.00
552 4 0.01
553 96 0.20
554 2 0.00
558 3 0.01
561 2 0.00
562 2 0.00
565 204 0.43
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.43
Consensus pattern (552 bp):
TTAATAAAATTATTAAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTAT
GTCACATTGCATATTATATGGCTCATAAATAATAGTACATGTCATATTAATTTCATTTGCATAAT
TAATATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGACCATTTATTTTGTTGTTATGAATA
AGTAATAATAAAACCAAAATAACATAGAGTCCATTTACATTAGTTTACATAAGCCCAATACATAA
GCCCACTATTTTATTACAAATATATATGCATTAGTGCTAGTATATTTATATTATGGTTTAGTGTT
TAGAGTTTACGGTTTAAATTAGGTTTAAGATTTAAGGTTTAAGATTTCTATAAAACTATATACTT
TATTACTTTATATAGTCTATGCATAGTATTTCTATAAACTATATAAGTAATTTACTTTATATAGA
ATTATATATATATACTTTATATAGTATATATATATATATATACTATACATGGTTTATACATACAT
ACATACATATTATATAAAATTATTTAATAAAA
Found at i:738697 original size:17 final size:17
Alignment explanation
Indices: 738657--738699 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
738647 ATTTCTATAA
738657 ACTATATA-AGTAATTT
1 ACTATATATAGTAATTT
*
738673 ACTTTATATAGTAATTAT
1 ACTATATATAGTAATT-T
738691 A-TATATATA
1 ACTATATATA
738700 CTTTATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (17 bp):
ACTATATATAGTAATTT
Found at i:738720 original size:28 final size:28
Alignment explanation
Indices: 738672--738743 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
738662 ATAAGTAATT
*
738672 TACTTTATATAG-TAAT-TATATATATA
1 TACTTTATATAGTTTATATATATATATA
738698 TACTTTATATAGTTTATATATATATATA
1 TACTTTATATAGTTTATATATATATATA
* * *
738726 TACTATACATGGTTTATA
1 TACTTTATATAGTTTATA
738744 CATACATGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 12 0.30
27 3 0.08
28 25 0.62
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (28 bp):
TACTTTATATAGTTTATATATATATATA
Found at i:738725 original size:26 final size:26
Alignment explanation
Indices: 738672--738723 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 26
738662 ATAAGTAATT
738672 TACTTTATATAGTAATTATATATATA
1 TACTTTATATAGTAATTATATATATA
738698 TACTTTATATAGT--TTATATATATA
1 TACTTTATATAGTAATTATATATATA
738722 TA
1 TA
738724 TATACTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 13 0.50
26 13 0.50
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (26 bp):
TACTTTATATAGTAATTATATATATA
Found at i:738732 original size:24 final size:24
Alignment explanation
Indices: 738672--738732 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
738662 ATAAGTAATT
*
738672 TACTTTATATAGTAATTATATATATA
1 TACTATATATAGT--TTATATATATA
*
738698 TACTTTATATAGTTTATATATATA
1 TACTATATATAGTTTATATATATA
738722 TA-TATACTATA
1 TACTATA-TATA
738733 CATGGTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 3 0.09
24 17 0.52
26 13 0.39
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (24 bp):
TACTATATATAGTTTATATATATA
Found at i:738743 original size:26 final size:28
Alignment explanation
Indices: 738688--738758 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
738678 ATATAGTAAT
* * *
738688 TATATATATATACTTTATATAGTTTATA
1 TATATATATATACTATACATAGGTTATA
738716 TATATATATATACTATACAT-GGTT-TA
1 TATATATATATACTATACATAGGTTATA
* * *
738742 TACATACATGTACTATA
1 TATATATATATACTATA
738759 AGTTACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
26 16 0.43
27 3 0.08
28 18 0.49
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.46
Consensus pattern (28 bp):
TATATATATATACTATACATAGGTTATA
Found at i:738794 original size:7 final size:7
Alignment explanation
Indices: 738772--738838 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
738762 TACATATATA
738772 GTTTAGG
1 GTTTAGG
*
738779 GGTTAGG
1 GTTTAGG
738786 GTTTAGG
1 GTTTAGG
* *
738793 GTTAAAG
1 GTTTAGG
738800 GTTTAGG
1 GTTTAGG
* *
738807 GTTCATG
1 GTTTAGG
* *
738814 TTTTAGA
1 GTTTAGG
738821 GTTTAGG
1 GTTTAGG
738828 GTTTAGG
1 GTTTAGG
738835 GTTT
1 GTTT
738839 TTTTTTTATA
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.18, C:0.01, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:738904 original size:2 final size:2
