Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_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: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:617718 original size:19 final size:20
Alignment explanation
Indices: 617682--617720 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
617672 ATTTTAGTTC
* *
617682 ATCCCCTTAAGTTTAAATTT
1 ATCCCCTTAAGATAAAATTT
617702 ATCCCC-TAAGATAAAATTT
1 ATCCCCTTAAGATAAAATTT
617721 TATGTTCGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
ATCCCCTTAAGATAAAATTT
Found at i:618331 original size:33 final size:33
Alignment explanation
Indices: 618289--618376 Score: 97
Period size: 32 Copynumber: 2.6 Consensus size: 33
618279 ATAAAAAATA
*
618289 CGGGTTCGGGTTGAGTTTTTTTAAGTTTGATATT
1 CGGG-TCGGGTTGAGTTTTTTTAAGTGTGATATT
* * *
618323 CGGGTCGGGTCG-GATTTTTTAAGTGTGGTATT
1 CGGGTCGGGTTGAGTTTTTTTAAGTGTGATATT
**
618355 TAGGTCGGGTTCGAGTTTTTTT
1 CGGGTCGGGTT-GAGTTTTTTT
618377 TAAATTCAGG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
32 25 0.57
33 8 0.18
34 11 0.25
ACGTcount: A:0.12, C:0.08, G:0.33, T:0.47
Consensus pattern (33 bp):
CGGGTCGGGTTGAGTTTTTTTAAGTGTGATATT
Found at i:621939 original size:2 final size:2
Alignment explanation
Indices: 621928--621967 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
621918 GCTTAGCGTC
621928 TA TA -A 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 TA T
621968 GATTAGAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:622294 original size:2 final size:2
Alignment explanation
Indices: 622287--622316 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
622277 CTTAGCGTCC
622287 TA TA TA TA TA TA T- 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
622317 GATTAGAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:624504 original size:4 final size:4
Alignment explanation
Indices: 624495--624540 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
624485 TTTAATGCAC
* *
624495 TTAT TTA- TT-T TTAT TTAT TTAT TTAT TTAT TCAT TTCAT TGAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TTA
624541 AATCATGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 4 0.11
4 28 0.80
5 3 0.09
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:630017 original size:29 final size:29
Alignment explanation
Indices: 629975--630030 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
629965 ATCGAATTTC
629975 CTGCATTATATGATCTTATTATAAGATTG
1 CTGCATTATATGATCTTATTATAAGATTG
630004 CTGCATTATATGATCTTATTATAAGAT
1 CTGCATTATATGATCTTATTATAAGAT
630031 ACTTATCGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (29 bp):
CTGCATTATATGATCTTATTATAAGATTG
Found at i:630412 original size:53 final size:52
Alignment explanation
Indices: 630349--630453 Score: 174
Period size: 53 Copynumber: 2.0 Consensus size: 52
630339 CATAAATTTC
*
630349 GTGTAAGATGGTACAGAAAGTAGACTGAATTAACATATTCAATGCAAATGCAA
1 GTGTAAGATGGTACAGAAAGTAGACAGAA-TAACATATTCAATGCAAATGCAA
* *
630402 GTGTAAGATGGTACAGAAAGTAGACAGAATAGCATATTCGATGCAAATGCAA
1 GTGTAAGATGGTACAGAAAGTAGACAGAATAACATATTCAATGCAAATGCAA
630454 TGGCTTGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 21 0.43
53 28 0.57
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (52 bp):
GTGTAAGATGGTACAGAAAGTAGACAGAATAACATATTCAATGCAAATGCAA
Found at i:631963 original size:141 final size:142
Alignment explanation
Indices: 631709--631991 Score: 559
Period size: 141 Copynumber: 2.0 Consensus size: 142
631699 ATCAAATGAA
631709 AAGCTGTACGTTACGTTCTAATCTCCAAAACCACAACTTAATTGAAATCATCGATAAAACCCATA
1 AAGCTGTACGTTACGTTCTAATCTCCAAAACCACAACTTAATTGAAATCATCGATAAAACCCATA
631774 TGTAAACTGTAAGCACAGGCACGCAACAGAAAAATGGCACAAACCC-AAAAGGCAAAATATTCTC
66 TGTAAACTGTAAGCACAGGCACGCAACAGAAAAATGGCACAAACCCAAAAAGGCAAAATATTCTC
631838 AATTTACGCACG
131 AATTTACGCACG
631850 AAGCTGTACGTTACGTTCTAATCTCCAAAACCACAACTTAATTGAAATCATCGATAAAACCCATA
1 AAGCTGTACGTTACGTTCTAATCTCCAAAACCACAACTTAATTGAAATCATCGATAAAACCCATA
631915 TGTAAACTGTAAGCACAGGCACGCAACAGAAAAATGGCACAAACCCAAAAAGGCAAAATATTCTC
66 TGTAAACTGTAAGCACAGGCACGCAACAGAAAAATGGCACAAACCCAAAAAGGCAAAATATTCTC
631980 AATTTACGCACG
131 AATTTACGCACG
631992 CTGTCATCTA
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 111 0.79
142 30 0.21
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.20
Consensus pattern (142 bp):
AAGCTGTACGTTACGTTCTAATCTCCAAAACCACAACTTAATTGAAATCATCGATAAAACCCATA
TGTAAACTGTAAGCACAGGCACGCAACAGAAAAATGGCACAAACCCAAAAAGGCAAAATATTCTC
AATTTACGCACG
Found at i:636376 original size:2 final size:2
Alignment explanation
Indices: 636371--636399 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
636361 CTCTCTCTAT
636371 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 T
636400 CTATGTAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:640600 original size:17 final size:17
Alignment explanation
Indices: 640558--640602 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
640548 ATTTTTATAT
*
640558 AATATATCTTTTAAAACA
1 AATATAT-TTTTAAAAAA
*
640576 ATTA-ATTTTTAAAAAA
1 AATATATTTTTAAAAAA
640592 AATATATTTTT
1 AATATATTTTT
640603 CTGAAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 12 0.52
17 8 0.35
18 3 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATTTTTAAAAAA
Found at i:640948 original size:38 final size:35
Alignment explanation
Indices: 640905--640991 Score: 93
Period size: 39 Copynumber: 2.3 Consensus size: 35
640895 AACTAAACAT
640905 TAAATTTTAAACAAGATACTAAAATGAAAAAAAAAAC
1 TAAATTTTAAACAAGATACT-AAATG-AAAAAAAAAC
* * *
640942 TAAAATTTTTAACAACATGGTACTAAATGAAACAAAAAC
1 T-AAA-TTTT-A-AACAAGATACTAAATGAAAAAAAAAC
640981 TAAATTTTAAA
1 TAAATTTTAAA
640992 TATAATTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
35 2 0.05
36 1 0.02
37 5 0.12
38 6 0.14
39 14 0.33
40 6 0.14
41 9 0.21
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (35 bp):
TAAATTTTAAACAAGATACTAAATGAAAAAAAAAC
Found at i:644302 original size:17 final size:16
Alignment explanation
Indices: 644269--644299 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
644259 AAATAAAATT
644269 ATTAATTTACTTTTTA
1 ATTAATTTACTTTTTA
644285 ATTAATTTACTTTTT
1 ATTAATTTACTTTTT
644300 TAAAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTAATTTACTTTTTA
Found at i:656710 original size:6 final size:6
Alignment explanation
Indices: 656699--656724 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
656689 AACTTCTCTC
656699 ATCCCT ATCCCT ATCCCT ATCCCT AT
1 ATCCCT ATCCCT ATCCCT ATCCCT AT
656725 AGATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.46, G:0.00, T:0.35
Consensus pattern (6 bp):
ATCCCT
Found at i:661532 original size:229 final size:229
Alignment explanation
Indices: 661095--661552 Score: 900
Period size: 228 Copynumber: 2.0 Consensus size: 229
661085 ACTTAGCATG
661095 GGTGAATTTAACTTTAATTGGACAAATGTTCTATCATAGTAAGTATAAACAAATATGATGCACAA
1 GGTGAATTTAACTTTAATTGGACAAATGTTCTATCATAGTAAGTATAAACAAATATGATGCACAA
661160 ATAGTTCTGTTTTTCCTTATTGGTTGAAAATCAAGGCCCCTTCAAAACAAAGTAAAAGTGATTGT
66 ATAGTTCTGTTTTTCCTTATTGGTTGAAAATCAAGGCCCCTTCAAAACAAAGTAAAAGTGATTGT
661225 ATGAACATACAAAAATGGAAACGCTTTTATGAGCAAATGAAGCCACAAGGAAGCTCATTTAATTA
131 ATGAACATACAAAAATGGAAACGCTTTTATGAGCAAATGAAGCCACAAGGAAGCTCATTTAATTA
661290 CACTACAATACCAAATGCCTAACGGTATGTAACC
196 CACTACAATACCAAATGCCTAACGGTATGTAACC
661324 GGTGAA-TTAACTTTAATTGGACAAATGTTCTATCATAGTAAGTATAAACAAATATGATGCACAA
1 GGTGAATTTAACTTTAATTGGACAAATGTTCTATCATAGTAAGTATAAACAAATATGATGCACAA
661388 ATAGTTCTGTTTTTCCTTATTGGTTGAAAATCAAGGCCCCTTCAAAACAAAGTAAAAGTGATTGT
66 ATAGTTCTGTTTTTCCTTATTGGTTGAAAATCAAGGCCCCTTCAAAACAAAGTAAAAGTGATTGT
661453 ATGAACATACAAAAATGGAAAACGCTTTTATGAGCAAATGAAGCCACAAGGAAGCTCATTTAATT
131 ATGAACATACAAAAATGG-AAACGCTTTTATGAGCAAATGAAGCCACAAGGAAGCTCATTTAATT
661518 ACACTACAATACCAAATGCCTAACGGTATGTAACC
195 ACACTACAATACCAAATGCCTAACGGTATGTAACC
661553 CCAGAATGAC
Statistics
Matches: 228, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
228 141 0.62
229 87 0.38
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (229 bp):
GGTGAATTTAACTTTAATTGGACAAATGTTCTATCATAGTAAGTATAAACAAATATGATGCACAA
ATAGTTCTGTTTTTCCTTATTGGTTGAAAATCAAGGCCCCTTCAAAACAAAGTAAAAGTGATTGT
ATGAACATACAAAAATGGAAACGCTTTTATGAGCAAATGAAGCCACAAGGAAGCTCATTTAATTA
CACTACAATACCAAATGCCTAACGGTATGTAACC
Found at i:663933 original size:54 final size:53
Alignment explanation
Indices: 663851--663959 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 53
663841 ATGATTTCTT
663851 ATAAGAGGAATGACCTAACTTACCTGTTGAAGTATTGAAAATGCCTCCGAAAAC
1 ATAAGAGGAATGACCTAACTTACCTGTTGAAGTATTGAAAATGCCTCC-AAAAC
663905 ATAAGAGGAATGACCTAACTTACCTGTTGAAGTATTGAAAATGCCTCCAAAAC
1 ATAAGAGGAATGACCTAACTTACCTGTTGAAGTATTGAAAATGCCTCCAAAAC
663958 AT
1 AT
663960 TTGTATGCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
53 7 0.13
54 48 0.87
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (53 bp):
ATAAGAGGAATGACCTAACTTACCTGTTGAAGTATTGAAAATGCCTCCAAAAC
Found at i:666845 original size:39 final size:39
Alignment explanation
Indices: 666786--666976 Score: 294
Period size: 39 Copynumber: 4.9 Consensus size: 39
