Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 85 of 210
Found at i:29475553 original size:43 final size:43
Alignment explanation
Indices: 29475477--29475606 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
29475467 CATAGGACCT
* **
29475477 TCGATATGTGTTTTTGTGTAAGACCACGTCTGGGAC-GTCGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGT-GGCA
*
29475520 TCGACT-TGTGCTTACGTGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGA-TATGTGATTACGTGTAAGACCAC-GTCTGGGACAGTGGCA
* * *
29475563 TTGATATGTGATTACATGTAAGACCACGTCTGGGACATTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTGGCA
29475606 T
1 T
29475607 TGTACGAGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
42 2 0.03
43 69 0.92
44 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACAGTGGCA
Found at i:29476750 original size:15 final size:14
Alignment explanation
Indices: 29476729--29476764 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
29476719 ATAATCTTTA
*
29476729 ATAATTATCTTAAT
1 ATAATTATCCTAAT
29476743 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
29476758 ATAATTA
1 ATAATTA
29476765 AAATAGAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:29478740 original size:110 final size:111
Alignment explanation
Indices: 29478612--29478832 Score: 435
Period size: 110 Copynumber: 2.0 Consensus size: 111
29478602 GGGTTAGGGT
29478612 GTTACATATCATATTAATTTTAATTAAATTAATTATTTAATTTAATTTAAATTTCCTTGATCAAA
1 GTTACATATCATATTAATTTTAATTAAATTAATTATTTAATTTAATTTAAATTTCCTTGATCAAA
29478677 ATTAATTTTTCCAAAAATCACTTAGATTTTCTAAA-TATTTTTTCA
66 ATTAATTTTTCCAAAAATCACTTAGATTTTCTAAATTATTTTTTCA
29478722 GTTACATATCATATTAATTTTAATTAAATTAATTATTTAATTTAATTTAAATTTCCTTGATCAAA
1 GTTACATATCATATTAATTTTAATTAAATTAATTATTTAATTTAATTTAAATTTCCTTGATCAAA
29478787 ATTAATTTTTCCAAAAATCACTTAGATTTTCTAAATTATTTTTTCA
66 ATTAATTTTTCCAAAAATCACTTAGATTTTCTAAATTATTTTTTCA
29478833 AGAAAATTCT
Statistics
Matches: 110, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
110 100 0.91
111 10 0.09
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (111 bp):
GTTACATATCATATTAATTTTAATTAAATTAATTATTTAATTTAATTTAAATTTCCTTGATCAAA
ATTAATTTTTCCAAAAATCACTTAGATTTTCTAAATTATTTTTTCA
Found at i:29481271 original size:19 final size:19
Alignment explanation
Indices: 29481247--29481284 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
29481237 AAAGTTAAAA
29481247 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTATGGTGG
29481266 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTATGGTGG
29481285 GTGGCGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (19 bp):
ACAAATTTGATTATGGTGG
Found at i:29484367 original size:21 final size:22
Alignment explanation
Indices: 29484320--29484369 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29484310 TAAAATAATT
*
29484320 AGAATTAAAATTTTAGGTTACG
1 AGAATTAAAATTTAAGGTTACG
29484342 A-AATTAAAA-TTAAGAG-TACG
1 AGAATTAAAATTTAAG-GTTACG
29484362 AGAATTAA
1 AGAATTAA
29484370 TTTGGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 9 0.36
21 15 0.60
22 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.16, T:0.30
Consensus pattern (22 bp):
AGAATTAAAATTTAAGGTTACG
Found at i:29490166 original size:8 final size:8
Alignment explanation
Indices: 29490149--29490181 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
29490139 AAGAAAAAAA
*
29490149 ATATAAAT
1 ATATACAT
29490157 ATATACAT
1 ATATACAT
29490165 ATATACAT
1 ATATACAT
29490173 ATATACAT
1 ATATACAT
29490181 A
1 A
29490182 AATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATACAT
Found at i:29490946 original size:23 final size:22
Alignment explanation
Indices: 29490902--29491016 Score: 61
Period size: 19 Copynumber: 5.6 Consensus size: 22
29490892 AAAAGGTATC
* *
29490902 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
29490923 TACAAAATCATATCTTCTACGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
29490946 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
29490965 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
29490984 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
29491003 TACATATCATATCT
1 TACAAATCATATCT
29491017 AAGATTGCAT
Statistics
Matches: 82, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
19 55 0.67
21 3 0.04
22 15 0.18
23 9 0.11
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:29490965 original size:19 final size:19
Alignment explanation
Indices: 29490938--29491029 Score: 166
Period size: 19 Copynumber: 4.8 Consensus size: 19
29490928 AATCATATCT
*
29490938 TCTACGATTGCATATCATA
1 TCTAAGATTGCATATCATA
29490957 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
29490976 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
29490995 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
29491014 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
29491030 CTTGAATATT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 70 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:29490989 original size:38 final size:38
Alignment explanation
Indices: 29490915--29491029 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
29490905 AAATTAAATC
* *
29490915 TCTAAGATTACAAAATCATATCTTCTACGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
*
29490957 TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
29490995 TCTAAGATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
29491030 CTTGAATATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
38 52 0.75
41 7 0.10
42 10 0.14
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:29493709 original size:16 final size:16
Alignment explanation
Indices: 29493685--29493722 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29493675 TTTGGTTCGC
* *
29493685 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
29493701 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
29493717 TGTAAT
1 TGTAAT
29493723 AGCAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:29493765 original size:45 final size:44
Alignment explanation
Indices: 29493701--29493795 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
29493691 GGATTAGAGG
29493701 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
29493746 TGTAATGGAATAGAGGTGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
29493790 TGTAAT
1 TGTAAT
29493796 AGAAGTGTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 22 0.48
45 24 0.52
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGTGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:29493977 original size:18 final size:17
Alignment explanation
Indices: 29493956--29493990 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29493946 TTATTATTAA
*
29493956 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29493974 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29493991 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29499897 original size:467 final size:469
Alignment explanation
Indices: 29498974--29499899 Score: 1768
Period size: 467 Copynumber: 2.0 Consensus size: 469
29498964 TCAAGCATTG
* *
29498974 GCATCTCTTTTATAATTATAAACCCACCATAAAATTAGTTTTCTTATTATTATTTTTTTATTCAA
1 GCATCTCTTTTATAATTATAAACCCACCAGAAAATTAGTTTTCTTATTATTATTTTTTGATTCAA
29499039 TTAATTAAAAGTGGATTGCTGAAATAAATACTATATGAGCAAAGTTAATAGACATTATTTATTCC
66 TTAATTAAAAGTGGATTGCTGAAATAAATACTATATGAGCAAAGTTAATAGACATTATTTATTCC
29499104 CTCCATTTTGAGATGATTTGTCCAACCACGCAAATTCAATGACTAAAAGATGTGAAAGATTAAAT
131 CTCCATTTTGAGATGATTTGTCCAACCACGCAAATTCAATGACTAAAAGATGTGAAAGATTAAAT
29499169 GTAGGGCTAAAATGATTTATTTATTTTTTGTAAAGTTAAAGGGCTAAGTAAATCATAATGCCTTC
196 GTAGGGCTAAAATGA-TTATTTATTTTTTGTAAAGTTAAAGGGCTAAGTAAATCATAATGCCTTC
29499234 TTTTTAGGTTACAATAACAAATAAAAAAAGGGAGAGGGAAACCTTTACAAATTTATTATATATGA
260 TTTTTAGGTTACAATAACAAATAAAAAAAGGGAGAGGGAAACCTTTACAAATTTATTATATATGA
29499299 TAAATCAGAAAATATCTATAAACTAGTAAATAAGGCCTACTGGAAGCAGAAAACGTTATTGGTAA
325 TAAATCAGAAAATATCTATAAACTAGTAAATAAGGCCTACTGGAAGCAGAAAACGTTATTGGTAA
29499364 TATTAACTTGCTTACCAAAGCTAAATTATTAGTAACATCTAATTGCATAGACGTAAATTAGAGAA
390 TATTAACTTGCTTACCAAAGCTAAATTATTAGTAACATCTAATTGCATAGACGTAAATTAGAGAA
29499429 CATCAGCAACCAACT
455 CATCAGCAACCAACT
*
29499444 GCATCTCTTTTATAATTATAAACCCACCAGAAAATTTGTTTTCTTATTATTATTATTTTGATTCA
1 GCATCTCTTTTATAATTATAAACCCACCAGAAAATTAGTTTTCTTATTATTATT-TTTTGATTCA
*
29499509 ATTAATTAAAAGTGGATTGCTGGAATAAATACTATATGAGCAAAGTTAATAGACATTATTTATTC
65 ATTAATTAAAAGTGGATTGCTGAAATAAATACTATATGAGCAAAGTTAATAGACATTATTTATTC
29499574 CCTCCATTTTGAGATGATTTGTCCAACCACGCAAATTCAATGACTAAAAGATGTGAAAGATTAAA
130 CCTCCATTTTGAGATGATTTGTCCAACCACGCAAATTCAATGACTAAAAGATGTGAAAGATTAAA
29499639 TGTAGGGCTAAAATGA-T-TTT-TTTTTTGTAAAGTTAAAGGGCTAAGTAAATCATAATGCCTTC
195 TGTAGGGCTAAAATGATTATTTATTTTTTGTAAAGTTAAAGGGCTAAGTAAATCATAATGCCTTC
29499701 TTTTTAGGTTACAATAACAAATAAAAAAAGGGAGAGGGAAACCTTTACAAATTTATTATATATGA
260 TTTTTAGGTTACAATAACAAATAAAAAAAGGGAGAGGGAAACCTTTACAAATTTATTATATATGA
29499766 TAAATCAGAAAATATCTATAAACTAGTAAATAAGGCCTACTGGAAGCAGAAAACGTTATTGGTAA
325 TAAATCAGAAAATATCTATAAACTAGTAAATAAGGCCTACTGGAAGCAGAAAACGTTATTGGTAA
*
29499831 TATTAACTTGCTTACCAAAGCTAAATTATTAGTAACATCTAATTGCATAGACGTAAATTGGAGAA
390 TATTAACTTGCTTACCAAAGCTAAATTATTAGTAACATCTAATTGCATAGACGTAAATTAGAGAA
29499896 CATC
455 CATC
29499900 CGCAGCCTAT
Statistics
Matches: 450, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
467 240 0.53
468 3 0.01
469 1 0.00
470 52 0.12
471 154 0.34
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (469 bp):
GCATCTCTTTTATAATTATAAACCCACCAGAAAATTAGTTTTCTTATTATTATTTTTTGATTCAA
TTAATTAAAAGTGGATTGCTGAAATAAATACTATATGAGCAAAGTTAATAGACATTATTTATTCC
CTCCATTTTGAGATGATTTGTCCAACCACGCAAATTCAATGACTAAAAGATGTGAAAGATTAAAT
GTAGGGCTAAAATGATTATTTATTTTTTGTAAAGTTAAAGGGCTAAGTAAATCATAATGCCTTCT
TTTTAGGTTACAATAACAAATAAAAAAAGGGAGAGGGAAACCTTTACAAATTTATTATATATGAT
AAATCAGAAAATATCTATAAACTAGTAAATAAGGCCTACTGGAAGCAGAAAACGTTATTGGTAAT
ATTAACTTGCTTACCAAAGCTAAATTATTAGTAACATCTAATTGCATAGACGTAAATTAGAGAAC
ATCAGCAACCAACT
Found at i:29510315 original size:19 final size:19
Alignment explanation
Indices: 29510291--29510328 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29510281 AAAGTTAAAA
29510291 ACAAATTTGATTACGGTGG
1 ACAAATTTGATTACGGTGG
*
29510310 ACAAATTTGATTATGGTGG
1 ACAAATTTGATTACGGTGG
29510329 GTGGCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTGATTACGGTGG
Found at i:29518283 original size:17 final size:18
Alignment explanation
Indices: 29518261--29518297 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29518251 TTTTGGGTTG
29518261 TGTGGG-CCACACGGGCA
1 TGTGGGCCCACACGGGCA
*
29518278 TGTGGGCCCACATGGGCA
1 TGTGGGCCCACACGGGCA
29518296 TG
1 TG
29518298 CAGCATGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.16, C:0.27, G:0.41, T:0.16
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCA
Found at i:29519619 original size:31 final size:31
Alignment explanation
Indices: 29519581--29519643 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
29519571 CATTCTTCAG
*
29519581 TCAACCTTTCGTAAAGTAGAATAAATTTGAA
1 TCAACCTTTCGTAAAGTAGAATAAATCTGAA
*
29519612 TCAACCTTTGGTAAAGTAGAATAAATCTGAA
1 TCAACCTTTCGTAAAGTAGAATAAATCTGAA
29519643 T
1 T
29519644 GGTTTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (31 bp):
TCAACCTTTCGTAAAGTAGAATAAATCTGAA
Found at i:29520118 original size:11 final size:10
Alignment explanation
Indices: 29520093--29520117 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29520083 TACTAACATC
29520093 TTTTTCATAG
1 TTTTTCATAG
29520103 TTTTTCATAG
1 TTTTTCATAG
29520113 TTTTT
1 TTTTT
29520118 TATATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTCATAG
Found at i:29523901 original size:28 final size:27
Alignment explanation