Alignment explanation
Indices: 738893--738935 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
738883 ATAGTGTTTC
738893 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
738934 TA
1 TA
738936 ATTTATAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:739460 original size:21 final size:20
Alignment explanation
Indices: 739413--739495 Score: 114
Period size: 20 Copynumber: 4.1 Consensus size: 20
739403 AATAGAATGT
*
739413 CCAGAGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
739433 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
739453 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
739474 CCAGGGGGTA-ACGATTCCCC
1 CCAGGGGGTACA-GATTCCCC
739494 CC
1 CC
739496 TGTCTAACGG
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
20 39 0.70
21 17 0.30
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:739494 original size:40 final size:40
Alignment explanation
Indices: 739413--739495 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 40
739403 AATAGAATGT
* *
739413 CCAGAGGGTACAGATTCCCCCCAGGGGGTACCGATTCCCC
1 CCAGAGGGAACAGATTCCCCCCAGGGGGTAACGATTCCCC
*
739453 CCAGGGGGAACAGATTCCCCCCCAGGGGGTAACGATTCCCC
1 CCAGAGGGAACAGATT-CCCCCCAGGGGGTAACGATTCCCC
739494 CC
1 CC
739496 TGTCTAACGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 14 0.36
41 25 0.64
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (40 bp):
CCAGAGGGAACAGATTCCCCCCAGGGGGTAACGATTCCCC
Found at i:739882 original size:34 final size:32
Alignment explanation
Indices: 739843--739912 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
739833 TTTTGTAAAT
*
739843 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
739877 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
739909 GGGA
1 GGGA
739913 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:740320 original size:19 final size:19
Alignment explanation
Indices: 740269--740330 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
740259 ATAAAATCTC
*
740269 AATTCTCAATTTCCCTCCA
1 AATTCTCAATTTCCCTCTA
* * *
740288 GATTTTTCTA-TTCCCTCTA
1 -AATTCTCAATTTCCCTCTA
740307 AATTCTCAATTTCCCTCTA
1 AATTCTCAATTTCCCTCTA
740326 AATTC
1 AATTC
740331 CCAAATAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 6 0.18
19 22 0.65
20 6 0.18
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.44
Consensus pattern (19 bp):
AATTCTCAATTTCCCTCTA
Found at i:740709 original size:16 final size:16
Alignment explanation
Indices: 740688--740726 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
740678 CATTTAATAG
740688 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
740704 ATAAACGAACACGAAT
1 ATAAACGAACACGAAC
740720 ATAAACG
1 ATAAACG
740727 TTGGAGACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:741837 original size:14 final size:14
Alignment explanation
Indices: 741820--741875 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
741810 AATGAACATA
741820 AACGAACATAACCG
1 AACGAACATAACCG
741834 AACGAACAT-A---
1 AACGAACATAACCG
* *
741844 AACGAACATAAACA
1 AACGAACATAACCG
741858 AACGAACATAACCG
1 AACGAACATAACCG
741872 AACG
1 AACG
741876 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 25 0.69
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:741874 original size:10 final size:10
Alignment explanation
Indices: 741813--741856 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 10
741803 ATAAATGAAT
741813 GAACATAAAC
1 GAACATAAAC
741823 GAACATAACCGAAC
1 GAACAT-A---AAC
741837 GAACATAAAC
1 GAACATAAAC
741847 GAACATAAAC
1 GAACATAAAC
741857 AAACGAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 19 0.63
11 1 0.03
13 1 0.03
14 9 0.30
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (10 bp):
GAACATAAAC
Found at i:741885 original size:24 final size:24
Alignment explanation
Indices: 741800--741874 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