666776 TCAACAACAA
*
666786 CAGACTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
**
666825 CAGATTTTGAAGAATCAGTTGCTGCATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
* *
666864 TAGATTTTGAAGAATCAGATGCCACATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
666903 CAGATTTTGAAGAATCAGTTGCC-CTATTAACCTCTCCCT
1 CAGATTTTGAAGAATCAGTTGCCAC-ATTAACCTCTCCCT
* * *
666942 CAGATTTTGTAGAATCAGTTTCCATATTAACCTCT
1 CAGATTTTGAAGAATCAGTTGCCACATTAACCTCT
666977 TCGTCTATTT
Statistics
Matches: 138, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
38 1 0.01
39 137 0.99
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (39 bp):
CAGATTTTGAAGAATCAGTTGCCACATTAACCTCTCCCT
Found at i:667407 original size:53 final size:53
Alignment explanation
Indices: 667327--667432 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
667317 CAAATTATAT
667327 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
1 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
667380 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
1 ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
667433 GCTCCTCTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.26
Consensus pattern (53 bp):
ATAACATGCAGTTCTAGCTCAGATTAGCATATACAATAAAAAAGATATCCATC
Found at i:669500 original size:242 final size:243
Alignment explanation
Indices: 669072--669554 Score: 842
Period size: 242 Copynumber: 2.0 Consensus size: 243
669062 GAACAAAGTA
669072 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
1 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
* * *
669137 TAGAAGAGGGAGGAAACTGAACAACATAACTTCTCAGAGGAATCATAACTGATTAATCCAGGGGA
66 TAGAAGAGGGAGGAAACTG-A-AACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGA
*
669202 AACAGAAAATATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAA
129 AACAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAA
*
669267 GGAACACTAACATGTGAAAGCACTCAGGATCAGTCGGTTTTATAGGCAAC
194 GGAACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGGCAAC
*
669317 ATAAATGAATTGATAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
1 ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
* * *
669382 TAGATGAGGGAGGAAACTG-AACATAACTCCTCAGAGAAATCATAACTGATTATTCCAGAGGCAA
66 TAGAAGAGGGAGGAAACTGAAACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGAAA
669446 CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
131 CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
* *
669511 AACACTAACATGTGAAAGCACTCGGGATCAGTTGGATTTATAGG
196 AACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGG
669555 TGGTATACAT
Statistics
Matches: 227, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
242 145 0.64
245 82 0.36
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (243 bp):
ATAAATGAATTGACAAACTGCTAAGAGATGCCTAAGCCTAAGGATTTTCAAATAATATCACAAAC
TAGAAGAGGGAGGAAACTGAAACATAACTCCTCAGAGAAATCATAACTGATTAATCCAGAGGAAA
CAGAAAAGATAACACAGTTAGCAAAGCATCCTAAAATTCTCAAACAAATGCAGAGTTTTTTAAGG
AACACTAACATGTGAAAGCACTCAGGATCAGTCGGATTTATAGGCAAC
Found at i:670761 original size:22 final size:21
Alignment explanation
Indices: 670733--670775 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
670723 AGAAGAATCA
670733 GCTTTTGCAATACAACAATACT
1 GCTTTTGCAATACAAC-ATACT
*
670755 GCTTTTGCAATGCAACATACT
1 GCTTTTGCAATACAACATACT
670776 TAAATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
GCTTTTGCAATACAACATACT
Found at i:677357 original size:21 final size:22
Alignment explanation
Indices: 677331--677378 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
677321 CAAAGTTCGC
*
677331 TTCAATG-GTATTAAATCGTGG
1 TTCAATGCATATTAAATCGTGG
677352 TTCAATGCATATTAAATCGTGG
1 TTCAATGCATATTAAATCGTGG
677374 TTCAA
1 TTCAA
677379 GATAGTCGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (22 bp):
TTCAATGCATATTAAATCGTGG
Found at i:681415 original size:8 final size:8
Alignment explanation
Indices: 681402--681440 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
681392 TCGACATTGT
681402 GGCGGGTG
1 GGCGGGTG
681410 GGCGGGTG
1 GGCGGGTG
681418 GGCGGGTG
1 GGCGGGTG
*
681426 GGCGGGCG
1 GGCGGGTG
681434 GGCGGGT
1 GGCGGGT
681441 CGAGGACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.00, C:0.15, G:0.74, T:0.10
Consensus pattern (8 bp):
GGCGGGTG
Found at i:682619 original size:24 final size:24
Alignment explanation
Indices: 682587--682636 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
682577 AATTCCAACC
682587 ATCATATTATAATAGGATGATTAA
1 ATCATATTATAATAGGATGATTAA
* *
682611 ATCATATTATAGTAGGATGCTTAA
1 ATCATATTATAATAGGATGATTAA
682635 AT
1 AT
682637 TCGAGACGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (24 bp):
ATCATATTATAATAGGATGATTAA
Found at i:682942 original size:22 final size:22
Alignment explanation
Indices: 682914--682985 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
682904 TTCCATTTCG
682914 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
682936 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
682955 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
682977 CGTTGCGAT
1 CGTTGCGAT
682986 TTTTCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:682959 original size:19 final size:19
Alignment explanation
Indices: 682935--683003 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
682925 TCTACAGTTG
*
682935 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTACAAAT
* **
682954 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
682975 GTCGTTGCGATTTTTCAAAT
1 -TCGTTGCGATTTTACAAAT
682995 TCGTTGCGA
1 TCGTTGCGA
683004 AAATTCGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 19 0.49
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:682959 original size:41 final size:41
Alignment explanation
Indices: 682914--683003 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
682904 TTCCATTTCG
682914 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
682955 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
682996 CGTTGCGA
1 CGTTGCGA
683004 AAATTCGTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:683108 original size:6 final size:6
Alignment explanation
Indices: 683097--683146 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
683087 AGACACGTAT
*
683097 GACCAC GACCAC GACCAC GACC-C GA-GAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
683143 GACC
1 GACC
683147 CGAGACGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
5 6 0.15
6 34 0.85
ACGTcount: A:0.32, C:0.48, G:0.20, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:683137 original size:28 final size:28
Alignment explanation
Indices: 683097--683154 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
683087 AGACACGTAT
683097 GACCACGACCACGACCACGACCCGAGAC
1 GACCACGACCACGACCACGACCCGAGAC
683125 GACCACGACCACGACCACGACCCGAGAC
1 GACCACGACCACGACCACGACCCGAGAC
683153 GA
1 GA
683155 GACGGACGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.45, G:0.22, T:0.00
Consensus pattern (28 bp):
GACCACGACCACGACCACGACCCGAGAC
Found at i:683656 original size:6 final size:6
Alignment explanation
Indices: 683635--683671 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
683625 TCTCGTCTCG
683635 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
683672 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:683820 original size:20 final size:20
Alignment explanation
Indices: 683795--683887 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
683785 ACTGTAGACT
683795 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
683815 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
683835 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* *
683856 ATCACAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
*
683876 AGCGCAACGCGA
1 ATCGCAACGCGA
683888 TTTTCAACTA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:683865 original size:21 final size:21
Alignment explanation
Indices: 683835--683908 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
683825 GAAATGAAAA
683835 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
683856 ATCACAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
683876 AGCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
683897 ATCGCAACGCGA
1 ATCGCAACGCGA
683909 AATGCAACGC
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 13 0.34
21 25 0.66
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:683929 original size:41 final size:41
Alignment explanation
Indices: 683819--683912 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
683809 TGAAAAATCG
* *
683819 CAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCA
1 CAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCA
*
683860 CAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCG
1 CAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCA
683901 CAACGCGAAATG
1 CAACGCGAAATG
683913 CAACGCGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACGCGAAATGGAAAAGCGCAACGCGATTTTCAACTATCA
Found at i:684325 original size:16 final size:16
Alignment explanation