Indices: 29523861--29523957 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 27
29523851 AGTATAAAAC
*
29523861 ATACAGTAGCAGTCTGGG-CTTAAGCCCA
1 ATACAGTAACAGT-TGGGCCTT-AGCCCA
*
29523889 ATAAAGTAACAGTTGGGGCCTTAGCCCA
1 ATACAGTAACAGTT-GGGCCTTAGCCCA
29523917 ATACAGTAACAGTGTGGGCCTTAGCCCA
1 ATACAGTAACAGT-TGGGCCTTAGCCCA
29523945 ATACAGTAACAGT
1 ATACAGTAACAGT
29523958 ACAATGCAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
27 1 0.02
28 58 0.92
29 4 0.06
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.22
Consensus pattern (27 bp):
ATACAGTAACAGTTGGGCCTTAGCCCA
Found at i:29524315 original size:27 final size:27
Alignment explanation
Indices: 29524293--29524575 Score: 310
Period size: 27 Copynumber: 10.5 Consensus size: 27
29524283 AGGGGTATAA
*
29524293 CAGTCATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
29524320 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TAATTTTACCTTTCGAGGGTATTT
* * *
29524347 CAATACTCTTTCCCTTT-GAGGGTATTT
1 CAGTAAT-TTTACCTTTCGAGGGTATTT
*
29524374 CAGTAATTTTACCTTT-TAGGGGTATTT
1 CAGTAATTTTACCTTTCGA-GGGTATTT
29524401 CAGTAATTTTACCTTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
29524428 CAGTAATTTTACCTATCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
* *
29524455 TAGTAATTTTACCCTTCGAGGGTATTT
1 CAGTAATTTTACCTTTCGAGGGTATTT
*
29524482 C-GATAATTTTACCCTTCGAGGGTATTT
1 CAG-TAATTTTACCTTTCGAGGGTATTT
* *
29524509 C-GATAATTTTA-CTTATCAACGGTATTT
1 CAG-TAATTTTACCTT-TCGAGGGTATTT
* * *
29524536 TAGTAGTTTTACCCTATCGAGGGTATTT
1 CAGTAATTTTA-CCTTTCGAGGGTATTT
*
29524564 -GGTAATTTTACC
1 CAGTAATTTTACC
29524576 CACGAATCGT
Statistics
Matches: 220, Mismatches: 26, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
26 15 0.07
27 184 0.84
28 19 0.09
29 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (27 bp):
CAGTAATTTTACCTTTCGAGGGTATTT
Found at i:29524420 original size:81 final size:81
Alignment explanation
Indices: 29524293--29524576 Score: 351
Period size: 81 Copynumber: 3.5 Consensus size: 81
29524283 AGGGGTATAA
* *
29524293 CAGTCATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATACTCTTT
1 CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAAT-TTT
* *
29524358 CCCT-TTGAGGGTATTT
65 ACCTATCGAGGGTATTT
* * *
29524374 CAGTAATTTTACCTTT-TAGGGGTATTTC-AGTAATTTTACCTTTCGAGGGTATTTCAGTAATTT
1 CAGTAATTTTACCTTTCGA-GGGTATTTCGA-TAATTTTACCCTTCGAGGGTATTTCAATAATTT
29524437 TACCTATCGAGGGTATTT
64 TACCTATCGAGGGTATTT
* * *
29524455 TAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGATAATTTTA
1 CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAATTTTA
* * *
29524520 CTTATCAACGGTATTT
66 CCTATCGAGGGTATTT
* * * *
29524536 TAGTAGTTTTACCCTATCGAGGGTATTT-GGTAATTTTACCC
1 CAGTAATTTTA-CCTTTCGAGGGTATTTCGATAATTTTACCC
29524577 ACGAATCGTA
Statistics
Matches: 177, Mismatches: 20, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
80 8 0.05
81 153 0.86
82 16 0.09
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.43
Consensus pattern (81 bp):
CAGTAATTTTACCTTTCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATAATTTTA
CCTATCGAGGGTATTT
Found at i:29529482 original size:32 final size:32
Alignment explanation
Indices: 29529395--29529533 Score: 127
Period size: 32 Copynumber: 4.4 Consensus size: 32
29529385 GAATGGCTAC
* * *
29529395 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * ** *
29529426 AAACAATCAATAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
29529458 CAGCCATCAGTAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
29529490 AAGCCATCAGTAACAATAATATGATCGGTAAA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
29529522 AAACCATCAGTA
1 AAGCCATCAGTA
29529534 GCATCGCAGC
Statistics
Matches: 82, Mismatches: 25, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
31 7 0.09
32 75 0.91
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:29529717 original size:24 final size:24
Alignment explanation
Indices: 29529690--29529738 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29529680 AGTTATACCA
*
29529690 ATCACAGACAAATCAGTCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
29529714 ATCACGGACAAATTAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
29529738 A
1 A
29529739 CTCGAGGGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.27
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:29529759 original size:26 final size:24
Alignment explanation
Indices: 29529690--29529763 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
29529680 AGTTATACCA
*
29529690 ATCACAGAC-AAATCAGTCATTTAC
1 ATCACGGACAAAAT-AGTCATTTAC
* *
29529714 ATCACGGACAAATTAATCATTTAC
1 ATCACGGACAAAATAGTCATTTAC
* *
29529738 ACTCGAGGGGCAAAATAGTCATTTAC
1 A-TC-ACGGACAAAATAGTCATTTAC
29529764 CCTCTAAGGG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 18 0.45
25 5 0.12
26 17 0.43
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.26
Consensus pattern (24 bp):
ATCACGGACAAAATAGTCATTTAC
Found at i:29529789 original size:27 final size:27
Alignment explanation
Indices: 29529755--29530033 Score: 173
Period size: 27 Copynumber: 10.4 Consensus size: 27
29529745 GGGCAAAATA
*
29529755 GTCA-TTTACCCTCTAAGGGTATTATG
1 GTCATTTTACCCTCTAAGGGTATTACG
* *
29529781 GTCATTTTA-ACTAAC-AAGGGTATTATG
1 GTCATTTTACCCT--CTAAGGGTATTACG
*
29529808 GTTATTTT--CC-CTACAGGGTTATTACG
1 GTCATTTTACCCTCTA-AGGG-TATTACG
* * *
29529834 GTCATTTAACCCTATAGGGGTATTACG
1 GTCATTTTACCCTCTAAGGGTATTACG
* * *
29529861 ATTATTTTACCC-C-ACAGAGGCATTACG
1 GTCATTTTACCCTCTA-AG-GGTATTACG
*
29529888 GTCATTTTACCCTAC-AAGGGTATTACA
1 GTCATTTTACCCT-CTAAGGGTATTACG
* * * *
29529915 GTAATTTAACCCTATGAGGGTATTACG
1 GTCATTTTACCCTCTAAGGGTATTACG
*
29529942 GTCATTTTACCCTAC-AGGGGTATTACG
1 GTCATTTTACCCT-CTAAGGGTATTACG
* * * ** *
29529969 ATCATTTAACCCTATGGGGGTATTACA
1 GTCATTTTACCCTCTAAGGGTATTACG
* * * **
29529996 GTCATTTAACCCTATGAGGGTATTATA
1 GTCATTTTACCCTCTAAGGGTATTACG
29530023 GTCATTTTACC
1 GTCATTTTACC
29530034 TTACAGAGGG
Statistics
Matches: 200, Mismatches: 37, Indels: 31
0.75 0.14 0.12
Matches are distributed among these distances:
23 1 0.00
24 1 0.00
25 5 0.03
26 20 0.10
27 161 0.81
28 8 0.04
29 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTCTAAGGGTATTACG
Found at i:29529900 original size:54 final size:54
Alignment explanation
Indices: 29529798--29530087 Score: 261
Period size: 54 Copynumber: 5.4 Consensus size: 54
29529788 TAACTAACAA
* *
29529798 GGGTATTATGGTTATTTT-CCCTACAG-GGTTATTACGGTCATTTAACCCTATAG
1 GGGTATTACGATTATTTTACCCTACAGAGG-TATTACGGTCATTTAACCCTATAG
* * * * *
29529851 GGGTATTACGATTATTTTACCCCACAGAGGCATTACGGTCATTTTACCCTACAA
1 GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
* * * * *
29529905 GGGTATTAC-AGTAATTTAACCCTA-TGAGGGTATTACGGTCATTTTACCCTACAG
1 GGGTATTACGA-TTATTTTACCCTACAGA-GGTATTACGGTCATTTAACCCTATAG
* * ** * *
29529959 GGGTATTACGATCATTTAACCCTATGGGGGTATTACAGTCATTTAACCCTAT-G
1 GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
* * * * *
29530012 AGGGTATTA-TAGTCATTTTACCTTACAGAGGGCATTACGGTTATTTAACCCTAT-G
1 -GGGTATTACGA-TTATTTTACCCTACAGA-GGTATTACGGTCATTTAACCCTATAG
29530067 GGGATATTACGATTATTTTAC
1 GGG-TATTACGATTATTTTAC
29530088 AACCTTTTCG
Statistics
Matches: 196, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
53 21 0.11
54 135 0.69
55 39 0.20
56 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (54 bp):
GGGTATTACGATTATTTTACCCTACAGAGGTATTACGGTCATTTAACCCTATAG
Found at i:29529926 original size:81 final size:80
Alignment explanation
Indices: 29529816--29530064 Score: 304
Period size: 81 Copynumber: 3.1 Consensus size: 80
29529806 TGGTTATTTT
* * *
29529816 CCCTACAGGGTTATTACGGTCATTTAACCCTAT-AGGGGTATTACGATTATTTTACCCCACAGAG
1 CCCTACAGGG-TATTACAGTCATTTAACCCTATGA-GGGTATTACGATCATTTTACCCTACAGAG
*
29529880 GCATTACGGTCATTTTA
64 GCATTACGGTCATTTAA
* * *
29529897 CCCTACAAGGGTATTACAGTAATTTAACCCTATGAGGGTATTACGGTCATTTTACCCTACAGGGG
1 CCCTAC-AGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGATCATTTTACCCTACAGAGG
* *
29529962 TATTACGATCATTTAA
65 CATTACGGTCATTTAA
** * *
29529978 CCCTATGGGGGTATTACAGTCATTTAACCCTATGAGGGTATTA-TAGTCATTTTACCTTACAGAG
1 CCCTA-CAGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGA-TCATTTTACCCTACAGA-
*
29530042 GGCATTACGGTTATTTAA
63 GGCATTACGGTCATTTAA
29530060 CCCTA
1 CCCTA
29530065 TGGGGATATT
Statistics
Matches: 144, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
81 119 0.83
82 25 0.17
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (80 bp):
CCCTACAGGGTATTACAGTCATTTAACCCTATGAGGGTATTACGATCATTTTACCCTACAGAGGC
ATTACGGTCATTTAA
Found at i:29530075 original size:27 final size:26
Alignment explanation
Indices: 29529827--29530077 Score: 205
Period size: 27 Copynumber: 9.3 Consensus size: 26
29529817 CCTACAGGGT
29529827 TATTACGGTCATTTAACCCTATAGGGG
1 TATTACGGTCATTTAACCCTAT-GGGG
* * * * * *
29529854 TATTACGATTATTTTACCCCACAGAGG
1 TATTACGGTCATTTAACCCTA-TGGGG
* * **
29529881 CATTACGGTCATTTTACCCTACAAGGG
1 TATTACGGTCATTTAACCCTA-TGGGG
* *
29529908 TATTACAGTAATTTAACCCTATGAGGG
1 TATTACGGTCATTTAACCCTATG-GGG
* *
29529935 TATTACGGTCATTTTACCCTACAGGGG
1 TATTACGGTCATTTAACCCTA-TGGGG
*
29529962 TATTACGATCATTTAACCCTATGGGGG
1 TATTACGGTCATTTAACCCTAT-GGGG
*
29529989 TATTACAGTCATTTAACCCTATGAGGG
1 TATTACGGTCATTTAACCCTATG-GGG
** * * *
29530016 TATTATAGTCATTTTACCTTACAGAGGG
1 TATTACGGTCATTTAACCCTA-TG-GGG
* *
29530044 CATTACGGTTATTTAACCCTATGGGG
1 TATTACGGTCATTTAACCCTATGGGG
29530070 ATATTACG
1 -TATTACG
29530078 ATTATTTTAC
Statistics
Matches: 178, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
26 4 0.02
27 153 0.86
28 21 0.12
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (26 bp):
TATTACGGTCATTTAACCCTATGGGG
Found at i:29530906 original size:32 final size:32
Alignment explanation
Indices: 29530824--29530962 Score: 120
Period size: 32 Copynumber: 4.4 Consensus size: 32
29530814 GAATGGCTAC
* * *
29530824 AAGCCATAAGT-ACATTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
29530855 AAGCCATCAGTAGTAGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
29530887 CAA-CCATCAGTAACGGTAATATGATCGGGAAA
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
*** * * *
29530919 AATATATTAGTAACAGTAATATAATCGGCTCA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
29530951 AAGCCATCAGTA
1 AAGCCATCAGTA
29530963 GCATCGCAGC
Statistics
Matches: 82, Mismatches: 23, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
31 12 0.15
32 68 0.83
33 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:29531261 original size:27 final size:27
Alignment explanation
Indices: 29531231--29531543 Score: 288
Period size: 27 Copynumber: 11.6 Consensus size: 27
29531221 CTCTCAGGGC
* * *
29531231 ATTATGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * * *
29531258 ATTACGATTATTTTATCCTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
29531285 ATTACGGTTATTTAACCCTATATGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
29531312 ATTACGATCATTTTACCCTACAGAGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
*
29531339 ATTAAGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
** *
29531366 ATTATAGTCATTAT-CCCTATAGGGGAT
1 ATTACGGTCATTTTACCCTATAGGGG-T
* *
29531393 ATTACGGTCATTTTACCTTACAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * * *
29531420 ATTATGATCATTTAACCCTATGGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
29531447 ATTACGGTTATTTAACCTTATAGGGGT
1 ATTACGGTCATTTTACCCTATAGGGGT
* * *
29531474 ATTACGATCATTTTACCCAATTGGGGCT
1 ATTACGGTCATTTTACCCTATAGGGG-T
* * * *
29531502 -TTACGGTTATTTGACCCTATTGGAGT
1 ATTACGGTCATTTTACCCTATAGGGGT
*
29531528 ATTACGGTTATTTTAC
1 ATTACGGTCATTTTAC
29531544 AACCTTTTCA
Statistics
Matches: 231, Mismatches: 51, Indels: 8
0.80 0.18 0.03
Matches are distributed among these distances:
26 12 0.05
27 209 0.90
28 10 0.04
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTATAGGGGT
Found at i:29531323 original size:81 final size:81
Alignment explanation
Indices: 29531238--29531490 Score: 337
Period size: 81 Copynumber: 3.1 Consensus size: 81
29531228 GGCATTATGG
* * * *
29531238 TCATTTTACCTTACAGGGGTATTACGATTATTTTATCCTACAGGGGTATTACGGTTATTTAACCC
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
*
29531303 TATATGGGTATTACGA
66 TATAGGGGTATTACGA
* * * ** * *
29531319 TCATTTTACCCTACAGAGGTATTAAGGTCATTTTACCCTATAGGGGTATTATAGTCA-TTATCCC
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
*
29531383 TATAGGGGATATTACGG
66 TATAGGGG-TATTACGA
* * * *
29531400 TCATTTTACCTTACAGGGGTATTATGATCATTTAACCCTATGGGGGTATTACGGTTATTTAACCT
1 TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
29531465 TATAGGGGTATTACGA
66 TATAGGGGTATTACGA
29531481 TCATTTTACC
1 TCATTTTACC
29531491 CAATTGGGGC
Statistics
Matches: 145, Mismatches: 25, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
80 13 0.09
81 119 0.82
82 13 0.09
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (81 bp):
TCATTTTACCTTACAGGGGTATTAAGATCATTTTACCCTATAGGGGTATTACGGTTATTTAACCC
TATAGGGGTATTACGA
Found at i:29531519 original size:81 final size:81
Alignment explanation
Indices: 29531238--29531540 Score: 322
Period size: 81 Copynumber: 3.7 Consensus size: 81
29531228 GGCATTATGG
* * * * * * *
29531238 TCATTTTACCTTACAGGGGTATTACGATTATTTTATCCTACAGGGGTATTACGGTTATTTAACCC
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
*
29531303 TATATGGGTATTACGA
66 TATAGGGGTATTACGA
* * ** * *
29531319 TCATTTTACCCTACAGAGGTATTAAGGTCATTTTACCCTATAGGGGTATTATAGTCA-TTATCCC
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
*
29531383 TATAGGGGATATTACGG
66 TATAGGGG-TATTACGA
* * * * *
29531400 TCATTTTACCTTACAGGGGTATTATGATCATTTAACCCTATGGGGGTATTACGGTTATTTAACCT
1 TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
29531465 TATAGGGGTATTACGA
66 TATAGGGGTATTACGA
* ** * * * * *
29531481 TCATTTTACCCAATTGGGGCT-TTACGGTTATTTGACCCTATTGGAGTATTACGGTTATTT
1 TCATTTTACCCTACAGGGG-TATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTT
29531541 TACAACCTTT
Statistics
Matches: 184, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
80 13 0.07
81 157 0.85
82 14 0.08
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (81 bp):
TCATTTTACCCTACAGGGGTATTAAGGTCATTTAACCCTATAGGGGTATTACGGTTATTTAACCC
TATAGGGGTATTACGA
Found at i:29532036 original size:24 final size:23
Alignment explanation
Indices: 29532009--29532053 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
29531999 GCTGTATCGT
29532009 CAGC-TTTCCGACATTTCGACATCC
1 CAGCATTT-CGACATTT-GACATCC
29532033 CAGCATTTCGACATTTGACAT
1 CAGCATTTCGACATTTGACAT
29532054 TCTTAAACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (23 bp):
CAGCATTTCGACATTTGACATCC
Found at i:29533520 original size:13 final size:11
Alignment explanation
Indices: 29533491--29533557 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
29533481 TATTTTTTTA
29533491 TTTTAAAATAC
1 TTTTAAAATAC
29533502 TTTTAAAATAC
1 TTTTAAAATAC
29533513 TTTTTTAAAAT--
1 --TTTTAAAATAC
*
29533524 TTTTTAAAT--
1 TTTTAAAATAC
*
29533533 TTTT-AAATAT
1 TTTTAAAATAC
29533543 TTTTAAAATAC
1 TTTTAAAATAC
29533554 TTTT
1 TTTT
29533558 TTTATTTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
8 4 0.08
9 12 0.24
10 4 0.08
11 20 0.41
13 9 0.18
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:29533537 original size:18 final size:19
Alignment explanation
Indices: 29533514--29533551 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29533504 TTAAAATACT
*
29533514 TTTTTAAA-ATTTTTTAAA
1 TTTTTAAATATTTTTAAAA
29533532 TTTTTAAATATTTTTAAAA
1 TTTTTAAATATTTTTAAAA
29533551 T
1 T
29533552 ACTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAAATATTTTTAAAA
Found at i:29533586 original size:40 final size:39
Alignment explanation
Indices: 29533477--29533677 Score: 183
Period size: 40 Copynumber: 5.3 Consensus size: 39
29533467 ATAATAAATA
*
29533477 TTTTT-ATTTTTTTA-TTTTAAAATACTTTTAAAATACT
1 TTTTTAATTTTTTTATTTTTAAAATATTTTTAAAATACT
*
29533514 TTTTTAAAATTTTTTAAATTTTT-AAATATTTTTAAAATACT
1 TTTTT--AATTTTTT-TATTTTTAAAATATTTTTAAAATACT
* *
29533555 TTTTTTATTTTTTTATTTTTAAAATAATTTTT----T--G
1 TTTTTAATTTTTTTATTTTTAAAAT-ATTTTTAAAATACT
* * * *
29533589 GTATT-ATTTTTTAAATTTTT-AAATTTTTTTAAAATACT
1 TTTTTAATTTTTT-TATTTTTAAAATATTTTTAAAATACT
*
29533627 TTTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATA-T
1 TTTTTAA-TTTTTTTATTTTTAAAATATTTTTAAAATACT
29533666 TTTTTAATTTTT
1 TTTTTAATTTTT
29533678 AAAATAAATT
Statistics
Matches: 132, Mismatches: 15, Indels: 33
0.73 0.08 0.18
Matches are distributed among these distances:
32 5 0.04
33 11 0.08
34 9 0.07
36 2 0.02
37 5 0.04
38 14 0.11
39 25 0.19
40 34 0.26
41 23 0.17
42 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTTTAATTTTTTTATTTTTAAAATATTTTTAAAATACT
Found at i:29533672 original size:12 final size:11
Alignment explanation
Indices: 29533644--29533669 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
29533634 TTTTTTTTAA
29533644 TTTTAAAATAT
1 TTTTAAAATAT
29533655 TTTTAAAATAT
1 TTTTAAAATAT
29533666 TTTT
1 TTTT
29533670 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:29533689 original size:20 final size:19
Alignment explanation
Indices: 29533653--29533690 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29533643 ATTTTAAAAT
*
29533653 ATTTTTAAAATATTTTTTA
1 ATTTTTAAAATAATTTTTA
29533672 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAAT-AATTTTT
29533691 GGTATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTTAAAATAATTTTTA
Found at i:29533690 original size:72 final size:69
Alignment explanation
Indices: 29533502--29533680 Score: 236
Period size: 72 Copynumber: 2.6 Consensus size: 69
29533492 TTTAAAATAC
* *
29533502 TTTTAAAATACTTTTTTAAAAT-TTTTTAAATTTTTAAATATTTTTAAAATACTTTTTTTATTTT
1 TTTTAAAATA-TTTTTTAAAATATTTTTTAATTTTTAAATATTTTTAAAATACTTTTTTAATTTT
*
29533566 TTTAT
65 TTTAA
** * *
29533571 TTTTAAAATAATTTTTTGGTATTATTTTTTAAATTTTTAAATTTTTTTAAAATACTTTTTTAATT
1 TTTTAAAAT-ATTTTTT-AAAATATTTTTT-AATTTTTAAATATTTTTAAAATACTTTTTTAA-T
29533636 TTTTTTAA
62 TTTTTTAA
29533644 TTTTAAAATA-TTTTTAAAATATTTTTTAATTTTTAAA
1 TTTTAAAATATTTTTTAAAATATTTTTTAATTTTTAAA
29533681 ATAAATTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
69 25 0.26
70 12 0.13
71 10 0.11
72 31 0.33
73 17 0.18
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (69 bp):
TTTTAAAATATTTTTTAAAATATTTTTTAATTTTTAAATATTTTTAAAATACTTTTTTAATTTTT
TTAA
Found at i:29536802 original size:28 final size:28
Alignment explanation
Indices: 29536771--29536886 Score: 142
Period size: 28 Copynumber: 4.1 Consensus size: 28
29536761 CATGCAGTAG
* * *
29536771 CAGTCTGGGCCTGAGCCCAATACAACAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
29536799 CAGTGTGGGCCTTAGCCTAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* * *
29536827 CAGTGTAGGCATTAGCCCAATACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
* *
29536855 CAGTGTGAGCCTTAGGCCAATACAATAA
1 CAGTGTGGGCCTTAGCCCAATACAATAA
29536883 CAGT
1 CAGT
29536887 ACAATGCAGT
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 75 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAATAA
Found at i:29537279 original size:27 final size:27
Alignment explanation
Indices: 29537249--29537607 Score: 465
Period size: 27 Copynumber: 13.3 Consensus size: 27
29537239 TATTTTAGCT
* * *
29537249 ATTTTACCCTTTGGGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537276 ATTTTACCCTT-GAAGGGTATTTCG-TA
1 ATTTTACCCTTCG-AGGGTATTTCGATA
* ** *
29537302 ATCTTACCCTTTAAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
29537329 ATCTTACCCTTTGAGGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537356 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
29537383 ATTTTACCCTTCGAGGATATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
29537410 AATTTAGCCTTCGAGGGTATTT-TAGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
29537437 ATTTTACCCATT-GAGGGTATTTCGATA
1 ATTTTACCC-TTCGAGGGTATTTCGATA
* * *
29537464 GTTTTACCATTCGAAGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537491 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537518 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537545 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
29537572 ATTTTACCCTTCGAGGTTAGTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
29537599 ATTTTACCC
1 ATTTTACCC
29537608 ACGAATCGCA
Statistics
Matches: 297, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
26 26 0.09
27 268 0.90
28 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:29539219 original size:42 final size:42
Alignment explanation
Indices: 29539171--29539270 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
29539161 GCTTTCGGTA
* *
29539171 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
* *
29539213 TCGCACACTTAGTGCCTATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
29539255 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
29539271 GTTCATATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
Found at i:29544971 original size:29 final size:29
Alignment explanation
Indices: 29544742--29544971 Score: 173
Period size: 29 Copynumber: 8.0 Consensus size: 29
29544732 TTTTTTGTAG
* *
29544742 AATAGTGGTAAAACTGTAAAATCT-AAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* *
29544770 AATAGTGGAAAAACTGTAAAATCTAGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * *
29544799 AATAATGGC-AAATTATAAAATCTGGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
** *
29544827 ACCAGTGGCAAAACTGTAAAATTTAGG-AA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * *
29544856 AATTGTGGTAGAACTGTAAAAT-TGGGAAA
1 AATAGTGGCAAAACTGTAAAATCT-GGAAA
* * ** *
29544885 AATAGTGGCAGAACTATAAAAGATGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
** * *
29544914 ACCAGTGGCAAAATTGTAAAAT-TTGAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
* * * *
29544942 AACAGTGGCAGAACTATAAAATCTGTAAA
1 AATAGTGGCAAAACTGTAAAATCTGGAAA
29544971 A
1 A
29544972 TGGCAGTACA
Statistics
Matches: 158, Mismatches: 38, Indels: 11
0.76 0.18 0.05
Matches are distributed among these distances:
28 70 0.44
29 85 0.54
30 3 0.02
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.23
Consensus pattern (29 bp):
AATAGTGGCAAAACTGTAAAATCTGGAAA
Found at i:29548005 original size:65 final size:65
Alignment explanation
Indices: 29547896--29548026 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
29547886 TTTTAAAAAG
*
29547896 ATTACTTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
* *
29547961 ATTAATTTCCATCTTTCTTGATAGACATGAGATACACTGACAATTACCGTAAAGTATTATTAGTC
1 ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
29548026 A
1 A
29548027 AGAACCTACT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (65 bp):
ATTAATTTCCATCTTGCTTGATAGACATGAGATACACTGACAATTACCATAAAGTATTATTAGTC
Found at i:29552983 original size:13 final size:13
Alignment explanation
Indices: 29552952--29552989 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
29552942 AATTTCAAGT
29552952 ATTGT-ATAAAAA
1 ATTGTGATAAAAA
29552964 ATATGTGATAAAAA
1 AT-TGTGATAAAAA
*
29552978 CTTGTGATAAAA
1 ATTGTGATAAAA
29552990 TTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 13 0.57
14 8 0.35
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (13 bp):
ATTGTGATAAAAA
Found at i:29554675 original size:19 final size:19
Alignment explanation
Indices: 29554651--29554689 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
29554641 AGCAGACCAA
*
29554651 TTAAGTCTGTTGGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
*