741790 GATTAGGTTA
* *
741800 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
741824 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
741848 AACATAAACAAACGAACATAACCG
1 AACATAAACGAACGAACATAAACG
741872 AAC
1 AAC
741875 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:742074 original size:18 final size:17
Alignment explanation
Indices: 742051--742117 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
742041 AGGCCTAATT
742051 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
742069 ATATAGTTTATATATAA
1 ATATAGTTTATATATAA
*
742086 ACT-TA-TATTATATATAT
1 A-TATAGT-TTATATATAA
*
742103 ATATA-TATATATATA
1 ATATAGTTTATATATA
742118 TTATATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.23
17 22 0.50
18 12 0.27
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:742084 original size:2 final size:2
Alignment explanation
Indices: 742059--742123 Score: 57
Period size: 2 Copynumber: 33.5 Consensus size: 2
742049 TTATATAGTT
* * *
742059 TA TA -A TA TA AA TA TA GTT TA TA TA TA AA CT- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA
742100 TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
742124 TTTTTAATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
1 4 0.08
2 46 0.90
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:744490 original size:6 final size:6
Alignment explanation
Indices: 744479--744582 Score: 138
Period size: 6 Copynumber: 17.3 Consensus size: 6
744469 CATACATGTG
* * *
744479 TATATA TATATA TATATA TATATA TATGTA TATGTA TATATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
744527 TATATA TATATG TATATA TATGTA TATATA TATATA TATAAA TAGTA-A
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA-TATA
744575 TATATA TA
1 TATATA TA
744583 AAGAATATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
5 2 0.02
6 83 0.95
7 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (6 bp):
TATATA
Found at i:744494 original size:10 final size:10
Alignment explanation
Indices: 744479--744582 Score: 138
Period size: 10 Copynumber: 10.4 Consensus size: 10
744469 CATACATGTG
744479 TATATATATA
1 TATATATATA
744489 TATATATATA
1 TATATATATA
*
744499 TATATATGTA
1 TATATATATA
*
744509 TATGTATATA
1 TATATATATA
*
744519 TATGTATATA
1 TATATATATA
*
744529 TATATATATG
1 TATATATATA
*
744539 TATATATATG
1 TATATATATA
744549 TATATATATA
1 TATATATATA
*
744559 TATATATAAA
1 TATATATATA
744569 TAGTA-ATATA
1 TA-TATATATA
744579 TATA
1 TATA
744583 AAGAATATTT
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
9 2 0.02
10 81 0.95
11 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
TATATATATA
Found at i:744584 original size:16 final size:16
Alignment explanation
Indices: 744479--744582 Score: 147
Period size: 16 Copynumber: 6.5 Consensus size: 16
744469 CATACATGTG
*
744479 TATATATATATATATA
1 TATATATATATGTATA
744495 TATATATATATGTATA
1 TATATATATATGTATA
*
744511 TGTATATATATGTATA
1 TATATATATATGTATA
744527 TATATATATATGTATA
1 TATATATATATGTATA
* *
744543 TATATGTATATATATA
1 TATATATATATGTATA
*
744559 TATATATAAATAGTA-A
1 TATATATATAT-GTATA
744575 TATATATA
1 TATATATA
744583 AAGAATATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
16 77 0.97
17 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TATATATATATGTATA
Found at i:764837 original size:5 final size:5
Alignment explanation
Indices: 764827--764876 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
764817 GAACCGGTCT
* *
764827 GACCC GACCC GACTC GA-TC GACCC GACCC GACCC GACCGC TGACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC-C -GACCC GACC
764877 TGACTGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 4 0.10
5 30 0.75
6 2 0.05
7 4 0.10
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:764854 original size:24 final size:22
Alignment explanation
Indices: 764827--764876 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
764817 GAACCGGTCT
764827 GACCCGACCCGACTCGATCGACCC