Indices: 684284--684327 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
684274 GCACAGGAGC
* *
684284 ATGACAGATATCGTTA
1 ATGACACATGTCGTTA
*
684300 GTGACACATGTCGTTA
1 ATGACACATGTCGTTA
684316 ATGACACATGTC
1 ATGACACATGTC
684328 AATACATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (16 bp):
ATGACACATGTCGTTA
Found at i:684592 original size:10 final size:10
Alignment explanation
Indices: 684577--684612 Score: 54
Period size: 10 Copynumber: 3.4 Consensus size: 10
684567 TTGATAATGG
684577 TAAAAGAAAA
1 TAAAAGAAAA
684587 TAAAAGAAAA
1 TAAAAGAAAA
684597 TAAAAGTAAAAA
1 TAAAAG--AAAA
684609 TAAA
1 TAAA
684613 TTAGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 16 0.67
12 8 0.33
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (10 bp):
TAAAAGAAAA
Found at i:685735 original size:32 final size:33
Alignment explanation
Indices: 685676--685780 Score: 88
Period size: 32 Copynumber: 3.2 Consensus size: 33
685666 ACACCATCAC
* * * *
685676 TTATGTTATATACACGTGATATATATCATGTCA
1 TTATTTTATATACACATAATATGTATCATGTCA
* **
685709 TTATTTT-TATACATATAATATGTATCACATCA
1 TTATTTTATATACACATAATATGTATCATGTCA
* * * *
685741 TT-TTTTATGTACACGTAGTATGTATTATGTCA
1 TTATTTTATATACACATAATATGTATCATGTCA
*
685773 TTACTTTA
1 TTATTTTA
685781 AAGATGTAAT
Statistics
Matches: 55, Mismatches: 15, Indels: 4
0.74 0.20 0.05
Matches are distributed among these distances:
31 4 0.07
32 41 0.75
33 10 0.18
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (33 bp):
TTATTTTATATACACATAATATGTATCATGTCA
Found at i:694500 original size:15 final size:15
Alignment explanation
Indices: 694480--694530 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
694470 TTTCAGAAAA
694480 TGAATTACTGAAATT
1 TGAATTACTGAAATT
**
694495 TGAATTACTGAAAAA
1 TGAATTACTGAAATT
694510 TGAATTACT-ATAATT
1 TGAATTACTGA-AATT
694525 TGAATT
1 TGAATT
694531 CTGGAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 1 0.03
15 30 0.97
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:694508 original size:29 final size:29
Alignment explanation
Indices: 694475--694546 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 29
694465 TGGTTTTTCA
694475 GAAAATGAATTACTGA-AATTTGAATTACTG
1 GAAAATGAATTACT-ATAATTTGAATT-CTG
*
694505 AAAAATGAATTACTATAATTTGAATTCTG
1 GAAAATGAATTACTATAATTTGAATTCTG
694534 GAAAATGAATTAC
1 GAAAATGAATTAC
694547 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (29 bp):
GAAAATGAATTACTATAATTTGAATTCTG
Found at i:694552 original size:20 final size:20
Alignment explanation
Indices: 694529--694598 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
694519 ATAATTTGAA
694529 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
694549 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
694569 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
694589 TTCTAGAAAA
1 TTCTGGAAAA
694599 CATCTGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:694851 original size:28 final size:29
Alignment explanation
Indices: 694762--694861 Score: 86
Period size: 29 Copynumber: 3.5 Consensus size: 29
694752 CTTTACTAAA
*
694762 ATATTATTGAA-ATAT-ATAAATAATATTAT
1 ATATTATT-AATATATAAAAAAT-ATATTAT
*
694791 -TCATTATTAATATATAAAAAATTTATTAT
1 AT-ATTATTAATATATAAAAAATATATTAT
694820 ATATTATTAA-A-ATAAAAATATATATCT-T
1 ATATTATTAATATATAAAAA-ATATAT-TAT
*
694848 ATATTATTTATATA
1 ATATTATTAATATA
694862 ATTGATTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
27 7 0.12
28 19 0.32
29 26 0.44
30 7 0.12
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
ATATTATTAATATATAAAAAATATATTAT
Found at i:694862 original size:28 final size:27
Alignment explanation
Indices: 694774--694862 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
694764 ATTATTGAAA
* *
694774 TATATAAATAATATTATTCAT-TATTA-A
1 TATATAAAAAATA-TATT-ATATATTATT
*
694801 TATATAAAAAATTTATTATATATTATT
1 TATATAAAAAATATATTATATATTATT
* *
694828 AAAATAAAAATATATATCT-TATATTATT
1 TATATAAAAA-ATATAT-TATATATTATT
694856 TATATAA
1 TATATAA
694863 TTGATTATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.04
26 9 0.18
27 19 0.38
28 19 0.38
29 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TATATAAAAAATATATTATATATTATT
Found at i:694892 original size:31 final size:30
Alignment explanation
Indices: 694857--694922 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
694847 TATATTATTT
*
694857 ATATAATTGATTATTTTATATAATATTAA-AA
1 ATATAATTGA-TATTAT-TATAATATTAATAA
*
694888 ATATAATTTATATTATTATAATATTAATAA
1 ATATAATTGATATTATTATAATATTAATAA
694918 ATATA
1 ATATA
694923 TTTTAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 11 0.34
30 12 0.38
31 9 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAATTGATATTATTATAATATTAATAA
Found at i:694925 original size:29 final size:28
Alignment explanation
Indices: 694867--694927 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
694857 ATATAATTGA
*
694867 TTATTTTATATAATATTAAAAATATAAT
1 TTATATTATATAATATTAAAAATATAAT
*
694895 TTATATTATTATAATATTAATAAATATATT
1 TTATATTA-TATAATATTAA-AAATATAAT
694925 TTA
1 TTA
694928 AATATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.24
29 11 0.38
30 11 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATATTATATAATATTAAAAATATAAT
Found at i:694933 original size:29 final size:30
Alignment explanation
Indices: 694875--694946 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
694865 GATTATTTTA
*
694875 TATAATATTAA-AAATATAATTTATATTAT
1 TATAATATTAATAAATATAATTTATAATAT
*
694904 TATAATATTAATAAATATATTTTA-AATAT
1 TATAATATTAATAAATATAATTTATAATAT
*
694933 TTTAATAATTAATA
1 TATAAT-ATTAATA
694947 TTTTGATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 20 0.53
30 18 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TATAATATTAATAAATATAATTTATAATAT
Found at i:695180 original size:42 final size:42
Alignment explanation
Indices: 695121--695240 Score: 177
Period size: 42 Copynumber: 2.8 Consensus size: 42
695111 ATGAATTACA
** *
695121 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
* *
695163 TTCCGGAAAACGAATTACGTGAAATAAACACGAAAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
*
695205 TTTCGAAAAACGAATTACGTGAAACAAACACAGAAA
1 TTCCGAAAAACGAATTACGTGAAACAAACAC-GAAA
695241 TTCGGGAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
42 65 0.94
43 4 0.06
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.17
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
Found at i:696454 original size:12 final size:12
Alignment explanation
Indices: 696437--696465 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
696427 GAAACTAACC
696437 TTTTTTTTTCTT
1 TTTTTTTTTCTT
696449 TTTTTTTTTCTT
1 TTTTTTTTTCTT
696461 TTTTT
1 TTTTT
696466 GCATCTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:700872 original size:122 final size:123
Alignment explanation
Indices: 700714--700940 Score: 323
Period size: 122 Copynumber: 1.9 Consensus size: 123
700704 TTGAATTTTT
* * ** *
700714 TTGAAAGTTTAGGTACTAAAACGGACCAAATTTGATAGTTTAGGTACTAAATGCGTTAAATTTTT
1 TTGAAAGTGTAGATACTAAAACGGACCAAAAATGATAATTTAGGTACTAAATGCGTTAAATTTTT
** * *
700779 AATGGTAGGGTAC-GAAAATGAAACT-AAAACTAAATGTTATGTATGATTTTAAAAAAA
66 AATGACAGGGTACTAAAAATGAAA-TAAAAACTAAACGTTATGTATGATTTTAAAAAAA
* *
700836 TTGAAAGTGTAGATACTAAAATGGACCAAAAATGATAATTTAGGTACTAAATGCGTTAAGTTTTT
1 TTGAAAGTGTAGATACTAAAACGGACCAAAAATGATAATTTAGGTACTAAATGCGTTAAATTTTT
*
700901 AATGACAGTGTACTAAAAATGAAATAAAAACTAAACGTTA
66 AATGACAGGGTACTAAAAATGAAATAAAAACTAAACGTTA
700941 GTCATTGTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
122 69 0.76
123 22 0.24
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (123 bp):
TTGAAAGTGTAGATACTAAAACGGACCAAAAATGATAATTTAGGTACTAAATGCGTTAAATTTTT
AATGACAGGGTACTAAAAATGAAATAAAAACTAAACGTTATGTATGATTTTAAAAAAA
Found at i:706856 original size:16 final size:16
Alignment explanation
Indices: 706835--706883 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
706825 TTGATTTACC
706835 TTTTCTCTTCTTCATT
1 TTTTCTCTTCTTCATT
706851 TTTTCTCTTCCTCTTCATT
1 TTTTCTC-T--TCTTCATT
*
706870 TTCTTATCTTCTTC
1 TT-TTCTCTTCTTC
706884 TTCATGCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 7 0.25
17 6 0.21
19 11 0.39
20 4 0.14
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTCTCTTCTTCATT
Found at i:706882 original size:17 final size:18
Alignment explanation
Indices: 706840--706888 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
706830 TTACCTTTTC
706840 TCTTCTTCATTTTTTCTCT
1 TCTTCTTCA-TTTTTCTCT
* *
706859 TCCTCTTCATTTTCTTATCT
1 TCTTCTTCA-TTT-TTCTCT
706879 TCTTCTTCAT
1 TCTTCTTCAT
706889 GCTTCTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (18 bp):
TCTTCTTCATTTTTCTCT
Found at i:706885 original size:20 final size:19
Alignment explanation
Indices: 706840--706888 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
706830 TTACCTTTTC
*
706840 TCTTCTTCATTTTTTCTCT
1 TCTTCTTCATTTTTTATCT
*
706859 TCCTCTTCATTTTCTTATCT
1 TCTTCTTCATTTT-TTATCT
706879 TCTTCTTCAT
1 TCTTCTTCAT
706889 GCTTCTCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTTCTTCATTTTTTATCT
Found at i:715734 original size:14 final size:14