29554670 TTAAGTTTGTTAGGGTTGT
1 TTAAGTCTGTTAGGGTTGT
29554689 T
1 T
29554690 AACTTCAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.33, T:0.51
Consensus pattern (19 bp):
TTAAGTCTGTTAGGGTTGT
Found at i:29560327 original size:27 final size:26
Alignment explanation
Indices: 29560283--29560614 Score: 278
Period size: 27 Copynumber: 12.3 Consensus size: 26
29560273 GTAATGGGCC
*
29560283 TAAAATGACAGAAATACCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
* *
29560310 TAAAATAACCAAACTACCCTCGAAAGG
1 TAAAATGACCAAA-TACCCTCGAAGGG
* *
29560337 TAAAATGATCGAAATACCCCCGAAGGG
1 TAAAATGA-CCAAATACCCTCGAAGGG
* * * *
29560364 TCAAATGACTGAAATACCCTCAAAGGA
1 TAAAATGAC-CAAATACCCTCGAAGGG
* * *
29560391 TAAAATGACCGAAATACCTTCAAAGGT
1 TAAAATGACC-AAATACCCTCGAAGGG
* *
29560418 TAAAATGACTGAAATACCC-CTAAAGGG
1 TAAAATGAC-CAAATACCCTC-GAAGGG
* * *
29560445 TAAAAAGACTAAAATATCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
*
29560472 TAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGAC-CAAATACCCTCGAAGGG
29560499 TAAAATGACCGAAATACTCC-CGAAGGG
1 TAAAATGACC-AAATAC-CCTCGAAGGG
* *
29560526 TAAAACGACCGAAATA-CCTCCGAAAGG
1 TAAAATGACC-AAATACCCT-CGAAGGG
*
29560553 TAAAATGATCGAAATACCC-CTGAAGGG
1 TAAAATGA-CCAAATACCCTC-GAAGGG
* *
29560580 TAAAATGACAGAAATACCC-CGAAGGA
1 TAAAATGAC-CAAATACCCTCGAAGGG
29560606 TAAAATGAC
1 TAAAATGAC
29560615 TATTATAGCC
Statistics
Matches: 258, Mismatches: 32, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.01
26 21 0.08
27 225 0.87
28 10 0.04
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (26 bp):
TAAAATGACCAAATACCCTCGAAGGG
Found at i:29560382 original size:54 final size:53
Alignment explanation
Indices: 29560283--29560614 Score: 352
Period size: 54 Copynumber: 6.2 Consensus size: 53
29560273 GTAATGGGCC
* * *
29560283 TAAAATGACAGAAATACCCTCGAAGGGTAAAATAAC-CAAACTACCCTCGAAAGG
1 TAAAATGAC-GAAATACCCCCGAAGGGTAAAATGACTGAAA-TACCCTCGAAAGG
*
29560337 TAAAATGATCGAAATACCCCCGAAGGGTCAAATGACTGAAATACCCTC-AAAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
** * * *
29560390 ATAAAATGACCGAAATACCTTCAAAGGTTAAAATGACTGAAATACCC-CTAAAGGG
1 -TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAA-GG
* * * * *
29560445 TAAAAAGACTAAAATATCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGAC-GAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
* * *
29560499 TAAAATGACCGAAATACTCCCGAAGGGTAAAACGACCGAAATA-CCTCCGAAAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCT-CGAAAGG
* *
29560553 TAAAATGATCGAAATACCCCTGAAGGGTAAAATGACAGAAATACCC-CG-AAGG
1 TAAAATGA-CGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
29560605 ATAAAATGAC
1 -TAAAATGAC
29560615 TATTATAGCC
Statistics
Matches: 236, Mismatches: 31, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
52 5 0.02
53 20 0.08
54 199 0.84
55 12 0.05
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (53 bp):
TAAAATGACGAAATACCCCCGAAGGGTAAAATGACTGAAATACCCTCGAAAGG
Found at i:29560422 original size:81 final size:82
Alignment explanation
Indices: 29560283--29560615 Score: 362
Period size: 81 Copynumber: 4.1 Consensus size: 82
29560273 GTAATGGGCC
* * *
29560283 TAAAATGACAGAAATACCCTCGAAGGGTAAAATAACC-AAACTACCCTCGAAA-GGTAAAATGAT
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAA-TACCCTCGAAAGGGTAAAATGA-
29560346 C-GAAATACCCCCGAAGGG
64 CAGAAATACCCCCGAAGGG
* * * * *
29560364 TCAAATGACTGAAATACCCTCAAAGGATAAAATGACCGAAATACCTTC-AAAGGTTAAAATGACT
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
**
29560428 GAAATACCCCTAAAGGG
66 GAAATACCCCCGAAGGG
* * * * * *
29560445 TAAAAAGACTAAAATATCCTCGAAGGGTAAAATGACTGAAATACCCTCG-AAGGGTAAAATGACC
1 TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
*
29560509 GAAATACTCCCGAAGGG
66 GAAATACCCCCGAAGGG
* * *
29560526 TAAAACGACCGAAATA-CCTCCGAAA-GGTAAAATGATCGAAATACCC-CTG-AAGGGTAAAATG
1 TAAAATGACTGAAATACCCT-C-AAAGGGTAAAATGACCGAAATACCCTC-GAAAGGGTAAAATG
*
29560587 ACAGAAATA-CCCCGAAGGA
63 ACAGAAATACCCCCGAAGGG
29560606 TAAAATGACT
1 TAAAATGACT
29560616 ATTATAGCCC
Statistics
Matches: 212, Mismatches: 33, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
80 24 0.11
81 183 0.86
82 5 0.02
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (82 bp):
TAAAATGACTGAAATACCCTCAAAGGGTAAAATGACCGAAATACCCTCGAAAGGGTAAAATGACA
GAAATACCCCCGAAGGG
Found at i:29560850 original size:26 final size:26
Alignment explanation
Indices: 29560794--29560864 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
29560784 ACATATACTA
* **
29560794 TTACTGGCAGCTTTACTGCATTGCTG
1 TTACTGGCAGCTTTGCTGCATCACTG
*
29560820 TTACTGGCAGCTTTGCTGCATCATTAG
1 TTACTGGCAGCTTTGCTGCATCACT-G
* *
29560847 -TACTGGTAACTTTGCTGC
1 TTACTGGCAGCTTTGCTGC
29560865 GATTTTGGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 37 0.97
27 1 0.03
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCATCACTG
Found at i:29584353 original size:97 final size:96
Alignment explanation
Indices: 29584166--29584358 Score: 282
Period size: 96 Copynumber: 2.0 Consensus size: 96
29584156 GGTTTGCAGC
*
29584166 ATAATATTAAATGCTACACTAATTTTATATTTTTTTTACTTATAGAGTTTAAATTTTTCTACAAA
1 ATAAGATTAAATGCTACACTAATTTTATATTTTTTTTACTTATAGAGTTTAAATTTTTCTACAAA
* **
29584231 AGGTTAAACATTTTTTACATTATAAAAAAAA
66 AAGTTAAACATTTGCTACATTATAAAAAAAA
* *
29584262 ATAAGATTAAATGCTACACTATATTTTATA-TTTTTTTACTTATAGAGTTTAATTTTTTTTTTAC
1 ATAAGATTAAATGCTACACTA-ATTTTATATTTTTTTTACTTATAGAGTTTAA--ATTTTTCTAC
*
29584326 AAAAAGTT-AACATTTGCTACATTATAAATAAAA
63 AAAAAGTTAAACATTTGCTACATTATAAAAAAAA
29584359 CTTTTAAACT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
96 42 0.48
97 30 0.34
98 15 0.17
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (96 bp):
ATAAGATTAAATGCTACACTAATTTTATATTTTTTTTACTTATAGAGTTTAAATTTTTCTACAAA
AAGTTAAACATTTGCTACATTATAAAAAAAA
Found at i:29585523 original size:18 final size:19
Alignment explanation
Indices: 29585500--29585536 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29585490 TTTTTAAAAA
29585500 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
29585518 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
29585537 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:29585537 original size:18 final size:18
Alignment explanation
Indices: 29585500--29585553 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
29585490 TTTTTAAAAA
29585500 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAA-TTT
29585518 TATAAATATTTAGAATTT
1 TATAAATATTTAGAATTT
* *
29585536 TAAAAATTATTTTGAATT
1 TATAAA-TATTTAGAATT
29585554 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TATAAATATTTAGAATTT
Found at i:29587026 original size:30 final size:30
Alignment explanation
Indices: 29586992--29587098 Score: 114
Period size: 30 Copynumber: 3.6 Consensus size: 30
29586982 ACCCCTTAAT
* *
29586992 TTTCTTTAAATTGTATTTTGGACCCTAAAC
1 TTTCTTAAAATTATATTTTGGACCCTAAAC
*
29587022 TTTCTTAAAATT-TCATTTT-GACCCCTTAAC
1 TTTCTTAAAATTAT-ATTTTGGA-CCCTAAAC
* * *
29587052 TTTCTAAAAATTATATTTTGG-CCC-ATAT
1 TTTCTTAAAATTATATTTTGGACCCTAAAC
29587080 TTTCTTAAAATTATATTTT
1 TTTCTTAAAATTATATTTT
29587099 TCTCCAGAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
28 19 0.29
29 6 0.09
30 39 0.59
31 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50
Consensus pattern (30 bp):
TTTCTTAAAATTATATTTTGGACCCTAAAC
Found at i:29587700 original size:16 final size:16
Alignment explanation
Indices: 29587664--29587713 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
29587654 TTCGGGAAAA
*
29587664 AGAGAAGAGAGAA-AG
1 AGAGAAGAGAGAAGGG
*
29587679 -GAGAAGGGA-AAGGGG
1 AGAGAAGAGAGAA-GGG
29587694 AGAGAAGAGAGAAGGG
1 AGAGAAGAGAGAAGGG
29587710 AGAG
1 AGAG
29587714 TCCGGCCACC
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.07
14 8 0.29
15 1 0.04
16 15 0.54
17 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGAGAAGGG
Found at i:29587804 original size:20 final size:20
Alignment explanation
Indices: 29587777--29587831 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
29587767 TAGGGTTTTT
29587777 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGTAGAA
* *
29587797 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGTAGAA
29587816 GAAAGAA-AAGAAAAGT
1 GAAAGAAGAA-AAAAGT
29587832 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGTAGAA
Found at i:29587821 original size:16 final size:16
Alignment explanation
Indices: 29587779--29587824 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
29587769 GGGTTTTTGA
*
29587779 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
29587795 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
29587811 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
29587825 GAAAAGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:29596122 original size:75 final size:75
Alignment explanation
Indices: 29595909--29596575 Score: 787
Period size: 75 Copynumber: 8.7 Consensus size: 75
29595899 AGAATTATAT
29595909 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGG-CT
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
*
29595973 ATACACCGAGGTA
65 AT-C-CTGAGGTA
* *
29595986 TTTTTAATTTATGTTTTTC-AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
29596050 TCCTGAGGTA
66 TCCTGAGGTA
* *
29596060 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCAAGAGGTAAGTTGAGCCTCGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
29596125 TCCTGAGGTA
66 TCCTGAGGTA
** * *
29596135 TTTTCAATTTCTGCCTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
29596200 TCCTGAGGTA
66 TCCTGAGGTA
* * *
29596210 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCTGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
29596275 TCCTGAGGTA
66 TCCTGAGGTA
* * * * *
29596285 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTG
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-GGGT-
29596350 CA-CGCTGAGGTA
64 CATC-CTGAGGTA
* * * *
29596362 TTTTTTAATTTATTTTTTAAAAAATCAAATCAAAACCAACTCATAATGCGAGAGGTGAGTTGAGC
1 -TTTTCAATTTCTGTTTT------TCAAA--AAAATCAACTCATAATGCGAGAGGTGAGTTGAGC
29596427 CTCGGG-CTATACACTGAGGTA
57 CTCGGGTC-AT-C-CTGAGGTA
* * * * *
29596448 TTTTTAATTTTTGTTTTTC--AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTTGGGTCA
1 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC-
29596511 TATGCC-GAGGTA
65 -AT-CCTGAGGTA
* ** *
29596523 TTTTTCAATTTCTATTTTTC--AAAGGTCAACTCATAAT-CTGAGAAGTGAGTTGA
1 -TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
29596576 ACATCGAATC
Statistics
Matches: 526, Mismatches: 43, Indels: 43
0.86 0.07 0.07
Matches are distributed among these distances:
74 24 0.05
75 297 0.56
76 91 0.17
77 33 0.06
78 13 0.02
79 2 0.00
83 1 0.00
84 6 0.01
85 17 0.03
86 42 0.08
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (75 bp):
TTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCA
TCCTGAGGTA
Found at i:29596444 original size:86 final size:86
Alignment explanation
Indices: 29596307--29596475 Score: 232
Period size: 86 Copynumber: 2.0 Consensus size: 86
29596297 GCTTTTCAAA
* * * *
29596307 AAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCAGGCTGCACGCTGAGGTATTTTTTAATT
1 AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTA-TTTTTAATT
29596372 TAT-TTTTTAAAAAATCAAATC
65 TATGTTTTTAAAAAATCAAATC
* * * *
29596393 AAAACCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCTATACACTGAGGTATTTTTAATTT
1 AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTATTTTTAATTT
* *
29596458 TTGTTTTTCAAAAATCAA
66 ATGTTTTTAAAAAATCAA
29596476 CTTATATTGC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 11 0.15
86 61 0.85
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (86 bp):
AAAACCAACTCATAATGCGAGAAGTGAGTTAAGCCTCAGGCTACACACTGAGGTATTTTTAATTT
ATGTTTTTAAAAAATCAAATC