1 GACCCGACCCGAC-CGAT-GACCC
*
764851 GACCCGACCCGACCGCTGACCC
1 GACCCGACCCGACCGATGACCC
764873 GACC
1 GACC
764877 TGACTGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 3 0.12
24 13 0.52
ACGTcount: A:0.20, C:0.52, G:0.22, T:0.06
Consensus pattern (22 bp):
GACCCGACCCGACCGATGACCC
Found at i:764879 original size:10 final size:10
Alignment explanation
Indices: 764825--764880 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
764815 TCGAACCGGT
764825 CTGACCCGAC
1 CTGACCCGAC
* * *
764835 CCGACTCGAT
1 CTGACCCGAC
764845 C-GACCCGAC
1 CTGACCCGAC
*
764854 CCGACCCGACC
1 CTGACCCGA-C
764865 GCTGACCCGAC
1 -CTGACCCGAC
764876 CTGAC
1 CTGAC
764881 TGTTGACCGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 7 0.19
10 20 0.54
11 2 0.05
12 8 0.22
ACGTcount: A:0.20, C:0.50, G:0.21, T:0.09
Consensus pattern (10 bp):
CTGACCCGAC
Found at i:784363 original size:22 final size:21
Alignment explanation
Indices: 784335--784409 Score: 80
Period size: 22 Copynumber: 3.3 Consensus size: 21
784325 GCTTGAAGAG
784335 AAAAAAAGAAGTGAAAAAATGAAA
1 AAAAAAAGAA-TGAAAAAA--AAA
*
784359 AAAAAAA-AATAAAAAAAAAA
1 AAAAAAAGAATGAAAAAAAAA
784379 AAAAAAATGAATGAAAAAAAAA
1 AAAAAAA-GAATGAAAAAAAAA
784401 TGAAAAAAA
1 --AAAAAAA
784410 TGAGGGTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
20 10 0.22
22 19 0.42
23 2 0.04
24 14 0.31
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.08
Consensus pattern (21 bp):
AAAAAAAGAATGAAAAAAAAA
Found at i:784377 original size:18 final size:20
Alignment explanation
Indices: 784356--784400 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
784346 TGAAAAAATG
784356 AAAAAAAAAAAAT-AA-AAA
1 AAAAAAAAAAAATGAAGAAA
784374 AAAAAAAAAAAATGAATGAAA
1 AAAAAAAAAAAATGAA-GAAA
784395 AAAAAA
1 AAAAAA
784401 TGAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
21 9 0.38
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.07
Consensus pattern (20 bp):
AAAAAAAAAAAATGAAGAAA
Found at i:784400 original size:1 final size:1
Alignment explanation
Indices: 784356--784385 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
784346 TGAAAAAATG
*
784356 AAAAAAAAAAAATAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
784386 TGAATGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:784410 original size:24 final size:23
Alignment explanation
Indices: 784348--784412 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
784338 AAAAGAAGTG
**
784348 AAAAAATGAAAAAAAAAAAATAAA
1 AAAAAATG-AAAAAAATGAATAAA
*
784372 AAAAAA-AAAAAAAATGAATGAAA
1 AAAAAATGAAAAAAATGAAT-AAA
784395 AAAAAATGAAAAAAATGA
1 AAAAAATGAAAAAAATGA
784413 GGGTTCAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 10 0.29
23 9 0.26
24 16 0.46
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.09
Consensus pattern (23 bp):
AAAAAATGAAAAAAATGAATAAA
Found at i:785641 original size:55 final size:55
Alignment explanation
Indices: 785572--786264 Score: 868
Period size: 55 Copynumber: 12.9 Consensus size: 55
785562 CAGGTTCCCT
* *
785572 ACGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
785627 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * *
785682 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGGGAGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * * *
785737 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAGGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * * *
785792 GCGATTGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAAAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
785847 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * * *
785902 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTAAAGAAATAGGGGGCAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
** * * *
785957 GTGATTG-AGAAGATTG---G-GTCTTATA--CTCTGAAGAAATAGAGGG-GGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* * *
786004 GA-GATCGTTGAAGATTGTTCGAGTC-T-TACTCTCTGAGGAAATAGGGAGCGAAAC