Alignment explanation
Indices: 715715--715749 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
715705 CTACACCGGT
715715 TGAACCGCTACTAG
1 TGAACCGCTACTAG
715729 TGAACCGCTACTAG
1 TGAACCGCTACTAG
715743 TGAACCG
1 TGAACCG
715750 GTCAGAACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (14 bp):
TGAACCGCTACTAG
Found at i:715776 original size:17 final size:18
Alignment explanation
Indices: 715743--715776 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
715733 CCGCTACTAG
715743 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
715761 TGAACCGGTC-GAACCG
1 TGAACCGGTCAGAACCG
715777 GACCGGCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.26, C:0.32, G:0.29, T:0.12
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:727480 original size:22 final size:24
Alignment explanation
Indices: 727455--727500 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
727445 TGAAATATAA
*
727455 ATATCTAA-AATAA-ATTATTTTT
1 ATATCTAATAATAATATCATTTTT
*
727477 ATATTTAATAATAATATCATTTTT
1 ATATCTAATAATAATATCATTTTT
727501 TAATATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 5 0.25
24 8 0.40
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATCTAATAATAATATCATTTTT
Found at i:727504 original size:13 final size:13
Alignment explanation
Indices: 727488--727512 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
727478 TATTTAATAA
727488 TAATATCATTTTT
1 TAATATCATTTTT
727501 TAATATCATTTT
1 TAATATCATTTT
727513 AATAAATAAA
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:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATCATTTTT
Found at i:727529 original size:15 final size:15
Alignment explanation
Indices: 727511--727541 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
727501 TAATATCATT
727511 TTAATAAATAAAATA
1 TTAATAAATAAAATA
*
727526 TTAATTAATAAAATA
1 TTAATAAATAAAATA
727541 T
1 T
727542 ATTTATCAAA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAATAAATAAAATA
Found at i:730605 original size:12 final size:12
Alignment explanation
Indices: 730588--730612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
730578 TAACAAAAAT
730588 ATCAAATTTATC
1 ATCAAATTTATC
730600 ATCAAATTTATC
1 ATCAAATTTATC
730612 A
1 A
730613 GGTCTGAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCAAATTTATC
Found at i:732400 original size:2 final size:2
Alignment explanation
Indices: 732395--732424 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
732385 AAAGAAACAT
732395 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
732425 CCTCAAGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:739558 original size:2 final size:2
Alignment explanation
Indices: 739551--739576 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
739541 TTCTCGATGC
739551 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
739577 TAAAGAGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:742694 original size:12 final size:12
Alignment explanation
Indices: 742679--742713 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
742669 CGATCAGAAT
742679 GACGAAGATGAA
1 GACGAAGATGAA
*
742691 GACGATGATGAA
1 GACGAAGATGAA
*
742703 GATGAAGATGA
1 GACGAAGATGA
742714 TGATGGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.06, G:0.34, T:0.14
Consensus pattern (12 bp):
GACGAAGATGAA
Found at i:742703 original size:18 final size:18
Alignment explanation
Indices: 742677--742718 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
742667 GACGATCAGA
*
742677 ATGACGAAGATGAAGACG
1 ATGATGAAGATGAAGACG
*
742695 ATGATGAAGATGAAGATG
1 ATGATGAAGATGAAGACG
742713 ATGATG
1 ATGATG
742719 GAAAAGGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.05, G:0.33, T:0.19
Consensus pattern (18 bp):
ATGATGAAGATGAAGACG
Found at i:743160 original size:14 final size:16
Alignment explanation
Indices: 743138--743171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
743128 TTAGAATACG
* *
743138 AAAACATATTTTAAAA
1 AAAATATATATTAAAA
743154 AAAATATATATTAAAA
1 AAAATATATATTAAAA
743170 AA
1 AA
743172 TTTAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATATATTAAAA
Found at i:744158 original size:21 final size:20
Alignment explanation
Indices: 744072--744229 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
744062 AAATGACCAA
**
744072 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
744091 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
744111 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
744131 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
744152 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
744173 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
744193 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
744214 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
744230 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:744574 original size:20 final size:20
Alignment explanation
Indices: 744197--744587 Score: 450
Period size: 20 Copynumber: 19.4 Consensus size: 20
744187 GATTTTCAAT
* ** *
744197 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
744217 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
744237 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744257 AATCGCAACGTGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A
**
744278 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
744298 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744318 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
744338 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
744359 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744379 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
744399 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744419 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
744439 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744459 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
744479 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
744499 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
744519 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
744539 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
744559 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
744579 AATCACAAC
1 AATCGCAAC
744588 ACTGAAATTT
Statistics
Matches: 319, Mismatches: 40, Indels: 24
0.83 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 279 0.87
21 35 0.11
22 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:745303 original size:24 final size:24
Alignment explanation
Indices: 745264--745310 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
745254 AAATTTGGTC
745264 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
745288 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
745311 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:745502 original size:12 final size:12
Alignment explanation
Indices: 745485--745509 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
745475 ATATAATCCT
745485 GAAGAAGAAAAA
1 GAAGAAGAAAAA
745497 GAAGAAGAAAAA
1 GAAGAAGAAAAA
745509 G
1 G
745510 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:747813 original size:19 final size:19
Alignment explanation
Indices: 747791--748163 Score: 406
Period size: 19 Copynumber: 21.4 Consensus size: 19
747781 CGGAAAATAC
*
747791 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
747810 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
747824 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
747843 AATCGCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
747857 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
747877 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
747891 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
747910 AATC-CAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
747923 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
747943 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
747957 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
747976 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
747995 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
748009 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
748028 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
748047 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
748066 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
748085 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
748104 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
748118 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
748137 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
748156 AATCGCAA
1 AATCGCAA
748164 CGAGATAATC
Statistics
Matches: 304, Mismatches: 10, Indels: 80
0.77 0.03 0.20
Matches are distributed among these distances:
13 12 0.04
14 62 0.20
15 3 0.01
16 16 0.05
17 12 0.04
18 8 0.03
19 162 0.53
20 29 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:747846 original size:33 final size:33
Alignment explanation
Indices: 747791--748185 Score: 357