Found at i:29597789 original size:10 final size:10
Alignment explanation
Indices: 29597771--29597835 Score: 53
Period size: 10 Copynumber: 6.3 Consensus size: 10
29597761 AGGGTTTCCG
29597771 AAAGAAGAAA
1 AAAGAAGAAA
* *
29597781 AAAGTAGAAG
1 AAAGAAGAAA
*
29597791 GAAGAAGAAAA
1 AAAGAAG-AAA
29597802 AGAAGAAGAAAGA
1 A-AAGAAG-AA-A
29597815 AAAGAA-AAA
1 AAAGAAGAAA
29597824 AAAG-AGAAA
1 AAAGAAGAAA
29597833 AAA
1 AAA
29597836 AATTTAAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 1 0.02
9 11 0.24
10 15 0.33
11 2 0.04
12 14 0.31
13 2 0.04
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AAAGAAGAAA
Found at i:29597803 original size:19 final size:20
Alignment explanation
Indices: 29597770--29597832 Score: 69
Period size: 19 Copynumber: 3.2 Consensus size: 20
29597760 TAGGGTTTCC
*
29597770 GAAAGAAGAAAAAAGTAGAA
1 GAAAGAAGAAAAAAGAAGAA
*
29597790 GGAAGAAG-AAAAAGAAGAA
1 GAAAGAAGAAAAAAGAAGAA
29597809 GAAAGAAAAGAAAAAA-AAG-A
1 GAAAG--AAGAAAAAAGAAGAA
29597829 GAAA
1 GAAA
29597833 AAAAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.38
20 12 0.32
21 6 0.16
22 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
GAAAGAAGAAAAAAGAAGAA
Found at i:29597808 original size:12 final size:12
Alignment explanation
Indices: 29597791--29597836 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
29597781 AAAGTAGAAG
29597791 GAAGAAGAAAAA
1 GAAGAAGAAAAA
29597803 GAAGAAGAAAGAA
1 GAAGAAGAAA-AA
*
29597816 -AAGAAAAAAAA
1 GAAGAAGAAAAA
29597827 G-AGAA-AAAAA
1 GAAGAAGAAAAA
29597837 ATTTAAATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 18 0.58
13 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:29597814 original size:16 final size:16
Alignment explanation
Indices: 29597772--29597817 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
29597762 GGGTTTCCGA
*
29597772 AAGAAGAAA-AAAGTAG
1 AAGAAGAAAGAAA-AAG
29597788 AAGGAAG-AAGAAAAAG
1 AA-GAAGAAAGAAAAAG
29597804 AAGAAGAAAGAAAA
1 AAGAAGAAAGAAAA
29597818 GAAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:29598074 original size:70 final size:71
Alignment explanation
Indices: 29597992--29598132 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 71
29597982 AAAAAAGAAA
*
29597992 ACAGGCCATTTTTAGCAGGCCAACA-CAGGCCCGCCTACCAAGCCAGCCCAGCGCCCAGGC-AGC
1 ACAGGCCATTTTTAGCAGGCCAACAGCAGGCCAG-CTACCAAGCCAGCCCAGCGCCCAGGCGAGC
29598055 CAGTAGC
65 CAGTAGC
29598062 ACAGGCCATTTTTAGCAGGCCAACAGCAGGCCAGCTACCAAGCCAGCCCAGCGCCCAGGCGAGCC
1 ACAGGCCATTTTTAGCAGGCCAACAGCAGGCCAGCTACCAAGCCAGCCCAGCGCCCAGGCGAGCC
29598127 AGTAGC
66 AGTAGC
29598133 CCCCAGGCCC
Statistics
Matches: 68, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
70 51 0.75
71 17 0.25
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.10
Consensus pattern (71 bp):
ACAGGCCATTTTTAGCAGGCCAACAGCAGGCCAGCTACCAAGCCAGCCCAGCGCCCAGGCGAGCC
AGTAGC
Found at i:29598223 original size:16 final size:16
Alignment explanation
Indices: 29598202--29598238 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
29598192 CGGCAGCAGC
29598202 AAAAAAAA-GAGAAAAG
1 AAAAAAAAGGA-AAAAG
29598218 AAAAAAAAGGAAAAAG
1 AAAAAAAAGGAAAAAG
29598234 AAAAA
1 AAAAA
29598239 GAAAAAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGGAAAAAG
Found at i:29598249 original size:7 final size:6
Alignment explanation
Indices: 29598205--29598245 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
29598195 CAGCAGCAAA
*
29598205 AAAAAG AGAAAAG -AAAA- AAAAGG AAAAAG AAAAAG AAAAAG
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
29598246 GAAAGGCCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 7 0.23
6 18 0.60
7 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:29598830 original size:18 final size:18
Alignment explanation
Indices: 29598710--29598889 Score: 116
Period size: 17 Copynumber: 10.2 Consensus size: 18
29598700 AAAAATCAAT
29598710 AAAA-TTTCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
29598726 AAAATCTTT-GTG-TTTCC
1 AAAAT-TTTCGTGTTTTCA
29598743 AAAA-TTTCG-GTATTTCA
1 AAAATTTTCGTGT-TTTCA
*
29598760 AAAATTTTCCGTATTTTCA
1 AAAATTTT-CGTGTTTTCA
*
29598779 AAAATTTCCGTG-TTTCA
1 AAAATTTTCGTGTTTTCA
*
29598796 AAAATTTTTTTTTGTGTTTTCA
1 AAAA----TTTTCGTGTTTTCA
*
29598818 ACAATTTTCGTG--TT-A
1 AAAATTTTCGTGTTTTCA
*
29598833 AAAA-ATTCGTG-TTTCAA
1 AAAATTTTCGTGTTTTC-A
*
29598850 AATAATTCTCGTG-TTTCA
1 AA-AATTTTCGTGTTTTCA
*
29598868 TAAATTTTCGTGTTTTCA
1 AAAATTTTCGTGTTTTCA
29598886 AAAA
1 AAAA
29598890 AAAAATTCCC
Statistics
Matches: 129, Mismatches: 16, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
14 6 0.05
15 10 0.08
16 7 0.05
17 40 0.31
18 28 0.22
19 23 0.18
20 1 0.01
21 6 0.05
22 8 0.06
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (18 bp):
AAAATTTTCGTGTTTTCA
Found at i:29598953 original size:16 final size:16
Alignment explanation
Indices: 29598899--29598953 Score: 56
Period size: 17 Copynumber: 3.3 Consensus size: 16
29598889 AAAAAATTCC
* *
29598899 CGTGCTTCGAAAATTT
1 CGTGTTTCGAAATTTT
*
29598915 CGTGTTTTCAAAAGTTTT
1 CGTG-TTTCGAAA-TTTT
*
29598933 TGTGTTTCGAAATTTT
1 CGTGTTTCGAAATTTT
29598949 CGTGT
1 CGTGT
29598954 CTCAATAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 12 0.39
17 13 0.42
18 6 0.19
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (16 bp):
CGTGTTTCGAAATTTT
Found at i:29604636 original size:6 final size:6
Alignment explanation
Indices: 29604625--29604654 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
29604615 GATGATTTGA
29604625 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
1 GCCCTT GCCCTT GCCCTT GCCCTT GCCCTT
29604655 AGGCTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
GCCCTT
Found at i:29612538 original size:14 final size:14
Alignment explanation
Indices: 29612521--29612549 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29612511 ATTTAATTTC
29612521 TTTGAATTAATATT
1 TTTGAATTAATATT
29612535 TTTGAATTAATATT
1 TTTGAATTAATATT
29612549 T
1 T
29612550 AATTGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTGAATTAATATT
Found at i:29615704 original size:89 final size:88
Alignment explanation
Indices: 29615500--29615727 Score: 289
Period size: 89 Copynumber: 2.6 Consensus size: 88
29615490 AAGCCCATTT
* * * *
29615500 TTTTTGTTTGCACTCAATTGGGTATTTGAACTTTCAAAATGCATCAAAAAAGCTCTCAAACTATT
1 TTTTT-TTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCAT-TAAAAAGCCCGCAAAC-ATT
* *
29615565 TAAAAAAAAAGCAATTAAGCCCCTAC
63 TAAAAAAAAAACAATTAAGCCACTAC
29615591 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAAC-TTTAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACATTTAA
* *
29615655 AAAATAAAACAATTAAGCCATTGAG
66 AAAA-AAAACAATTAAGCCACT-AC
* ** *
29615680 TTTTTTTGGCACTCAATTTAGTACTTGAACTGT-AAAATGCATTAAAAA
1 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAA
29615728 TACTCTCTGA
Statistics
Matches: 123, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
87 9 0.07
88 29 0.24
89 43 0.35
90 37 0.30
91 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (88 bp):
TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATTAAAAAGCCCGCAAACATTTAA
AAAAAAAACAATTAAGCCACTAC
Found at i:29617690 original size:27 final size:27
Alignment explanation
Indices: 29617639--29618191 Score: 590
Period size: 27 Copynumber: 20.5 Consensus size: 27
29617629 AAAGGTTGTT
* **
29617639 AAATGACCATAATGTCCTTTGTAGGGTA
1 AAATGACCGTAATG-CCCCTGTAGGGTA
* * *
29617667 AAATAACCGTAATACCCCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* ***
29617694 AAATGACCGTAATACCCCCAAAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * **
29617721 AAATAACCGTAATACTCCC-ATAGAATA
1 AAATGACCGTAATGC-CCCTGTAGGGTA
* *
29617748 AAATAACCGTAATACCCC-GATAGGGTA
1 AAATGACCGTAATGCCCCTG-TAGGGTA
*
29617775 AAATAACCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *** * * *
29617802 AATTAATTATAATACCTCTATAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
29617829 AAATGATCGTAATACCCTTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
29617856 AAATGACCGTAATGCCATTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
29617883 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * * *
29617910 AAATGTCCATAATGCCTCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
29617937 AAATGACCGTAATGCCTCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
29617964 AAATAATCGTAATGTCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* *
29617991 AAATGACC-TAATGCCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
29618017 AAATGACCATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
29618044 AAATGACCGTAATGCCCCTAAAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
**
29618071 AAATGACTATAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
29618098 AAATGATCGTAATGCCCCTGTAGGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
* * *
29618125 AAATGATCGTAATGCCCTTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
*
29618152 AAATGACCGTAATGCCCCTGTAAGGTA
1 AAATGACCGTAATGCCCCTGTAGGGTA
29618179 AAATGACCGTAAT
1 AAATGACCGTAAT
29618192 ACCTTCGAGG
Statistics
Matches: 453, Mismatches: 68, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
26 26 0.06
27 412 0.91
28 15 0.03
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
AAATGACCGTAATGCCCCTGTAGGGTA
Found at i:29618466 original size:26 final size:26
Alignment explanation
Indices: 29618411--29618466 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
29618401 TATATTATAT
* * *
29618411 TGGCAGCTTTGCTGCGATACTGCTGC
1 TGGCAACTTTGCTGCGATACTACTGA
* *
29618437 TGGCAACTTTGTTGCGATGCTACTGA
1 TGGCAACTTTGCTGCGATACTACTGA
29618463 TGGC
1 TGGC
29618467 TTTGTGCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.32
Consensus pattern (26 bp):
TGGCAACTTTGCTGCGATACTACTGA
Found at i:29618499 original size:32 final size:32
Alignment explanation
Indices: 29618457--29618659 Score: 255
Period size: 32 Copynumber: 6.4 Consensus size: 32
29618447 GTTGCGATGC
* * *
29618457 TACTGATGGCTTTGTGCTGATCATATTATCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
29618489 CACTGATGGCTTTGTGCCAATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
29618521 TATTGATGGTTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
29618553 TACTGATGGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * *
29618585 TACTGATGGCTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
29618617 TACTGATGGCTTTGTGCCAAACATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
29618648 TACTTATGGCTT
1 TACTGATGGCTT
29618660 GTAGCCATTC
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
31 11 0.07
32 138 0.93
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:29618676 original size:22 final size:21
Alignment explanation
Indices: 29618651--29618712 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
29618641 ATTACTGTAC
29618651 TTATGGCTTGTAGCCATTCTGT
1 TTATGGCTT-TAGCCATTCTGT
* ** *
29618673 TTATAGCTTATAGTTATCCTGT
1 TTATGGCTT-TAGCCATTCTGT
*
29618695 TTACGGCTCTTAGCCATT
1 TTATGGCT-TTAGCCATT
29618713 TTGACTACTG
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.45
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTGT
Found at i:29619674 original size:21 final size:21
Alignment explanation
Indices: 29619639--29619697 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
29619629 ATAAAAATAT
*
29619639 AAAAATATTATTAAAATTAGGA
1 AAAAAAATTA-TAAAATTAGGA
* * *
29619661 AAAAAAATTATAAAAATCGTA
1 AAAAAAATTATAAAATTAGGA
*
29619682 AAAGAAATTATAAAAT
1 AAAAAAATTATAAAAT
29619698 ATTGTAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAAAATTATAAAATTAGGA
Found at i:29619675 original size:9 final size:9
Alignment explanation
Indices: 29619663--29619734 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