1 -ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCG-GAC
* * * **
786058 ACGATTGTTGAAGATTGTTCGGGTC-T-TACTCTCTGAGGAAATAGGGGGTAGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
786111 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCGGAC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
786166 GCGATCGTTGAAGATTGTTCGAGTCTTATACTCCCTGAAGAAATA---GG-GG--
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
* *
786215 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAG-AATAGGGGGC
1 ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGC
786265 AGACGTGATT
Statistics
Matches: 563, Mismatches: 58, Indels: 37
0.86 0.09 0.06
Matches are distributed among these distances:
47 7 0.01
48 28 0.05
49 36 0.06
50 10 0.02
51 7 0.01
52 20 0.04
53 26 0.05
54 54 0.10
55 375 0.67
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (55 bp):
ACGATCGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCGGAC
Found at i:785850 original size:165 final size:165
Alignment explanation
Indices: 785572--786284 Score: 1032
Period size: 165 Copynumber: 4.4 Consensus size: 165
785562 CAGGTTCCCT
* ** * * * *
785572 ACGATCGTTGAAGATTGTTCAAGTCTCATACTCTCTGAAGAAATAGGGGGCGGACACGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
* *
785637 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGGGCAGACGCGATCGTTGAAGATTGTTC
66 AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGAGGGCGGACGCGATCGTTGAAGATTGTTC
* *
785702 GAGTCTTATACTCTCTGAGGAAATAGGGAGCGGAC
131 GAGTCTTATACTCCCTGAAGAAATAGGGAGCGGAC
*
785737 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAGGAAATAGGGGGCAGACGCGATTGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
* *
785802 AAGATTGTTCGAGTCTTATACTCCCTGAAAAAATAGGGGGCGGACGCGATCGTTGAAGATTGTTC
66 AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGAGGGCGGACGCGATCGTTGAAGATTGTTC
*
785867 GAGTCTTATACTCCCTGAAGAAATAGGGGGCGGAC
131 GAGTCTTATACTCCCTGAAGAAATAGGGAGCGGAC
* * *
785902 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTAAAGAAATAGGGGGCAGACGTGATTG-AG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
*
785966 AAGATTG---G-GTCTTATACT--CTGAAGAAATAGAGGG-GGACGAGATCGTTGAAGATTGTTC
66 AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGAGGGCGGACGCGATCGTTGAAGATTGTTC
* * *
786024 GAGTC-T-TACTCTCTGAGGAAATAGGGAGCGAAAC
131 GAGTCTTATACTCCCTGAAGAAATAGGGAGCG-GAC
* * *
786058 ACGATTGTTGAAGATTGTTCGGGTC-T-TACTCTCTGAGGAAATAGGGGGTAGACGCGATCGTTG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
*
786121 AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGGGCGGACGCGATCGTTGAAGATTGTTC
66 AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGAGGGCGGACGCGATCGTTGAAGATTGTTC
786186 GAGTCTTATACTCCCTGAAGAAATA--G-G-GG--
131 GAGTCTTATACTCCCTGAAGAAATAGGGAGCGGAC
* *
786215 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAG-AATAGGGGGCAGACGTGATTGATG
1 ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
786279 AAGATT
66 AAGATT
786285 AAATGGGGGG
Statistics
Matches: 493, Mismatches: 42, Indels: 33
0.87 0.07 0.06
Matches are distributed among these distances:
154 29 0.06
155 30 0.06
156 28 0.06
157 53 0.11
158 42 0.09
159 21 0.04
160 11 0.02
161 17 0.03
162 29 0.06
163 1 0.00
164 23 0.05
165 209 0.42
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (165 bp):
ACGATTGTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGTTG
AAGATTGTTCGAGTCTTATACTCCCTGAAGAAATAGAGGGCGGACGCGATCGTTGAAGATTGTTC
GAGTCTTATACTCCCTGAAGAAATAGGGAGCGGAC
Found at i:788488 original size:20 final size:18
Alignment explanation
Indices: 788450--788488 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
788440 CTTGTTTAAC
*
788450 TTTTGATTATATGTTTAG
1 TTTTGATTATATATTTAG
788468 TTTTGATTTATTATATTTAG
1 TTTTGA-TTA-TATATTTAG
788488 T
1 T
788489 CACTTTTTTA
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:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (18 bp):