Period size: 33 Copynumber: 11.5 Consensus size: 33
747781 CGGAAAATAC
* *
747791 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
747824 AATCGCAATGCGGAAATG-AAATCGCAACATGAA
1 AATCGCAATGC-GAAATGAAAATCGCAACATGAA
*
747857 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGAA
747891 AATCGCAATGCGAAATGAAAATC-CAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
*
747923 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAAC-ATGAA
747957 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
* * *
747995 AATCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACATGAA
*
748028 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
748066 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
748104 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
*
748137 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAA
748170 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
748186 TATAAACGCA
Statistics
Matches: 317, Mismatches: 17, Indels: 56
0.81 0.04 0.14
Matches are distributed among these distances:
31 2 0.01
32 25 0.08
33 145 0.46
34 47 0.15
35 9 0.03
36 7 0.02
37 1 0.00
38 72 0.23
39 8 0.03
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAA
Found at i:748089 original size:109 final size:102
Alignment explanation
Indices: 747852--748144 Score: 234
Period size: 109 Copynumber: 2.8 Consensus size: 102
747842 AAATCGCAAC
*
747852 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGA-GAATCGCAATGCGAAATGAAAATC-
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAAATGAATCGCAA--CG--ATGAAAATCG
* * * * *
747914 CAA--C---ATGAAAATCGCAATGCGGAAAT-GAAAAT-CGCA
61 CAATGCGAAATGAAAATCGCAACGAGAAAATCG-CAATGCGAA
* *
747950 ACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCG
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG--AATCGCAACGATGAAAATCG
748014 CAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
61 CAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAA
*
748061 ATGGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGA--AAGAATCGC
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG--AATCGCAACGATGAA-AATCGC
748124 AATGCGAAATGAAAATCGCAA
62 AATGCGAAATGAAAATCGCAA
748145 TGCGAAATGA
Statistics
Matches: 163, Mismatches: 11, Indels: 31
0.80 0.05 0.15
Matches are distributed among these distances:
98 3 0.02
99 23 0.14
100 15 0.09
101 4 0.02
102 4 0.02
104 8 0.05
105 13 0.08
107 1 0.01
108 1 0.01
109 76 0.47
110 9 0.06
111 6 0.04
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (102 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAATCGCAACGATGAAAATCGCAATG
CGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAA
Found at i:748201 original size:52 final size:52
Alignment explanation
Indices: 747819--748185 Score: 484
Period size: 52 Copynumber: 7.0 Consensus size: 52
747809 AAATCCCAAC
*
747819 ATGAAAATCGCAATGCGGAAATG-AAATCGCAAC-ATGAAAATCGCAATGCGGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAA
* * * * *
747872 ATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGA-AAT-GAAAAT-CCAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
747917 CATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 -ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
747971 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
748023 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
748080 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
748132 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
748184 AT
1 AT
748186 TATAAACGCA
Statistics
Matches: 283, Mismatches: 13, Indels: 37
0.85 0.04 0.11
Matches are distributed among these distances:
45 2 0.01
46 15 0.05
47 7 0.02
48 12 0.04
49 1 0.00
50 1 0.00
51 2 0.01
52 147 0.52
53 36 0.13
54 8 0.03
55 5 0.02
56 1 0.00
57 46 0.16
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:748215 original size:14 final size:14
Alignment explanation
Indices: 748196--748283 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
748186 TATAAACGCA
748196 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
748210 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
748227 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
748243 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
748260 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
748276 TTGCGATT
1 TTGCGATT
748284 TTCATTTCGC
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
16 14 0.23
17 14 0.23
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:748215 original size:33 final size:33
Alignment explanation
Indices: 748192--748301 Score: 220
Period size: 33 Copynumber: 3.3 Consensus size: 33
748182 AAATTATAAA
748192 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
748225 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
748258 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
748291 CGCATTGCGAT
1 CGCATTGCGAT
748302 AGTCATTTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (33 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:748234 original size:19 final size:19
Alignment explanation
Indices: 748210--748301 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
748200 GATTCTCTCG
748210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
748229 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
748243 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
748262 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
748276 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
748295 TTGCGAT
1 TTGCGAT
748302 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:748248 original size:66 final size:66
Alignment explanation
Indices: 748178--748301 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
748168 ATAATCGCAA
748178 TGCGAAATT-ATAAACGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 TGCGAAATTCAT-AACGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
748242 GT
65 GT
** **
748244 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TGCGAAATTCATAACGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAT
748302 AGTCATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
TGCGAAATTCATAACGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG
T
Found at i:748309 original size:19 final size:17
Alignment explanation
Indices: 748192--748301 Score: 76
Period size: 16 Copynumber: 6.6 Consensus size: 17
748182 AAATTATAAA
*
748192 CGCATTGCGATTC-TCT
1 CGCATTGCGATTCATTT
748208 CG--TTGCGATTTTCATTT
1 CGCATTGCGA--TTCATTT
*
748225 CGCATTGCGATTC-TCT
1 CGCATTGCGATTCATTT
748241 CG--TTGCGATTTTCATTT
1 CGCATTGCGA--TTCATTT
*
748258 CGCATTGCGATTC-TCT
1 CGCATTGCGATTCATTT
748274 CG--TTGCGATTTTCATTT
1 CGCATTGCGA--TTCATTT
748291 CGCATTGCGAT
1 CGCATTGCGAT
748302 AGTCATTTTT
Statistics
Matches: 74, Mismatches: 5, Indels: 29
0.69 0.05 0.27
Matches are distributed among these distances:
14 18 0.24
16 19 0.26
17 19 0.26
19 18 0.24
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (17 bp):
CGCATTGCGATTCATTT
Found at i:748423 original size:13 final size:14
Alignment explanation
Indices: 748407--748442 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
748397 CATCAATTAC
748407 ACAAATCAAC-TTT
1 ACAAATCAACTTTT
*
748420 ACAAATCATCTTTT
1 ACAAATCAACTTTT
748434 ACAAATCAA
1 ACAAATCAA
748443 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:750373 original size:19 final size:19
Alignment explanation
Indices: 750333--750467 Score: 101
Period size: 19 Copynumber: 7.6 Consensus size: 19
750323 TAGTTTACTT
* *
750333 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
750353 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
750372 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
750391 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
750405 TCGCAATGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
750424 TCGCAA--CG-AA--AGAA
1 TCGCAACGCGAAACCAAAA
**
750438 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
750457 TCGCAATGCGA
1 TCGCAACGCGA
750468 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:750408 original size:14 final size:14
Alignment explanation
Indices: 750389--750445 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
750379 GCGAAATGAA
750389 AATCGCAACGACAG
1 AATCGCAACGACAG
*
750403 AATCGCAATGCGAAACCAA
1 AATCGCAA--CG--A-CAG
*
750422 AATCGCAACGAAAG
1 AATCGCAACGACAG
750436 AATCGCAACG
1 AATCGCAACG
750446 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.26, G:0.19, T:0.09
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:750416 original size:33 final size:33
Alignment explanation
Indices: 750370--750462 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
750360 GCGAAACCAA
*
750370 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* **
750403 AATCGCAATGCGAAACCAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
750436 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
750463 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:750459 original size:52 final size:54
Alignment explanation