29619653 AATTAGGAAA
29619663 AAAAATTAT
1 AAAAATTAT
*
29619672 AAAAATCGTAA
1 AAAAAT--TAT
29619683 AAGAAATTAT
1 AA-AAATTAT
*
29619693 AAAATATTGT
1 AAAA-ATTAT
29619703 AAAAATTTAT
1 AAAAA-TTAT
* *
29619713 AAAAGTCAT
1 AAAAATTAT
29619722 AAAAATTAT
1 AAAAATTAT
29619731 AAAA
1 AAAA
29619735 GGCATCAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
9 23 0.46
10 19 0.38
11 4 0.08
12 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29619712 original size:20 final size:20
Alignment explanation
Indices: 29619661--29619734 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
29619651 AAAATTAGGA
29619661 AAAAAAATTATAAAAATCGT
1 AAAAAAATTATAAAAATCGT
*
29619681 AAAAGAAATTATAAAATATTGT
1 AAAA-AAATTATAAAA-ATCGT
* *
29619703 -AAAAATTTATAAAAGTC--
1 AAAAAAATTATAAAAATCGT
*
29619720 ATAAAAATTATAAAA
1 AAAAAAATTATAAAA
29619735 GGCATCAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 12 0.27
19 1 0.02
20 14 0.31
21 14 0.31
22 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAAAATTATAAAAATCGT
Found at i:29619744 original size:19 final size:19
Alignment explanation
Indices: 29619702--29619745 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
29619692 TAAAATATTG
*
29619702 TAAAAATTTATAAAAGTCA
1 TAAAAATTTATAAAAGGCA
29619721 TAAAAA-TTATAAAAGGCA
1 TAAAAATTTATAAAAGGCA
29619739 TCAAAAA
1 T-AAAAA
29619746 GACTAACGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAATTTATAAAAGGCA
Found at i:29623387 original size:13 final size:13
Alignment explanation
Indices: 29623364--29623388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29623354 TTTATTTTAG
29623364 TATTTTATTTACT
1 TATTTTATTTACT
29623377 TATTTTATTTAC
1 TATTTTATTTAC
29623389 AGTTATACTT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTATTTACT
Found at i:29623489 original size:16 final size:16
Alignment explanation
Indices: 29623464--29623498 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
29623454 TAATTCTCAT
*
29623464 TTTATTTATTTACGTA
1 TTTATCTATTTACGTA
*
29623480 TTTATCTATTTACTTA
1 TTTATCTATTTACGTA
29623496 TTT
1 TTT
29623499 TTACAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTATCTATTTACGTA
Found at i:29636221 original size:132 final size:131
Alignment explanation
Indices: 29636036--29636293 Score: 419
Period size: 132 Copynumber: 2.0 Consensus size: 131
29636026 GAGCAGGTTG
* * *
29636036 ATGGTGGATTTTACCTCCTGAGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTA-TCTCCCTG
1 ATGGCGGATTTTACCTCCTGAGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTG
* * *
29636100 GGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATAAA
65 GGCAGCAGTGGAATAGATTGAAGATTTCAGAACTTATCTCCCAAAGTAGTAGCGGAGCAGATAAA
29636165 AA
130 AA
*
29636167 ATGGCGGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG
1 ATGGCGGATTTTACCT-CCTGAGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTG
*
29636232 GGCAGTAGTGGAATAGATTGAAGATTTCAGAACTTATCTCCCAAAGTAGTAGCGGAGCAGAT
65 GGCAGCAGTGGAATAGATTGAAGATTTCAGAACTTATCTCCCAAAGTAGTAGCGGAGCAGAT
29636294 TGAAGACGGC
Statistics
Matches: 117, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
131 15 0.13
132 101 0.86
133 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (131 bp):
ATGGCGGATTTTACCTCCTGAGATTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGG
GCAGCAGTGGAATAGATTGAAGATTTCAGAACTTATCTCCCAAAGTAGTAGCGGAGCAGATAAAA
A
Found at i:29636560 original size:50 final size:50
Alignment explanation
Indices: 29636424--29636590 Score: 172
Period size: 50 Copynumber: 3.3 Consensus size: 50
29636414 GTGGAGGGTT
* * *
29636424 GAATCTTACTTCTCCGGGCGGTGTAGTGGAACAGATTAAAGCTACAACGGC
1 GAATCTTACTTC-CCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
* * ** ** * ** *
29636475 AAATCTTGCTTCCCCAACATTGCAGTTAAAAAGATTAAAGCCACAACGAC
1 GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
* *
29636525 GAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTAAAGCCACAACGGC
1 GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
**
29636575 GAATCTTGTTTCCCCG
1 GAATCTTACTTCCCCG
29636591 ACATTGTAGT
Statistics
Matches: 88, Mismatches: 28, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
50 78 0.89
51 10 0.11
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (50 bp):
GAATCTTACTTCCCCGGCGGTGTAGTGGAAAAGATTAAAGCCACAACGGC
Found at i:29636599 original size:50 final size:50
Alignment explanation
Indices: 29636445--29636600 Score: 177
Period size: 50 Copynumber: 3.1 Consensus size: 50
29636435 CTCCGGGCGG
* * * *
29636445 TGTAGTGGAACAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCAACAT
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
* ** * * * * **
29636495 TGCAGTTAAAAAGATTAAAGCCACAACGACGAATCTTACTTCCCTGGCGG
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
* *
29636545 TGTAGTGGAATAGATTAAAGCCACAACGGCGAATCTTGTTTCCCCGACAT
1 TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
29636595 TGTAGT
1 TGTAGT
29636601 CAGACAGTAC
Statistics
Matches: 82, Mismatches: 24, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
TGTAGTGGAAAAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACAT
Found at i:29637409 original size:18 final size:19
Alignment explanation
Indices: 29637367--29637410 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
29637357 ATAGGCCAGC
*
29637367 ATAT-AAAAAACGGAAGAA
1 ATATAAAAAAAAGGAAGAA
29637385 ATAATAAAAAAAAGGAA-AA
1 AT-ATAAAAAAAAGGAAGAA
29637404 ATATAAA
1 ATATAAA
29637411 CCATTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.30
19 6 0.26
20 10 0.43
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.14
Consensus pattern (19 bp):
ATATAAAAAAAAGGAAGAA
Found at i:29638642 original size:94 final size:95
Alignment explanation
Indices: 29638538--29638723 Score: 356
Period size: 94 Copynumber: 2.0 Consensus size: 95
29638528 TGTTTTGCTT
29638538 TTTGATTGATTTTATATTCATTAGCCTTTGAATGTTAGCATAATATGTAATATAAGATGGTTGCC
1 TTTGATTGATTTTATATTCATTAGCCTTTGAATGTTAGCATAATATGTAATATAAGATGGTTGCC
29638603 CTTATGTAGGTAGTA-GTTTATATGTGTGC
66 CTTATGTAGGTAGTATGTTTATATGTGTGC
29638632 TTTGATTGATTTTATATTCATTAGCCTTTGAATGTTAGCATAATATGTAATATAAGATGGTTGCC
1 TTTGATTGATTTTATATTCATTAGCCTTTGAATGTTAGCATAATATGTAATATAAGATGGTTGCC
29638697 CTTATGTAGGTAGTATTGTTTATATGT
66 CTTATGTAGGTAGTA-TGTTTATATGT
29638724 ATTTTATCGA
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
94 80 0.89
96 10 0.11
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (95 bp):
TTTGATTGATTTTATATTCATTAGCCTTTGAATGTTAGCATAATATGTAATATAAGATGGTTGCC
CTTATGTAGGTAGTATGTTTATATGTGTGC
Found at i:29646611 original size:60 final size:60
Alignment explanation
Indices: 29646518--29646649 Score: 237
Period size: 60 Copynumber: 2.2 Consensus size: 60
29646508 TAAACGTGAG
* * *
29646518 ATTTATGTAAATCAAATGGTATATGATTTTTTTTATTCTGATCGTAATATTTAACACTTC
1 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
29646578 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
1 ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
29646638 ATTTATGTAAAT
1 ATTTATGTAAAT
29646650 CGTGTTTAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.33, C:0.09, G:0.10, T:0.48
Consensus pattern (60 bp):
ATTTATGTAAATAAAATGCTATATGATTTTTTTTATTCTGATCGTAATATTGAACACTTC
Found at i:29651263 original size:82 final size:82
Alignment explanation
Indices: 29651114--29651269 Score: 267
Period size: 82 Copynumber: 1.9 Consensus size: 82
29651104 CCACCTAATT
* *
29651114 TGGAGTAGAAGTTGAGATTTCTTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTGTTCCAAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
29651179 ATGCGTTTTTTAGTCCC
66 ATGCGTTTTTTAGTCCC
* *
29651196 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATTTATTCCGAA
1 TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
*
29651261 ATGGGTTTT
66 ATGCGTTTT
29651270 AATTCTTCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (82 bp):
TGGAGTAGAAGTTGAGATTTATTTGTTTTCATTGGTTTTCTATGCTTTCTTGCATCTATTCCAAA
ATGCGTTTTTTAGTCCC
Found at i:29651620 original size:6 final size:6
Alignment explanation
Indices: 29651609--29651647 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
29651599 GATAACTCTC
* *
29651609 TTTCCG TTTCCG TTTCCG TTTCCT TTTCCT TTATCCG TT
1 TTTCCG TTTCCG TTTCCG TTTCCG TTTCCG TT-TCCG TT
29651648 ACTCCTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.03, C:0.31, G:0.10, T:0.56
Consensus pattern (6 bp):
TTTCCG
Found at i:29652975 original size:14 final size:14
Alignment explanation
Indices: 29652956--29652984 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29652946 CAAAAAAAAT
29652956 AAATTCATTTTCTA
1 AAATTCATTTTCTA
29652970 AAATTCATTTTCTA
1 AAATTCATTTTCTA
29652984 A
1 A
29652985 CCAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTCATTTTCTA
Found at i:29653038 original size:59 final size:59
Alignment explanation
Indices: 29652925--29653039 Score: 203
Period size: 59 Copynumber: 1.9 Consensus size: 59
29652915 TCATCTAAAT
*
29652925 ACCAGAAAATATTAACTTTTTCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
1 ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
* *
29652984 ACCAGAAAATATTAGCTTTTCCAAAAAAAGTAAATTCATTTTCTAAAATTCATTTT
1 ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTT
29653040 TCGGAAACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.44, C:0.14, G:0.03, T:0.38
Consensus pattern (59 bp):
ACCAGAAAATATTAACTTTTCCAAAAAAAATAAATTCATTTTCTAAAATTCATTTTCTA
Found at i:29662183 original size:695 final size:695
Alignment explanation
Indices: 29660854--29662243 Score: 2780
Period size: 695 Copynumber: 2.0 Consensus size: 695
29660844 AAATCACTAG
29660854 TGTTACAGTTAAGGTTCAGGTGAGCGTCAAATTTTCTCAATTTCAATGAAATCTACTTTCTGATG
1 TGTTACAGTTAAGGTTCAGGTGAGCGTCAAATTTTCTCAATTTCAATGAAATCTACTTTCTGATG
29660919 TTTTTTATTCGATATCATTTTTTTTAGATTTTTTTTCTGTTATTCCTAAAAGCTTTTCCAAGCTT
66 TTTTTTATTCGATATCATTTTTTTTAGATTTTTTTTCTGTTATTCCTAAAAGCTTTTCCAAGCTT
29660984 CGTTCGGAAATGCAAAACGACAATTTTGCAACCGTCTATGGCGACCTCGCAGCCAAGCAATCGAA
131 CGTTCGGAAATGCAAAACGACAATTTTGCAACCGTCTATGGCGACCTCGCAGCCAAGCAATCGAA
29661049 AGATCACCAGAGCGACGGAGTTTTCTCTTCCTCCACCACCTCGTCCTCCACTTCCGCCGCTTCTG
196 AGATCACCAGAGCGACGGAGTTTTCTCTTCCTCCACCACCTCGTCCTCCACTTCCGCCGCTTCTG
29661114 TCTTCGCTCTTTACCATCCTCGCATCCTCATGCAACAACATCAAGATATGATCAACCGCCACAAC
261 TCTTCGCTCTTTACCATCCTCGCATCCTCATGCAACAACATCAAGATATGATCAACCGCCACAAC
29661179 CTCTGCCTCACTCGCCTCCGTGAAGCTGCAAAGGAAGCCGAGGCCCTCCGCCAAGAGAATACCTC
326 CTCTGCCTCACTCGCCTCCGTGAAGCTGCAAAGGAAGCCGAGGCCCTCCGCCAAGAGAATACCTC
29661244 CCTTCGATCTGCCAACCGAGACCTCAACAAGCAACTCAGCGCACTGATCCAAGCCTCTGTGCAGA
391 CCTTCGATCTGCCAACCGAGACCTCAACAAGCAACTCAGCGCACTGATCCAAGCCTCTGTGCAGA
29661309 ACCACTTTTCATCATCTGATTACAATACCACGCCGTTTGAGTTGGTGAACGCGTTGCGAGGACTT
456 ACCACTTTTCATCATCTGATTACAATACCACGCCGTTTGAGTTGGTGAACGCGTTGCGAGGACTT
29661374 TGTCTCGGTAGTGGCGGTGGAGGAGAGGTAGATGTTTCTGATGAGAGTCCGACGAGTGTGATGGA
521 TGTCTCGGTAGTGGCGGTGGAGGAGAGGTAGATGTTTCTGATGAGAGTCCGACGAGTGTGATGGA
29661439 AGGTGGTGCGGTGGACGTGGAGCGGGTCATGTTACCTAAGAGCATATCTGTTAGGTCTAATGGAT
586 AGGTGGTGCGGTGGACGTGGAGCGGGTCATGTTACCTAAGAGCATATCTGTTAGGTCTAATGGAT
29661504 ATCTGAAGATGATGAATCAAGCTGGAGCGAGTCATCGTGGTAAAA
651 ATCTGAAGATGATGAATCAAGCTGGAGCGAGTCATCGTGGTAAAA
29661549 TGTTACAGTTAAGGTTCAGGTGAGCGTCAAATTTTCTCAATTTCAATGAAATCTACTTTCTGATG
1 TGTTACAGTTAAGGTTCAGGTGAGCGTCAAATTTTCTCAATTTCAATGAAATCTACTTTCTGATG
29661614 TTTTTTATTCGATATCATTTTTTTTAGATTTTTTTTCTGTTATTCCTAAAAGCTTTTCCAAGCTT
66 TTTTTTATTCGATATCATTTTTTTTAGATTTTTTTTCTGTTATTCCTAAAAGCTTTTCCAAGCTT
29661679 CGTTCGGAAATGCAAAACGACAATTTTGCAACCGTCTATGGCGACCTCGCAGCCAAGCAATCGAA
131 CGTTCGGAAATGCAAAACGACAATTTTGCAACCGTCTATGGCGACCTCGCAGCCAAGCAATCGAA
29661744 AGATCACCAGAGCGACGGAGTTTTCTCTTCCTCCACCACCTCGTCCTCCACTTCCGCCGCTTCTG