TTTTGATTATATATTTAG
Found at i:790129 original size:3 final size:3
Alignment explanation
Indices: 790121--790148 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
790111 ACATATTAAA
790121 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
790149 TCGACTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:804907 original size:19 final size:19
Alignment explanation
Indices: 804880--804946 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 19
804870 TTGTTTTCCA
*
804880 TTTTCTTCTTTCATCTCTT
1 TTTTTTTCTTTCATCTCTT
*
804899 TTTTTTTCTCTC-TCTCTT
1 TTTTTTTCTTTCATCTCTT
* *** *
804917 TTTCTTTCGAACAACTCTT
1 TTTTTTTCTTTCATCTCTT
804936 TTTTTTTCTTT
1 TTTTTTTCTTT
804947 TTCGAACTGC
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.07, C:0.24, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTTTTCTTTCATCTCTT
Found at i:810338 original size:12 final size:12
Alignment explanation
Indices: 810305--810410 Score: 101
Period size: 12 Copynumber: 8.8 Consensus size: 12
810295 ACATTCATCA
810305 AGTATCAATACC
1 AGTATCAATACC
* *
810317 AATATGAATA-C
1 AGTATCAATACC
*
810328 ATGTATCAATATC
1 A-GTATCAATACC
810341 AGTATCAATACC
1 AGTATCAATACC
* *
810353 AATATGAATACTC
1 AGTATCAATAC-C
810366 -GTATCAATACC
1 AGTATCAATACC
810377 AGTATCAATACCC
1 AGTATCAATA-CC
*
810390 A-CATCAATACC
1 AGTATCAATACC
*
810401 ATTATCAATA
1 AGTATCAATA
810411 TTATACAATA
Statistics
Matches: 77, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
11 6 0.08
12 65 0.84
13 6 0.08
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (12 bp):
AGTATCAATACC
Found at i:810352 original size:36 final size:36
Alignment explanation
Indices: 810305--810411 Score: 146
Period size: 36 Copynumber: 3.0 Consensus size: 36
810295 ACATTCATCA
810305 AGTATCAATACCAATATGAATACATGTATCAATATC
1 AGTATCAATACCAATATGAATACATGTATCAATATC
*
810341 AGTATCAATACCAATATGAATAC-TCGTATCAATACC
1 AGTATCAATACCAATATGAATACAT-GTATCAATATC
* * *
810377 AGTATCAATACCCACATCAATACCAT-TATCAATAT
1 AGTATCAATACCAATATGAATA-CATGTATCAATAT
810412 TATACAATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 1 0.02
36 60 0.95
37 1 0.02
38 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (36 bp):
AGTATCAATACCAATATGAATACATGTATCAATATC
Found at i:811345 original size:32 final size:31
Alignment explanation
Indices: 811299--811416 Score: 155
Period size: 32 Copynumber: 3.7 Consensus size: 31
811289 ACTAGTAGTA
* * *
811299 TGTCGCATTCAGATAATACACACCAGTGTCAG
1 TGTCACATTCAGATAATGCACA-TAGTGTCAG
*
811331 TGTCACATTCAGATAATGCACAATAGTGTTAG
1 TGTCACATTCAGATAATGCAC-ATAGTGTCAG
*
811363 TGTCACATTCAGATAATGCACTATAGTTTCAG
1 TGTCACATTCAGATAATGCAC-ATAGTGTCAG
*
811395 TGTCGCATTCAGATAATGCACA
1 TGTCACATTCAGATAATGCACA
811417 ACAATTACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 1 0.01
32 75 0.97
33 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (31 bp):
TGTCACATTCAGATAATGCACATAGTGTCAG
Found at i:815119 original size:64 final size:64
Alignment explanation
Indices: 815051--815185 Score: 200
Period size: 64 Copynumber: 2.1 Consensus size: 64
815041 ACAATAATTA
** * *
815051 CATTCGATGTTTCAA-AGGAGCAGAAGTGCATCGATGCATGGTATGTGCATCGGTACATAAAATG
1 CATTCGATGTTTCAATAAAAGCAGAAGTGCATCAATGCATGGT-TGTGCATCGGTACACAAAATG
* *
815115 CATTCGATGTTTCAATAAAATCAGGAGTGCATCAATGCATGGTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAATAAAAGCAGAAGTGCATCAATGCATGGTTGTGCATCGGTACACAAAATG
815179 CATTCGA
1 CATTCGA
815186 ATTAGGGTGT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
64 42 0.66
65 22 0.34
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAAGCAGAAGTGCATCAATGCATGGTTGTGCATCGGTACACAAAATG
Found at i:815512 original size:13 final size:14
Alignment explanation
Indices: 815494--815529 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
815484 TTTAAGATTT
815494 TCTTTGAAAATC-A
1 TCTTTGAAAATCAA
815507 TCTTTG-AAATCAA
1 TCTTTGAAAATCAA
815520 T-TTTGAAAAT
1 TCTTTGAAAAT