Indices: 750333--750467 Score: 149
Period size: 52 Copynumber: 2.5 Consensus size: 54
750323 TAGTTTACTT
* *
750333 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
*
750391 TCGCAA-CGACA-G--AATCGCAATGCGAAACCAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
750438 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
750468 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 39 0.57
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:750485 original size:19 final size:19
Alignment explanation
Indices: 750463--750591 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
750453 AAAATCGCAA
750463 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
750482 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
750496 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
750515 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
750529 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
750548 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
750567 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
750587 TGCGA
1 TGCGA
750592 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:750505 original size:33 final size:33
Alignment explanation
Indices: 750463--750554 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
750453 AAAATCGCAA
750463 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
750496 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
750529 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
750555 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:750805 original size:92 final size:93
Alignment explanation
Indices: 750635--751013 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
750625 TTGAATGGAT
750635 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
750700 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
750728 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
750792 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
750820 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
750884 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
750912 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
750977 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
751005 AAATTTACT
1 AAATTTACT
751014 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:750964 original size:185 final size:185
Alignment explanation
Indices: 750635--751013 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
750625 TTGAATGGAT
750635 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
750700 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
750765 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
750820 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
750884 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
750949 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
751005 AAATTTACT
1 AAATTTACT
751014 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:752737 original size:14 final size:14
Alignment explanation
Indices: 752718--752840 Score: 93
Period size: 14 Copynumber: 7.7 Consensus size: 14
752708 TTGAAATGAA
752718 AATCGCAACGAGAG
1 AATCGCAACGAGAG
752732 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
752749 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
752765 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
752784 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
752798 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
752817 AATCGCAACGAGAG
1 AATCGCAACGAGAG
752831 AATCGCAACG
1 AATCGCAACG
752841 CGAAATGAAA
Statistics
Matches: 90, Mismatches: 4, Indels: 30
0.73 0.03 0.24
Matches are distributed among these distances:
14 38 0.42
15 2 0.02
16 10 0.11
17 10 0.11
18 2 0.02
19 28 0.31
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:752755 original size:33 final size:33
Alignment explanation
Indices: 752710--752857 Score: 278
Period size: 33 Copynumber: 4.5 Consensus size: 33
752700 TCTTTTGGTT
752710 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
752743 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
752776 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
752809 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
752842 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
752858 TGCGATTTTG
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 111 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:752756 original size:19 final size:18
Alignment explanation
Indices: 752717--752862 Score: 108
Period size: 19 Copynumber: 8.8 Consensus size: 18
752707 GTTGAAATGA
752717 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
752732 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
752749 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
752765 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
752782 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
752798 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
752815 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
752831 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
752848 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
752863 TTTTGGTTTC
Statistics
Matches: 105, Mismatches: 6, Indels: 36
0.71 0.04 0.24
Matches are distributed among these distances:
14 32 0.30
16 20 0.19
17 17 0.16
19 36 0.34
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:752893 original size:14 final size:14
Alignment explanation
Indices: 752874--752928 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
752864 TTTGGTTTCG
752874 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
752888 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
752907 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
752921 CGTTGCGA
1 CGTTGCGA
752929 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:752906 original size:33 final size:33
Alignment explanation
Indices: 752858--752928 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
752848 AAAATCGCAA
**
752858 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
752891 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
752924 TGCGA
1 TGCGA
752929 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:752936 original size:33 final size:33
Alignment explanation
Indices: 752869--752950 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
752859 GCGATTTTGG
***
752869 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
752902 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
752935 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
752951 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:752955 original size:20 final size:20
Alignment explanation
Indices: 752881--752969 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
752871 TCGCGTTGCG
752881 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
752901 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
752914 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
752934 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
752954 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
752970 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:753091 original size:33 final size:33
Alignment explanation
Indices: 753049--753119 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
753039 AATACTAACT
753049 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
***
753082 TGAAAATCGCAACGAGAGAATCTTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
753115 TGAAA
1 TGAAA
753120 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:753353 original size:22 final size:22
Alignment explanation
Indices: 753301--753355 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
753291 TGGTTGTGAG
**
753301 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
753323 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
753345 GGATTTCTTCG
1 GGATTTCTTCG
753356 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:753526 original size:20 final size:20
Alignment explanation
Indices: 753501--753694 Score: 212
Period size: 20 Copynumber: 9.6 Consensus size: 20
753491 CTTTAAATAT
753501 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
753521 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
753543 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
753562 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
753582 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
753602 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
753623 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
753643 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
753663 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
753683 CGCGTTGCGATT
1 CGCGTTGCGATT
753695 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.01
20 110 0.75
21 32 0.22
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:753578 original size:61 final size:60
Alignment explanation
Indices: 753501--753694 Score: 237
Period size: 61 Copynumber: 3.2 Consensus size: 60
753491 CTTTAAATAT