196 AGATCACCAGAGCGACGGAGTTTTCTCTTCCTCCACCACCTCGTCCTCCACTTCCGCCGCTTCTG
29661809 TCTTCGCTCTTTACCATCCTCGCATCCTCATGCAACAACATCAAGATATGATCAACCGCCACAAC
261 TCTTCGCTCTTTACCATCCTCGCATCCTCATGCAACAACATCAAGATATGATCAACCGCCACAAC
29661874 CTCTGCCTCACTCGCCTCCGTGAAGCTGCAAAGGAAGCCGAGGCCCTCCGCCAAGAGAATACCTC
326 CTCTGCCTCACTCGCCTCCGTGAAGCTGCAAAGGAAGCCGAGGCCCTCCGCCAAGAGAATACCTC
29661939 CCTTCGATCTGCCAACCGAGACCTCAACAAGCAACTCAGCGCACTGATCCAAGCCTCTGTGCAGA
391 CCTTCGATCTGCCAACCGAGACCTCAACAAGCAACTCAGCGCACTGATCCAAGCCTCTGTGCAGA
29662004 ACCACTTTTCATCATCTGATTACAATACCACGCCGTTTGAGTTGGTGAACGCGTTGCGAGGACTT
456 ACCACTTTTCATCATCTGATTACAATACCACGCCGTTTGAGTTGGTGAACGCGTTGCGAGGACTT
29662069 TGTCTCGGTAGTGGCGGTGGAGGAGAGGTAGATGTTTCTGATGAGAGTCCGACGAGTGTGATGGA
521 TGTCTCGGTAGTGGCGGTGGAGGAGAGGTAGATGTTTCTGATGAGAGTCCGACGAGTGTGATGGA
29662134 AGGTGGTGCGGTGGACGTGGAGCGGGTCATGTTACCTAAGAGCATATCTGTTAGGTCTAATGGAT
586 AGGTGGTGCGGTGGACGTGGAGCGGGTCATGTTACCTAAGAGCATATCTGTTAGGTCTAATGGAT
29662199 ATCTGAAGATGATGAATCAAGCTGGAGCGAGTCATCGTGGTAAAA
651 ATCTGAAGATGATGAATCAAGCTGGAGCGAGTCATCGTGGTAAAA
29662244 CTCGTGGACC
Statistics
Matches: 695, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
695 695 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (695 bp):
TGTTACAGTTAAGGTTCAGGTGAGCGTCAAATTTTCTCAATTTCAATGAAATCTACTTTCTGATG
TTTTTTATTCGATATCATTTTTTTTAGATTTTTTTTCTGTTATTCCTAAAAGCTTTTCCAAGCTT
CGTTCGGAAATGCAAAACGACAATTTTGCAACCGTCTATGGCGACCTCGCAGCCAAGCAATCGAA
AGATCACCAGAGCGACGGAGTTTTCTCTTCCTCCACCACCTCGTCCTCCACTTCCGCCGCTTCTG
TCTTCGCTCTTTACCATCCTCGCATCCTCATGCAACAACATCAAGATATGATCAACCGCCACAAC
CTCTGCCTCACTCGCCTCCGTGAAGCTGCAAAGGAAGCCGAGGCCCTCCGCCAAGAGAATACCTC
CCTTCGATCTGCCAACCGAGACCTCAACAAGCAACTCAGCGCACTGATCCAAGCCTCTGTGCAGA
ACCACTTTTCATCATCTGATTACAATACCACGCCGTTTGAGTTGGTGAACGCGTTGCGAGGACTT
TGTCTCGGTAGTGGCGGTGGAGGAGAGGTAGATGTTTCTGATGAGAGTCCGACGAGTGTGATGGA
AGGTGGTGCGGTGGACGTGGAGCGGGTCATGTTACCTAAGAGCATATCTGTTAGGTCTAATGGAT
ATCTGAAGATGATGAATCAAGCTGGAGCGAGTCATCGTGGTAAAA
Found at i:29662312 original size:6 final size:6
Alignment explanation
Indices: 29662301--29662334 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
29662291 GTGAGTTTGA
29662301 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCT
29662335 AGTTCTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:29662340 original size:18 final size:18
Alignment explanation
Indices: 29662301--29662340 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
29662291 GTGAGTTTGA
**
29662301 TTCTTTTTCTTTTTCTTT
1 TTCTTTTTCTTTTTCTAG
29662319 TTCTTTTTCTTTTTCTAG
1 TTCTTTTTCTTTTTCTAG
29662337 TTCT
1 TTCT
29662341 GTTTGGATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (18 bp):
TTCTTTTTCTTTTTCTAG
Found at i:29667717 original size:23 final size:23
Alignment explanation
Indices: 29667691--29667741 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29667681 TGGAAAGAAG
* *
29667691 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
29667714 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
29667737 AGTAA
1 TGTAA
29667742 GAAAGTACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:29668322 original size:23 final size:23
Alignment explanation
Indices: 29668296--29668346 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
29668286 TGGAAAGAAG
* *
29668296 TGTAATATCCTGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
29668319 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
29668342 AGTAA
1 TGTAA
29668347 GAAAGTACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:29668734 original size:605 final size:605
Alignment explanation
Indices: 29667584--29668794 Score: 2422
Period size: 605 Copynumber: 2.0 Consensus size: 605
29667574 AGGGTCATAC
29667584 ATCTTATGACATTATTGTTGGTGAGCCATTGAATGGCTATTACATGTCTAACTTATTCCATTGAT
1 ATCTTATGACATTATTGTTGGTGAGCCATTGAATGGCTATTACATGTCTAACTTATTCCATTGAT
29667649 TGTGTGTCTATATACTTGTATAGAGAATGAATTGGAAAGAAGTGTAATATCCTGAAAATTACTAC
66 TGTGTGTCTATATACTTGTATAGAGAATGAATTGGAAAGAAGTGTAATATCCTGAAAATTACTAC
29667714 TGTAATACCCCGAAAATTACTACAGTAAGAAAGTACGTATCCTTGATATAGTAAAATAAGGAAAT
131 TGTAATACCCCGAAAATTACTACAGTAAGAAAGTACGTATCCTTGATATAGTAAAATAAGGAAAT
29667779 AAAATGAAAAAAAGGGAAATTTTGAGTTATGACAACATTGGGAAGTATATTATGATATATTAATT
196 AAAATGAAAAAAAGGGAAATTTTGAGTTATGACAACATTGGGAAGTATATTATGATATATTAATT
29667844 CAAAAAAAGATTAAATCGCAAAAGTGAAAAAAGTTTTGTTGATTAAGAGTAAATACTCAAAATTT
261 CAAAAAAAGATTAAATCGCAAAAGTGAAAAAAGTTTTGTTGATTAAGAGTAAATACTCAAAATTT
29667909 GAGGGGGTAAAGTGTAAATATGAAAAAGTTAAAGGACCAATGGTGAAAATATTTTAAGGGTGAAA
326 GAGGGGGTAAAGTGTAAATATGAAAAAGTTAAAGGACCAATGGTGAAAATATTTTAAGGGTGAAA
29667974 TAATATAGAAACTAAGGAAAACGGATGAATTAGGACCAAATTGAAAATGTGAAGAATTTTGAAAG
391 TAATATAGAAACTAAGGAAAACGGATGAATTAGGACCAAATTGAAAATGTGAAGAATTTTGAAAG
29668039 ACTAAATCGTAATTTTATCAAATTAAGTGATGACTCAATGATGGAATTTTTAAAGATTATAAAGG
456 ACTAAATCGTAATTTTATCAAATTAAGTGATGACTCAATGATGGAATTTTTAAAGATTATAAAGG
29668104 GAAAAATGGTAAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTGGAGATATTTTAGAT
521 GAAAAATGGTAAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTGGAGATATTTTAGAT
29668169 TAATTAATTAAATAAATATT
586 TAATTAATTAAATAAATATT
29668189 ATCTTATGACATTATTGTTGGTGAGCCATTGAATGGCTATTACATGTCTAACTTATTCCATTGAT
1 ATCTTATGACATTATTGTTGGTGAGCCATTGAATGGCTATTACATGTCTAACTTATTCCATTGAT
29668254 TGTGTGTCTATATACTTGTATAGAGAATGAATTGGAAAGAAGTGTAATATCCTGAAAATTACTAC
66 TGTGTGTCTATATACTTGTATAGAGAATGAATTGGAAAGAAGTGTAATATCCTGAAAATTACTAC
29668319 TGTAATACCCCGAAAATTACTACAGTAAGAAAGTACGTATCCTTGATATAGTAAAATAAGGAAAT
131 TGTAATACCCCGAAAATTACTACAGTAAGAAAGTACGTATCCTTGATATAGTAAAATAAGGAAAT
29668384 AAAATGAAAAAAAGGGAAATTTTGAGTTATGACAACATTGGGAAGTATATTATGATATATTAATT
196 AAAATGAAAAAAAGGGAAATTTTGAGTTATGACAACATTGGGAAGTATATTATGATATATTAATT
29668449 CAAAAAAAGATTAAATCGCAAAAGTGAAAAAAGTTTTGTTGATTAAGAGTAAATACTCAAAATTT
261 CAAAAAAAGATTAAATCGCAAAAGTGAAAAAAGTTTTGTTGATTAAGAGTAAATACTCAAAATTT
29668514 GAGGGGGTAAAGTGTAAATATGAAAAAGTTAAAGGACCAATGGTGAAAATATTTTAAGGGTGAAA
326 GAGGGGGTAAAGTGTAAATATGAAAAAGTTAAAGGACCAATGGTGAAAATATTTTAAGGGTGAAA
29668579 TAATATAGAAACTAAGGAAAACGGATGAATTAGGACCAAATTGAAAATGTGAAGAATTTTGAAAG
391 TAATATAGAAACTAAGGAAAACGGATGAATTAGGACCAAATTGAAAATGTGAAGAATTTTGAAAG
29668644 ACTAAATCGTAATTTTATCAAATTAAGTGATGACTCAATGATGGAATTTTTAAAGATTATAAAGG
456 ACTAAATCGTAATTTTATCAAATTAAGTGATGACTCAATGATGGAATTTTTAAAGATTATAAAGG
29668709 GAAAAATGGTAAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTGGAGATATTTTAGAT
521 GAAAAATGGTAAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTGGAGATATTTTAGAT
29668774 TAATTAATTAAATAAATATT
586 TAATTAATTAAATAAATATT
29668794 A
1 A
29668795 GGTTATTAAT
Statistics
Matches: 606, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
605 606 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.30
Consensus pattern (605 bp):
ATCTTATGACATTATTGTTGGTGAGCCATTGAATGGCTATTACATGTCTAACTTATTCCATTGAT
TGTGTGTCTATATACTTGTATAGAGAATGAATTGGAAAGAAGTGTAATATCCTGAAAATTACTAC
TGTAATACCCCGAAAATTACTACAGTAAGAAAGTACGTATCCTTGATATAGTAAAATAAGGAAAT
AAAATGAAAAAAAGGGAAATTTTGAGTTATGACAACATTGGGAAGTATATTATGATATATTAATT
CAAAAAAAGATTAAATCGCAAAAGTGAAAAAAGTTTTGTTGATTAAGAGTAAATACTCAAAATTT
GAGGGGGTAAAGTGTAAATATGAAAAAGTTAAAGGACCAATGGTGAAAATATTTTAAGGGTGAAA
TAATATAGAAACTAAGGAAAACGGATGAATTAGGACCAAATTGAAAATGTGAAGAATTTTGAAAG
ACTAAATCGTAATTTTATCAAATTAAGTGATGACTCAATGATGGAATTTTTAAAGATTATAAAGG
GAAAAATGGTAAATTAGAAGAGAGAGAAATCTAGAAGGCAATGATGATGTGGAGATATTTTAGAT
TAATTAATTAAATAAATATT
Found at i:29679350 original size:20 final size:19
Alignment explanation
Indices: 29679305--29679351 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
29679295 AGCCCATTCC
*
29679305 AATTTAA-AAATTAATATA
1 AATTTAATAAATTAATAAA
**
29679323 AAGATAATAATATTAATAAA
1 AATTTAATAA-ATTAATAAA
29679343 AATTTAATA
1 AATTTAATA
29679352 TCAATAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AATTTAATAAATTAATAAA
Found at i:29689190 original size:25 final size:26
Alignment explanation
Indices: 29689149--29689280 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 26
29689139 TCCCGTTATG
*
29689149 TGGCTCTC-ACGAGCTTCTCGATTAA
1 TGGCTCTCTATGAGCTTCTCGATTAA
* * *
29689174 TGGCTCTCT-TGAACTTC-CCATTTA
1 TGGCTCTCTATGAGCTTCTCGATTAA
*
29689198 TGGCT-TGTATGAGCTT-TCCGA-TAA
1 TGGCTCTCTATGAGCTTCT-CGATTAA
29689222 TTGGCTCTCTA-GAGCTTCTCGA-TAA
1 -TGGCTCTCTATGAGCTTCTCGATTAA
29689247 TTGGCTCT-TATGAGCTT-TCCGATTAA
1 -TGGCTCTCTATGAGCTTCT-CGATTAA
29689273 TGGCTCTC
1 TGGCTCTC
29689281 CGGAGCTTCC
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
23 2 0.02
24 21 0.24
25 57 0.66
26 7 0.08
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (26 bp):
TGGCTCTCTATGAGCTTCTCGATTAA
Found at i:29689333 original size:25 final size:25
Alignment explanation
Indices: 29689304--29689351 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29689294 TATTAGCTCG
*
29689304 CATGAACTTCCTGTTACATGGCTTA
1 CATGAACTTCATGTTACATGGCTTA
* *
29689329 CATGAGCTTCATGTTATATGGCT
1 CATGAACTTCATGTTACATGGCT
29689352 CAAAAGAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (25 bp):
CATGAACTTCATGTTACATGGCTTA
Found at i:29697837 original size:25 final size:25
Alignment explanation
Indices: 29697809--29697861 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
29697799 ATGACAATCT
29697809 AATCCTTATTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
29697834 AATCCTTATTCAATCTATATCCTTA
1 AATCCTTATTCAATCTATATCCTTA
29697859 AAT
1 AAT
29697862 ATGGAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (25 bp):
AATCCTTATTCAATCTATATCCTTA
Found at i:29701126 original size:2 final size:2
Alignment explanation
Indices: 29701119--29701147 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29701109 AATAAAATGA
29701119 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 A
29701148 CTCATAACTN
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29701625 original size:7 final size:6
Alignment explanation
Indices: 29701580--29701609 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
29701570 TAAAAATCAA
29701580 AAAATC AAAATC AAAATC AAAATTC AAAAT
1 AAAATC AAAATC AAAATC AAAA-TC AAAAT
29701610 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATC
Found at i:29705123 original size:18 final size:19
Alignment explanation
Indices: 29705086--29705125 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29705076 TATTTTGTAT
29705086 AAATTAAATATAAGATTAA
1 AAATTAAATATAAGATTAA
29705105 AAATTGAAA-ATAA-ATTAA
1 AAATT-AAATATAAGATTAA
29705123 AAA
1 AAA
29705126 CATATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 9 0.45
20 3 0.15
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTAAATATAAGATTAA
Found at i:29707046 original size:13 final size:13
Alignment explanation
Indices: 29707028--29707052 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29707018 TATAAAAAAT
29707028 ATTAAAATATATA
1 ATTAAAATATATA
29707041 ATTAAAATATAT
1 ATTAAAATATAT
29707053 TAAAATACTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAAAATATATA
Found at i:29723576 original size:15 final size:16
Alignment explanation
Indices: 29723548--29723578 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29723538 AGGGGTTAAG
29723548 GGTTTAATGATTTTGA
1 GGTTTAATGATTTTGA
29723564 GGTTTAA-GATTTTGA
1 GGTTTAATGATTTTGA
29723579 TTTTAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (16 bp):
GGTTTAATGATTTTGA
Found at i:29723670 original size:62 final size:61
Alignment explanation
Indices: 29723550--29723678 Score: 134
Period size: 61 Copynumber: 2.1 Consensus size: 61
29723540 GGGTTAAGGG
* ** * * * * *
29723550 TTTAATGATTTTGAGGTTTAAGATTTTGATTTTAAGTTTAGGAATGGTAATTAGGTTTAATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTT-ATA
* *