815530 TACTCCCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (14 bp):
TCTTTGAAAATCAA
Found at i:815841 original size:25 final size:27
Alignment explanation
Indices: 815804--815887 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 27
815794 TCATTCAAAC
* *
815804 AAACCAAA-TATCCAAA-ATATATTCA
1 AAACCAAACAATCCAAACAAATATTCA
815829 AAA-CAAACAATCCAAACTAAATATTCA
1 AAACCAAACAATCCAAAC-AAATATTCA
*
815856 AAATCCAAACAA-ACAAAGCCAAATATTCA
1 AAA-CCAAACAATCCAAA--CAAATATTCA
815885 AAA
1 AAA
815888 TGTTTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.08
25 10 0.20
27 11 0.22
28 4 0.08
29 19 0.39
30 1 0.02
ACGTcount: A:0.60, C:0.21, G:0.01, T:0.18
Consensus pattern (27 bp):
AAACCAAACAATCCAAACAAATATTCA
Found at i:815864 original size:29 final size:28
Alignment explanation
Indices: 815822--815888 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
815812 TATCCAAAAT
* *
815822 ATATTCAAAA-CAAACAATCCAAA-CTAA
1 ATATTCAAAATCAAACAA-ACAAAGCCAA
815849 ATATTCAAAATCCAAACAAACAAAGCCAA
1 ATATTCAAAAT-CAAACAAACAAAGCCAA
815878 ATATTCAAAAT
1 ATATTCAAAAT
815889 GTTTTTAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 10 0.29
28 4 0.11
29 21 0.60
ACGTcount: A:0.58, C:0.21, G:0.01, T:0.19
Consensus pattern (28 bp):
ATATTCAAAATCAAACAAACAAAGCCAA
Found at i:817345 original size:13 final size:13
Alignment explanation
Indices: 817323--817365 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
817313 TCCTAATGGG
817323 CAAT-TTTGAAAA
1 CAATGTTTGAAAA
*
817335 CTATGTTTGAAAA
1 CAATGTTTGAAAA
817348 CAATGTTTGAAAA
1 CAATGTTTGAAAA
817361 TCAAT
1 -CAAT
817366 ATGGAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:817394 original size:14 final size:14
Alignment explanation
Indices: 817377--817407 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
817367 TGGAGTTTTC
817377 AAAACAACATAATT
1 AAAACAACATAATT
817391 AAAACAACATAATT
1 AAAACAACATAATT
817405 AAA
1 AAA
817408 TTAAAAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAACAACATAATT
Found at i:817917 original size:44 final size:44
Alignment explanation
Indices: 817842--817945 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 44
817832 AAACCTGACG
* *
817842 AGTGTATCGATGCACATTCAAGGCATACATCGGTGCA-TCTTCAT
1 AGTGTATCGATGCACATTCAAGGAATACATCGGTACACT-TTCAT
* * *
817886 AGTGCATCGATGCATATTCAAGGAATGCATCGGTACACTTTCAT
1 AGTGTATCGATGCACATTCAAGGAATACATCGGTACACTTTCAT
817930 AGTGTATCGATGCACA
1 AGTGTATCGATGCACA
817946 ATGCACAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 51 0.98
45 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATACATCGGTACACTTTCAT
Found at i:823937 original size:11 final size:13
Alignment explanation
Indices: 823905--823934 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
823895 TGGCCAAAGA
823905 TGAAAAGGTATGT
1 TGAAAAGGTATGT
823918 TGAAAAGGTATG-
1 TGAAAAGGTATGT
823930 TGAAA
1 TGAAA
823935 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:829163 original size:18 final size:19
Alignment explanation
Indices: 829130--829165 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
829120 GGGTCTTTCT
829130 CCTTCGATTCCGTTTGAAG
1 CCTTCGATTCCGTTTGAAG
*
829149 CCTTC-ATTTCGTTTGAA
1 CCTTCGATTCCGTTTGAA
829166 TTTTCTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (19 bp):
CCTTCGATTCCGTTTGAAG
Found at i:830878 original size:63 final size:64
Alignment explanation
Indices: 830768--830901 Score: 191
Period size: 63 Copynumber: 2.1 Consensus size: 64
830758 ACACTAATTA
* * * *
830768 CATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATGGTTGTGCATCGGTTCATAAAATG
1 CATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
* *
830832 CATTCGATGTTTCAATAA-AATCA-GAGTGCATCGATGCATGGCTGTGCATTGGTACACAAAATG
1 CATTCGATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
830895 CATTCGA
1 CATTCGA
830902 ATTAGGGTGT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
63 43 0.68
64 18 0.29