*
753501 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTAGCGTTGCGATTTACGGATA
* * ***
753562 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTA-GCGTTGCGA-TTTACGGATA
* * * * ** *
753623 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
753683 CGCGTTGCGATT
1 CGCGTTGCGATT
753695 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.02
60 30 0.27
61 78 0.70
62 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTAGCGTTGCGATTTACGGATA
Found at i:753671 original size:81 final size:81
Alignment explanation
Indices: 753500--753694 Score: 241
Period size: 81 Copynumber: 2.4 Consensus size: 81
753490 GCTTTAAATA
** * * *
753500 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACGC
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
753565 GTTGCGATATACGGAT
66 GTTGCGATATACGGAT
* * *
753581 ACGCATTGCGATTTACCCATACGCGTTGCGATTTTACGGA-TACACGTTGCGATTTACGGATACG
1 TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTA-ACGTTGCGATTTACGGATACG
* *
753645 CGTTGCGATTTATGTG-T
65 CGTTGCGATATACG-GAT
* * *
753662 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACACATACGCGTTGCGATT
753695 ATTGAAAATC
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
80 2 0.02
81 94 0.97
82 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (81 bp):
TCGCGTTGCGATTTACACATACGCGTTGCGATTTTACGGATTAACGTTGCGATTTACGGATACGC
GTTGCGATATACGGAT
Found at i:755408 original size:28 final size:27
Alignment explanation
Indices: 755376--755431 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
755366 GTCAATCGCT
*
755376 ATATT-TTTTAAAAATTTTAATAATAAAA
1 ATATTATTTTAAAAA-TATAA-AATAAAA
*
755404 ATATTATTTTTAAAATATAAAATAAAA
1 ATATTATTTTAAAAATATAAAATAAAA
755431 A
1 A
755432 AATAAACCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.32
28 9 0.36
29 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATATTATTTTAAAAATATAAAATAAAA
Found at i:756739 original size:14 final size:14
Alignment explanation
Indices: 756720--756760 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
756710 TTAGGATTAG
*
756720 GGTTTAAGATTTAA
1 GGTTTATGATTTAA
* *
756734 GGTTTATGATATAG
1 GGTTTATGATTTAA
756748 GGTTTATGATTTA
1 GGTTTATGATTTA
756761 TGATTCAGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
GGTTTATGATTTAA
Found at i:757103 original size:16 final size:18
Alignment explanation
Indices: 757082--757118 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
757072 TTTATTTATC
*
757082 TAAAATTATTA-A-AATA
1 TAAAATAATTATATAATA
757098 TAAAATAATTATATAATA
1 TAAAATAATTATATAATA
757116 TAA
1 TAA
757119 TTGTATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 1 0.06
18 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAATTATATAATA
Found at i:758079 original size:23 final size:25
Alignment explanation
Indices: 758038--758089 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
758028 ATTAGTTCTC
*
758038 TTTTTTTTATTTTATGTC-TTTAATA
1 TTTTTTTTACTTTATGTCTTTTAA-A
758063 TTTTTTTT-CTTTA-GTCTTTTAAA
1 TTTTTTTTACTTTATGTCTTTTAAA
758086 TTTT
1 TTTT
758090 GAATAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
24 9 0.36
25 8 0.32
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTTTTTTACTTTATGTCTTTTAAA
Found at i:758773 original size:2 final size:2
Alignment explanation
Indices: 758766--758790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
758756 GTTAGGAAGC
758766 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
758791 GCATGGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:760902 original size:35 final size:35
Alignment explanation
Indices: 760863--760932 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
760853 TTTTTTAGCT
* * *
760863 TCAATTCATGATTTCGAGTTCGAGTCGAGCTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAGCTTGAA
*
760898 TCAATTCATAATTTCAATTTCGAGTCAAGCTTGAA
1 TCAATTCATAATTTCAAGTTCGAGTCAAGCTTGAA
760933 AATTTTAGGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (35 bp):
TCAATTCATAATTTCAAGTTCGAGTCAAGCTTGAA
Found at i:763170 original size:12 final size:12
Alignment explanation
Indices: 763155--763218 Score: 58
Period size: 12 Copynumber: 5.4 Consensus size: 12
763145 TATTTAAACG
763155 GGTATTGGGCCA
1 GGTATTGGGCCA
* *
763167 GGTATTGGGTCG
1 GGTATTGGGCCA
*
763179 GGTATTGGGTC-
1 GGTATTGGGCCA
**
763190 GGTATTGGGCTG
1 GGTATTGGGCCA
* *
763202 GGAATCGGGCCA
1 GGTATTGGGCCA
763214 GGTAT
1 GGTAT
763219 ATATATATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 9 0.21
12 33 0.79
ACGTcount: A:0.14, C:0.12, G:0.45, T:0.28
Consensus pattern (12 bp):
GGTATTGGGCCA
Found at i:763195 original size:11 final size:12
Alignment explanation
Indices: 763155--763198 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
763145 TATTTAAACG
*
763155 GGTATTGGGCCA
1 GGTATTGGGTCA
*
763167 GGTATTGGGTCG
1 GGTATTGGGTCA
763179 GGTATTGGGTC-
1 GGTATTGGGTCA
763190 GGTATTGGG
1 GGTATTGGG
763199 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:763197 original size:23 final size:24
Alignment explanation
Indices: 763153--763218 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
763143 ATTATTTAAA
763153 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
763177 CGGGTATTGGGTC-GGTATTGGG-
1 CGGGTATTGGGCCAGGTATTGGGT
* *
763199 CTGGGAATCGGGCCAGGTAT
1 C-GGGTATTGGGCCAGGTAT
763219 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 18 0.50
24 17 0.47
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.27
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:763284 original size:2 final size:2
Alignment explanation
Indices: 763273--763312 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
763263 AAATTTATTA
763273 AT AT -T AT 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 AT AT AT AT A
763313 ATTATTTTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:772742 original size:66 final size:67
Alignment explanation
Indices: 772636--772769 Score: 218
Period size: 66 Copynumber: 2.0 Consensus size: 67
772626 ATTAGTAAGA
* *
772636 ACAGCTGACACTCGAACCTGAAAGAAAGGTTCATTGACAGCTATGTTAGATAAGAT-TATATCAA
1 ACAGCTAACACTCGAACCTGAAAGAAAGGTTCATTGACAGCTATGTTAGATAAGATAAATATCAA
772700 TG
66 TG
*
772702 ACAGCTAACACAT-GAACCTGAAAGAAAGGTTCATTGACAGCTATGTTAGATAATATAAATATCA
1 ACAGCTAACAC-TCGAACCTGAAAGAAAGGTTCATTGACAGCTATGTTAGATAAGATAAATATCA
772766 ATG
65 ATG
772769 A
1 A
772770 GTACTGCAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
66 52 0.83
67 11 0.17
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (67 bp):
ACAGCTAACACTCGAACCTGAAAGAAAGGTTCATTGACAGCTATGTTAGATAAGATAAATATCAA
TG
Found at i:778042 original size:21 final size:21
Alignment explanation
Indices: 777993--778056 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
777983 CATATGAAAT
* *
777993 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAATGACCTATGAA
*
778014 TATGTCCCGAATGACCTATGAG
1 T-TGTCCCGAATGACCTATGAA
778036 TTGTCCCGAATGACCTATGAA
1 TTGTCCCGAATGACCTATGAA
778057 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAATGACCTATGAA
Found at i:779447 original size:64 final size:63
Alignment explanation
Indices: 779349--779509 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
779339 TAATGAAGGT
* *
779349 ATGCATCGATGCACTACACCATGCATCGATGCATAAACCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAACCCTATTCGATGTTTTCTATTTAAAT--
*
779412 GG
62 GC
* *
779414 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAACCCTATTCGATGTTTTCTATTTAAATGC
* *
779478 ATGCATCGATGCACTACATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
779510 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAACCCTATTCGATGTTTTCTATTTAAATGC
Found at i:789207 original size:64 final size:65
Alignment explanation
Indices: 789131--789256 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 65
789121 TATAAATTTA
789131 ACTACCAATCTCTTTAAATATTATTTTATTTCCGTTGTGCAGTGGAAAGTGGTGC-TTATGGTGG
1 ACTACCAATCTCTTTAAATATTATTTTATTTCCGTTGTGCAGTGGAAAGTGGTGCATTATGGTGG
789195 ACTACCAATCTCTTTAAATATTATTTTATTTCCGTTGTGCAGTGGAAAGTGGTGCATTATGG
1 ACTACCAATCTCTTTAAATATTATTTTATTTCCGTTGTGCAGTGGAAAGTGGTGCATTATGG
789257 GGAGTATATG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
64 55 0.90
65 6 0.10
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (65 bp):
ACTACCAATCTCTTTAAATATTATTTTATTTCCGTTGTGCAGTGGAAAGTGGTGCATTATGGTGG
Found at i:801559 original size:69 final size:71
Alignment explanation
Indices: 801484--801626 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 71
801474 CTATTAAAAC
801484 TCGTCATACCTATTTAGCCAGTTTCAAGTTACTATAAC-AATGTCGT-TTCTCAAAATAAAATAT
1 TCGTCATACCTATTTAGCCAGTTTCAAGTTACTATAACAAATGTCGTATTCTCAAAATAAAATAT
801547 CTGACT
66 CTGACT
*
801553 TCGTCATACCTATTTAGCCAGTTTCAAGTTACTGTAACAAATGTCGTAATTCTCAAAATAAAATA
1 TCGTCATACCTATTTAGCCAGTTTCAAGTTACTATAACAAATGTCGT-ATTCTCAAAATAAAATA
801618 TCTGACT
65 TCTGACT
801625 TC
1 TC
801627 ATATTGAGTT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
69 37 0.53
70 8 0.11
72 25 0.36
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (71 bp):
TCGTCATACCTATTTAGCCAGTTTCAAGTTACTATAACAAATGTCGTATTCTCAAAATAAAATAT