29723612 TTTAATGATTTTAAGGTTTAAG-GGTTGATTTCGAGGTTAGGGACGATAATGTAAGTTTATA
1 TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAAT-TAAGTTTATA
*
29723673 ATTAAT
1 TTTAAT
29723679 TTTTTAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
61 28 0.51
62 27 0.49
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (61 bp):
TTTAATGATTTTAAGGTTTAAGAGGTTGATTTCAAGGTTAGGAACGATAATTAAGTTTATA
Found at i:29725350 original size:9 final size:9
Alignment explanation
Indices: 29725338--29725376 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
29725328 AAATATATTT
29725338 ATTTTTAAA
1 ATTTTTAAA
*
29725347 ATTTTTTAA
1 ATTTTTAAA
*
29725356 ATTTTAAAA
1 ATTTTTAAA
29725365 TATTTTTAAA
1 -ATTTTTAAA
29725375 AT
1 AT
29725377 ACTTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:29725360 original size:17 final size:18
Alignment explanation
Indices: 29725340--29725374 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
29725330 ATATATTTAT
29725340 TTTTAAAAT-TTTTTAAA
1 TTTTAAAATATTTTTAAA
29725357 TTTTAAAATATTTTTAAA
1 TTTTAAAATATTTTTAAA
29725375 ATACTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAAAATATTTTTAAA
Found at i:29725377 original size:11 final size:11
Alignment explanation
Indices: 29725337--29725383 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
29725327 TAAATATATT
29725337 TATTTTTAAAA
1 TATTTTTAAAA
29725348 T-TTTTT--AA
1 TATTTTTAAAA
29725356 -A-TTTTAAAA
1 TATTTTTAAAA
29725365 TATTTTTAAAA
1 TATTTTTAAAA
29725376 TACTTTTT
1 TA-TTTTT
29725384 TATTNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
7 4 0.13
8 2 0.07
9 2 0.07
10 6 0.20
11 11 0.37
12 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:29725482 original size:21 final size:20
Alignment explanation
Indices: 29725443--29725481 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
29725433 ATTTTAAAAT
29725443 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATACTTTTTTA
*
29725463 ATTTTTAAAATAATTTTTT
1 ATTTTTAAAATACTTTTTT
29725482 TGTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTTAAAATACTTTTTTA
Found at i:29733753 original size:29 final size:29
Alignment explanation
Indices: 29733711--29733769 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29733701 ATATAAAAAC
29733711 TAAAAAGCAAAGCAAAATGATGGTGGAGA
1 TAAAAAGCAAAGCAAAATGATGGTGGAGA
29733740 TAAAAAGCAAAGCAAAATGATGGTGGAGA
1 TAAAAAGCAAAGCAAAATGATGGTGGAGA
29733769 T
1 T
29733770 TTAGATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.51, C:0.07, G:0.27, T:0.15
Consensus pattern (29 bp):
TAAAAAGCAAAGCAAAATGATGGTGGAGA
Found at i:29735909 original size:29 final size:28
Alignment explanation
Indices: 29735838--29735909 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
29735828 AAGAACTAGA
* *
29735838 TAAAATATATATAGTTTTTGATGAATTGG
1 TAAAATATA-ATATTTTTTGATGAAATGG
* * *
29735867 TAAAAT-CACTATTTTTTTATGAAATGG
1 TAAAATATAATATTTTTTGATGAAATGG
29735894 TAAAAATATAATATTT
1 T-AAAATATAATATTT
29735910 GAGTTTGTAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
27 16 0.47
28 6 0.18
29 12 0.35
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (28 bp):
TAAAATATAATATTTTTTGATGAAATGG
Found at i:29737262 original size:13 final size:13
Alignment explanation
Indices: 29737244--29737268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29737234 CCCAATTGGT
29737244 AATTGAACTTGAA
1 AATTGAACTTGAA
29737257 AATTGAACTTGA
1 AATTGAACTTGA
29737269 GATCGTAAAT
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:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
AATTGAACTTGAA
Found at i:29737542 original size:26 final size:26
Alignment explanation
Indices: 29737506--29737557 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
29737496 TTAATGATTG
29737506 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
29737532 AGTGGTGGAAGAATTACACTCCTACT
1 AGTGGTGGAAGAATTACACTCCTACT
29737558 TAGACTCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
AGTGGTGGAAGAATTACACTCCTACT
Found at i:29737839 original size:25 final size:26
Alignment explanation
Indices: 29737789--29737840 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
29737779 AGTTGTAAAG
29737789 AGAAAATTTTCTAAAGAAATTATTTT
1 AGAAAATTTTCTAAAGAAATTATTTT
* * *
29737815 AGAAAA-TTTCTAGAGATATTTTTTT
1 AGAAAATTTTCTAAAGAAATTATTTT
29737840 A
1 A
29737841 TTTATAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (26 bp):
AGAAAATTTTCTAAAGAAATTATTTT
Found at i:29744856 original size:7 final size:7
Alignment explanation
Indices: 29744836--29744899 Score: 60
Period size: 7 Copynumber: 9.0 Consensus size: 7
29744826 GTTCAAATTC
*
29744836 AAAAAAC
1 AAAAAAG
29744843 AAAAAAG
1 AAAAAAG
29744850 AAAAAAGAG
1 -AAAAA-AG
29744859 AAAAAAG
1 AAAAAAG
29744866 AAAAAA-
1 AAAAAAG
*
29744872 AGAAGAAG
1 A-AAAAAG
29744880 AAAAAAG
1 AAAAAAG
*
29744887 AAAAGA-
1 AAAAAAG
29744893 AAAAAAG
1 AAAAAAG
29744900 GCAGGAGAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
6 6 0.13
7 28 0.60
8 11 0.23
9 2 0.04
ACGTcount: A:0.83, C:0.02, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:29744869 original size:21 final size:22
Alignment explanation
Indices: 29744845--29744897 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
29744835 CAAAAAACAA
29744845 AAAAGAAAAAAG-AGAAAAAAG
1 AAAAGAAAAAAGAAGAAAAAAG
*
29744866 AAAA-AAAGAAGAAGAAAAAAG
1 AAAAGAAAAAAGAAGAAAAAAG
29744887 AAAAGAAAAAA
1 AAAAGAAAAAA
29744898 AGGCAGGAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 17 0.61
22 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAAAAAAGAAGAAAAAAG
Found at i:29746398 original size:132 final size:132
Alignment explanation
Indices: 29746128--29747067 Score: 1292
Period size: 132 Copynumber: 7.2 Consensus size: 132
29746118 ACAAACCGGG
* * * *
29746128 GAAGACAATAATTCTATCTCCCTGGGTAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
* * * * *
29746193 CT----A--AGTGGAGAAGATTGAAGATGGCAGATTTTACTTCCCTGTGATTACAGTGGAGTATA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
29746252 TT
131 TT
** *
29746254 GAAGCCAATAATTCTATCTCATTGGTTGGCAGTGGAATAGATTGAAGACTACAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
* * * * *
29746319 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGGTTTTACCTCTCTGTGATTACAGTGGAGTATA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
29746384 TT
131 TT
** ** *
29746386 G-CCCTCAATAATTCTATCTCATTGGTTGGCAGTGGAATAGATTGAAGACTACAGATCTTATCTC
1 GAAGC-CAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTC
29746450 CCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTAC
65 CCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTAC
29746515 ATT
130 ATT
* *
29746518 GAAGCCAATAATTCTATCTCCCT-G-TGCAGCAGTGGAATAGATTGAAGATTTCAGATTTTATCT
1 GAAGCCAATAATTCTATCTCCCTGGTTG--GCAGTGGAATAGATTGAAGATTACAGATCTTATCT
* *
29746581 CCCTAAGCAATAATGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
64 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
29746646 CATT
129 CATT
* *
29746650 GAAGCCAATAATTCTATCTCCCT-G-TGCAGCAGTGGAATAGATTGAAGATTACATATTTTATCT
1 GAAGCCAATAATTCTATCTCCCTGGTTG--GCAGTGGAATAGATTGAAGATTACAGATCTTATCT
*
29746713 CCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
64 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTA
*
29746778 TATT
129 CATT
*** *
29746782 GAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATATTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
* * * *
29746847 CTAAGCAGTAGTGGAACAGATCGAAGATGGTAGATTTTATCTCCCTGTGGTTATAGTGGAGTACA
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
29746912 TT
131 TT
* * * * * *
29746914 GAAACCAGTAATTCTATTTCTCTGGTTGGCAGTAGAATAGATTGAAGATTTCAGATCTTATCTCC
1 GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
* * ** *
29746979 TTAAGCAGTAGTGGAGTAGATCGAAGATGGC-GAATTTTACCTCCCTGTGACTATAGTGGAGTAC
66 CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTAC
29747043 ATT
130 ATT
*
29747046 GAAGCCAGTAATTCTATCTCCC
1 GAAGCCAATAATTCTATCTCCC
29747068 CGACATTGCG
Statistics
Matches: 736, Mismatches: 65, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
126 60 0.08
130 3 0.00
131 3 0.00
132 668 0.91
133 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (132 bp):
GAAGCCAATAATTCTATCTCCCTGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCC
CTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACA
TT
Found at i:29746464 original size:44 final size:44
Alignment explanation
Indices: 29746416--29746892 Score: 215
Period size: 44 Copynumber: 10.8 Consensus size: 44
29746406 ATTGGTTGGC
* *
29746416 AGTGGAATAGATTGAAGACTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * * * **
29746460 AGTGGAGCAGATCGAAGA-TGGCAGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGACT-ACAGATTTTATCTCCCTAAGCAG-T
* * * * * ** *
29746503 ACAGTGGAGTACATTGAAGCCAATA-ATTCTATCTCCCTGTGCAGC
1 --AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * * *
29746548 AGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAAT
1 AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * * * * **
29746592 AATGGAGCAGATCGAAGA-TGGCAGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGACT-ACAGATTTTATCTCCCTAAGCAG-T
* * * * * ** *
29746635 ACAGTGGAGTACATTGAAGCCAATA-ATTCTATCTCCCTGTGCAGC
1 --AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * *
29746680 AGTGGAATAGATTGAAGATTACATATTTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * * **
29746724 AGTGGAGTAGATCGAAGA-TGGCAGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGACT-ACAGATTTTATCTCCCTAAGCAG-T
* * * * * ** *
29746767 ACAGTGGAGTATATTGAAGCCAATA-ATTCTATCTCCCTGGGCAGC
1 --AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
* * *
29746812 AGTGGAATAGATTGAAGATTACAGATATTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
** * **
29746856 AGTGGAACAGATCGAAGA-TGGTAGATTTTATCTCCCT
1 AGTGGAGTAGATTGAAGACT-ACAGATTTTATCTCCCT
29746893 GTGGTTATAG
Statistics
Matches: 310, Mismatches: 98, Indels: 50
0.68 0.21 0.11
Matches are distributed among these distances:
42 5 0.02
43 57 0.18
44 197 0.64
45 45 0.15
46 6 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGACTACAGATTTTATCTCCCTAAGCAGT
Found at i:29746552 original size:88 final size:88
Alignment explanation
Indices: 29746444--29746848 Score: 257
Period size: 88 Copynumber: 4.6 Consensus size: 88
29746434 CTACAGATCT
* * *
29746444 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTG
*
29746509 GAGTACATTGAAGCCAATAATTC
66 GAGTAGATTGAAGCCAATAATTC
* * * ** * ** **
29746532 TATCTCCCTGTGCAGCAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAATA-A-T
1 TATCTCCCTGAGCAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTG-GTTACAGT
* * ***** *
29746595 GGAGCAGATCGAAGATGGCAGATTT
65 GGAGTAGATTGAAGCCAATA-ATTC
* * * * * ***** * * *
29746620 TACCTCCCTGTGGTTA-CAGTGGAGTACATTGAAGCCAATA-ATTCTATCTCCCTGT-G-CAGCA
1 TATCTCCCTG-AG-CAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA-CA
* ** *
29746681 GTGGAATAGATTGAAGATTACAT-ATTT
63 GTGGAGTAGATTGAAG-CCA-ATAATTC
* *
29746708 TATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTG
1 TATCTCCCTGAGCAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTG
*
29746773 GAGTATATTGAAGCCAATAATTC
66 GAGTAGATTGAAGCCAATAATTC
* * * ** * *
29746796 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATATTATCTCCCT
1 TATCTCCCTGAGCAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCT
29746849 AAGCAGTAGT
Statistics
Matches: 230, Mismatches: 73, Indels: 28
0.69 0.22 0.08
Matches are distributed among these distances:
85 1 0.00
86 1 0.00
87 33 0.14
88 155 0.67
89 38 0.17
90 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (88 bp):
TATCTCCCTGAGCAGCAGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTG
GAGTAGATTGAAGCCAATAATTC
Done.