65 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (64 bp):
CATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACACAAAATG
Found at i:833980 original size:11 final size:11
Alignment explanation
Indices: 833961--834024 Score: 67
Period size: 11 Copynumber: 5.8 Consensus size: 11
833951 TCACGAACAT
833961 GTTCGTTTAGC
1 GTTCGTTTAGC
* *
833972 GTTCATTTAGT
1 GTTCGTTTAGC
833983 GTTCGTTTAGC
1 GTTCGTTTAGC
*
833994 GTT-GTTTTAGT
1 GTTCG-TTTAGC
* *
834005 GTTTGTTTATC
1 GTTCGTTTAGC
834016 GTTCGTTTA
1 GTTCGTTTA
834025 TATATTCGAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
10 1 0.02
11 41 0.95
12 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (11 bp):
GTTCGTTTAGC
Found at i:833988 original size:22 final size:22
Alignment explanation
Indices: 833960--834024 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
833950 TTCACGAACA
833960 TGTTCGTTTAGCGTTCATTTAG
1 TGTTCGTTTAGCGTTCATTTAG
**
833982 TGTTCGTTTAGCGTTGTTTTAG
1 TGTTCGTTTAGCGTTCATTTAG
* * *
834004 TGTTTGTTTATCGTTCGTTTA
1 TGTTCGTTTAGCGTTCATTTA
834025 TATATTCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (22 bp):
TGTTCGTTTAGCGTTCATTTAG
Found at i:834254 original size:12 final size:12
Alignment explanation
Indices: 834237--834277 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
834227 GAACGAGTTG
*
834237 ATAAACAAGCTC
1 ATAAACGAGCTC
*
834249 ATAAACGAGCTT
1 ATAAACGAGCTC
834261 ATAAACGAGCTC
1 ATAAACGAGCTC
834273 ATAAA
1 ATAAA
834278 TGAGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:834264 original size:24 final size:24
Alignment explanation
Indices: 834228--834283 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
834218 AACATAAATG
834228 AACGAGTTGATAAACAAGCTCATA
1 AACGAGTTGATAAACAAGCTCATA
*
834252 AACGAGCTT-ATAAACGAGCTCATA
1 AACGAG-TTGATAAACAAGCTCATA
*
834276 AATGAGTT
1 AACGAGTT
834284 TTTTCGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 25 0.86
25 2 0.07
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (24 bp):
AACGAGTTGATAAACAAGCTCATA
Found at i:835057 original size:2 final size:2
Alignment explanation
Indices: 835050--835088 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
835040 TTCTTAAAAT
835050 TA 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 TA T
835089 TAGAATCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:836151 original size:21 final size:18
Alignment explanation
Indices: 836109--836164 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 18
836099 TCCTCTGCAA
*
836109 TTATATAAATTACATATT
1 TTATATAAATGACATATT
836127 TTATATAAATAGATCATATTT
1 TTATATAAAT-GA-CATA-TT
*
836148 TTATATAAATTACATAT
1 TTATATAAATGACATAT
836165 CAATGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 11 0.33
19 5 0.15
20 5 0.15
21 12 0.36
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (18 bp):
TTATATAAATGACATATT
Found at i:836509 original size:19 final size:18
Alignment explanation
Indices: 836477--836514 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
836467 TATGATATAT
836477 AATTTTAAAGTTATCTTTA
1 AATTTTAAAGTTAT-TTTA
836496 AATTTCTAAA-TTATTTTA
1 AATTT-TAAAGTTATTTTA
836514 A
1 A
836515 TGGAATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTTTAAAGTTATTTTA
Found at i:840169 original size:57 final size:59
Alignment explanation
Indices: 840055--840171 Score: 141
Period size: 57 Copynumber: 2.0 Consensus size: 59
840045 GTACACATCA
* *
840055 ACATGTATCGATACACTCTTGAATAAAGAAAACATCGAATGCAATAAGTGTATCGATAC
1 ACATGTATCGATACACCCTTGAATAAAGAAAACATCGAATGCAATAAGTGTACCGATAC
* * * * *
840114 ACATGTA-CGATACACCCTTTAA-GATGAAAACATCGAATGTAATTTA-TGTACCGATAC
1 ACATGTATCGATACACCCTTGAATAAAGAAAACATCGAATGCAA-TAAGTGTACCGATAC
840171 A
1 A
840172 TAGGTAGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 28 0.56
58 15 0.30
59 7 0.14
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (59 bp):
ACATGTATCGATACACCCTTGAATAAAGAAAACATCGAATGCAATAAGTGTACCGATAC
Done.