CTGACT
Found at i:810202 original size:25 final size:25
Alignment explanation
Indices: 810170--810280 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 25
810160 TGAGTTGACC
810170 AAAAATAATTTAATGATTATATATA
1 AAAAATAATTTAATGATTATATATA
810195 AAAAATAATTTAA-GA--ATATA-A
1 AAAAATAATTTAATGATTATATATA
* ** ** * *
810216 AAATATAAAGTTTTCTCTTTATTTAAA
1 AAAAAT-AA-TTTAATGATTATATATA
*
810243 ATAAAAAAATTTAATGATTATATAT-
1 A-AAAATAATTTAATGATTATATATA
810268 AAAAATAATTTAA
1 AAAAATAATTTAA
810281 ATGCATATTT
Statistics
Matches: 64, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
21 6 0.09
22 7 0.11
23 3 0.05
24 13 0.20
25 14 0.22
26 14 0.22
27 4 0.06
28 3 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (25 bp):
AAAAATAATTTAATGATTATATATA
Found at i:810299 original size:26 final size:23
Alignment explanation
Indices: 810170--810302 Score: 74
Period size: 25 Copynumber: 5.4 Consensus size: 23
810160 TGAGTTGACC
810170 AAAAATAATTTAATGATTATATAT
1 AAAAATAATTTAATGATTATA-AT
*
810194 AAAAAATAATTTAA-GAATATAA-
1 -AAAAATAATTTAATGATTATAAT
* ** * *
810216 AAATATAAAGTTTTCTCTTTATTTAAAAT
1 AAAAAT-AA---TT-TAATGA-TTATAAT
810245 AAAAA-AATTTAATGATTATATAT
1 AAAAATAATTTAATGATTATA-AT
*
810268 AAAAATAATTTAAATGCATATTTAAT
1 AAAAATAATTT-AATG-AT-TATAAT
810294 AAAAATAAT
1 AAAAATAAT
810303 ATTTCAAGTG
Statistics
Matches: 82, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
21 5 0.06
22 6 0.07
23 11 0.13
24 13 0.16
25 19 0.23
26 14 0.17
27 6 0.07
28 4 0.05
29 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAAATAATTTAATGATTATAAT
Found at i:810455 original size:20 final size:19
Alignment explanation
Indices: 810430--810483 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
810420 GCGAAATAAA
810430 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
810450 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
810470 AATCGCAACGCGAT
1 AATCGCAACGCGAT
810484 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:810494 original size:21 final size:20
Alignment explanation
Indices: 810470--810809 Score: 82
Period size: 20 Copynumber: 16.8 Consensus size: 20
810460 CAGTTCCCAG
810470 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
*
810490 GAATCGCAATGCGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
810511 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
*
810533 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGATTATGAA
**
810553 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
810573 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
* * *
810593 TATCGCAA--TGAGTATCCGTAA
1 AATCGCAACGCGATTAT--G-AA
*
810614 AATCGCAACGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
* *
810634 AATCGCAACGACAATACAT-AA
1 AATCGCAACG-CGAT-TATGAA
*
810655 AATCGCAACGCG--TATAGTA
1 AATCGCAACGCGATTAT-GAA
* * * *
810674 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGATTATGAA
* *
810694 AATCGCAACGCG-TATCTGTA
1 AATCGCAACGCGAT-TATGAA
* * * *
810714 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGATTATGAA
* *
810734 AATCGCAATGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
* *
810754 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGATTATG-AA
*
810775 AATCGCAACGCG--TATCCGTA
1 AATCGCAACGCGATTAT--GAA
810795 AATCGCAACGCGATT
1 AATCGCAACGCGATT
810810 TTTAAAGCGC
Statistics
Matches: 237, Mismatches: 48, Indels: 67
0.67 0.14 0.19
Matches are distributed among these distances:
17 2 0.01
18 6 0.03
19 16 0.07
20 127 0.54
21 76 0.32
22 6 0.03
23 2 0.01
24 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:810558 original size:20 final size:20
Alignment explanation
Indices: 810533--810807 Score: 229
Period size: 20 Copynumber: 13.7 Consensus size: 20
810523 GATTTTCCAG
* *
810533 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGTA
* **
810553 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
810573 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * * *
810592 CTATCGCAATGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
810614 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
810634 AATCGCAACGAC-AATACATAA
1 AATCGCAACG-CGAATACGT-A
*
810655 AATCGCAACGCGTATA-GTA
1 AATCGCAACGCGAATACGTA
*
810674 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
810694 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
810714 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
810734 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
810754 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
810775 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
810795 AATCGCAACGCGA
1 AATCGCAACGCGA
810808 TTTTTAAAGC
Statistics
Matches: 207, Mismatches: 35, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.00
19 18 0.09
20 134 0.65
21 52 0.25
22 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:810582 original size:40 final size:40
Alignment explanation
Indices: 810533--810808 Score: 258
Period size: 40 Copynumber: 6.8 Consensus size: 40
810523 GATTTTCCAG
* ** *
810533 AATCGCAACGCGAATATGAAAATCGCAACGCGA-ACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGATACATA-A
* * * * * *
810573 AATCGCAACGCG-ATTC-TGACTATCGCAATGAGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGCG-ATACATAA
*
810614 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGATACATAA
* * *
810655 AATCGCAACGCGTAT-AGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-ATACATAA
* * *
810694 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-A
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-ATACATAA
* * *
810734 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGATACATAA
810775 AATCGCAACGCGTATCCGTAAATCGCAACGCGAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAT
810809 TTTTAAAGCG
Statistics
Matches: 199, Mismatches: 26, Indels: 22
0.81 0.11 0.09
Matches are distributed among these distances:
39 19 0.10
40 99 0.50
41 73 0.37
42 7 0.04
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGATACATAA
Found at i:811291 original size:20 final size:19
Alignment explanation
Indices: 811266--811343 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 19
811256 TTATAAACTT
811266 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
811286 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
** *
811306 ACTATCCCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
811327 AAAATCGCAACGAGAAA
1 AAAATCGCAAC-AGAAA
811344 CCAAAATCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
20 31 0.63
21 18 0.37
ACGTcount: A:0.53, C:0.19, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:811326 original size:21 final size:21
Alignment explanation
Indices: 811281--811341 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
811271 CGCAACATGA
*
811281 AAATGAAAATCGCAAC-ACGA-
1 AAATGAAAATCCCAACGA-GAG
**
811301 AAATGACTATCCCAACGAGAG
1 AAATGAAAATCCCAACGAGAG
*
811322 AAATGAAAATCGCAACGAGA
1 AAATGAAAATCCCAACGAGA
811342 AACCAAAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCCCAACGAGAG
Found at i:811372 original size:19 final size:19
Alignment explanation
Indices: 811350--811462 Score: 110
Period size: 20 Copynumber: 6.1 Consensus size: 19
811340 GAAACCAAAA
*
811350 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
811369 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
811383 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
811402 TCGCGTTGCGATATTCATT
1 TCGCGTTGCGATTTTCATT
**
811421 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
811441 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
811461 TC
1 TC
811463 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 9 0.11
16 3 0.04
17 3 0.04
19 31 0.39
20 32 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:812540 original size:21 final size:21
Alignment explanation
Indices: 812514--812558 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
812504 GATTTCTGGG
* *
812514 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
812535 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
812556 CAA
1 CAA
812559 ACGACAGAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:813351 original size:32 final size:32
Alignment explanation
Indices: 813310--813405 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
813300 GAGTCGAGGG
813310 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
813342 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
813373 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
813405 T
1 T
813406 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:813522 original size:29 final size:30
Alignment explanation
Indices: 813397--813519 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
813387 AAGGAACATA
813397 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
813427 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
813457 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
813487 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
813516 TGGA
1 TGGA
813520 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Done.