Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 126 of 173
Found at i:38578516 original size:69 final size:69
Alignment explanation
Indices: 38578310--38578583 Score: 217
Period size: 69 Copynumber: 4.0 Consensus size: 69
38578300 TATTATCATT
* * * * * *
38578310 AAATTAATCATTAATATTATCTAAGTTTAT-TGTATATTATTATTTTAGATTTATCATGTTTTAT
1 AAATTTATCATTAATATT-TTTAAATTTATATATATACTATTATTTTAGATTTATCATG-TATAT
*
38578374 TATTTG
64 TATTTC
* * * * * *
38578380 TAATTTATCAATATTATTATTTTAAATTCATCGT-TA-AC-ATTATTTTAAATTTATCATGTATA
1 AAATTTATCATTAATA-T-TTTTAAATTTAT-ATATATACTATTATTTTAGATTTATCATGTATA
38578442 TTTATTTC
63 -TTATTTC
* *
38578450 AAATTTATCATTAATATTTTTAAATTTAT-TATATACTATTATTTTGGATTTATCACGTATGATT
1 AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTAT-ATT
38578514 A-TTC
65 ATTTC
* * * * *
38578518 TAGAA-TTATCATCAAAATTTTTAAATTT-TATATATATTATTATTTTAAATTTAT--TATATAT
1 -A-AATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATAT
38578579 TATTT
64 TATTT
38578584 ATTGTAAATT
Statistics
Matches: 166, Mismatches: 25, Indels: 29
0.75 0.11 0.13
Matches are distributed among these distances:
66 5 0.03
67 7 0.04
68 17 0.10
69 70 0.42
70 53 0.32
71 10 0.06
72 3 0.02
73 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.55
Consensus pattern (69 bp):
AAATTTATCATTAATATTTTTAAATTTATATATATACTATTATTTTAGATTTATCATGTATATTA
TTTC
Found at i:38578564 original size:17 final size:18
Alignment explanation
Indices: 38578542--38578579 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38578532 AAATTTTTAA
*
38578542 ATTTTATATATATTAT-T
1 ATTTTAAATATATTATAT
*
38578559 ATTTTAAATTTATTATAT
1 ATTTTAAATATATTATAT
38578577 ATT
1 ATT
38578580 ATTTATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTAAATATATTATAT
Found at i:38579435 original size:10 final size:11
Alignment explanation
Indices: 38579411--38579440 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38579401 CAAATGTTAA
38579411 TTTTAAAACGT
1 TTTTAAAACGT
38579422 TTTTAAAACGT
1 TTTTAAAACGT
*
38579433 TTTCAAAA
1 TTTTAAAA
38579441 TTAATACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (11 bp):
TTTTAAAACGT
Found at i:38588287 original size:18 final size:18
Alignment explanation
Indices: 38588264--38588306 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38588254 ACCCAATCCA
*
38588264 AACCCAAGTATACAACCC
1 AACCCAAGTACACAACCC
* *
38588282 AACCCAATTACCCAACCC
1 AACCCAAGTACACAACCC
38588300 AACCCAA
1 AACCCAA
38588307 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.44, G:0.02, T:0.09
Consensus pattern (18 bp):
AACCCAAGTACACAACCC
Found at i:38588495 original size:9 final size:9
Alignment explanation
Indices: 38588410--38588494 Score: 91
Period size: 9 Copynumber: 9.4 Consensus size: 9
38588400 GTAGTGATTC
38588410 AATTCGGTT
1 AATTCGGTT
38588419 AATTCGGTT
1 AATTCGGTT
*
38588428 AATTCGGGT
1 AATTCGGTT
38588437 AATTCGGTT
1 AATTCGGTT
* *
38588446 AATTTGGAT
1 AATTCGGTT
* *
38588455 AATCCGATT
1 AATTCGGTT
*
38588464 AATTCGGCT
1 AATTCGGTT
38588473 AATTCGAG-T
1 AATTCG-GTT
*
38588482 AATTTGGTT
1 AATTCGGTT
38588491 AATT
1 AATT
38588495 TTTAACCAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
8 1 0.02
9 60 0.97
10 1 0.02
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:38591130 original size:15 final size:14
Alignment explanation
Indices: 38591109--38591144 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
38591099 ATAATCCTTA
*
38591109 ATAATTATCTTAAT
1 ATAATTATCCTAAT
38591123 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
38591138 ATAATTA
1 ATAATTA
38591145 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:38592396 original size:19 final size:19
Alignment explanation
Indices: 38592350--38592403 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
38592340 GTAAGTATGA
*
38592350 TTTTTTATTTTATCTTAGTT
1 TTTTTTA-TGTATCTTAGTT
* **
38592370 ATCATTATGTATCTTAGTT
1 TTTTTTATGTATCTTAGTT
38592389 TTTTTTATGTTATCT
1 TTTTTTATG-TATCT
38592404 CAAGGTAGGG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (19 bp):
TTTTTTATGTATCTTAGTT
Found at i:38595517 original size:45 final size:45
Alignment explanation
Indices: 38595442--38595527 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
38595432 TATACGCCTA
*
38595442 AAATGAGTAAGACCATAGCTAAAAGATGCTATTACATCATGATAT
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATGATAT
* * *
38595487 AAATGAGTAAGACCATGGCTGAAAGGTGCTATGACATCATG
1 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATG
38595528 TGAAAGTACG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATGATAT
Found at i:38595710 original size:27 final size:27
Alignment explanation
Indices: 38595680--38595771 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
38595670 TCGACGAGAC
*
38595680 GTTAAACACGGGATAGTCTGTTAGGAT
1 GTTAAACACGGGATAGTCTGATAGGAT
* * *
38595707 GTTAAACA-GGGTATAGCCTAATGGGAT
1 GTTAAACACGGG-ATAGTCTGATAGGAT
* *
38595734 GTTAAATACAGGATAGTCTGATAGGAT
1 GTTAAACACGGGATAGTCTGATAGGAT
38595761 GTTAAACACGG
1 GTTAAACACGG
38595772 TGTAGTACTC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
26 3 0.06
27 47 0.90
28 2 0.04
ACGTcount: A:0.34, C:0.11, G:0.28, T:0.27
Consensus pattern (27 bp):
GTTAAACACGGGATAGTCTGATAGGAT
Found at i:38603292 original size:27 final size:27
Alignment explanation
Indices: 38603261--38603361 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
38603251 ATCATAGATT
*
38603261 GTCCGATAGGACGTTAAACATGGGATA
1 GTCCGATGGGACGTTAAACATGGGATA
* *
38603288 GTCCGATGGGACGTTAAACACGAGATA
1 GTCCGATGGGACGTTAAACATGGGATA
* * *
38603315 GTCCGACGGGAAGTTAAACATGGCATA
1 GTCCGATGGGACGTTAAACATGGGATA
*
38603342 GTCTGATGGGACGTTAAACA
1 GTCCGATGGGACGTTAAACA
38603362 CAAGGTAGTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.21
Consensus pattern (27 bp):
GTCCGATGGGACGTTAAACATGGGATA
Found at i:38603370 original size:27 final size:28
Alignment explanation
Indices: 38603261--38603373 Score: 110
Period size: 27 Copynumber: 4.2 Consensus size: 28
38603251 ATCATAGATT
* **
38603261 GTCCGATAGGACGTTAAACA-TGGGATA
1 GTCCGATGGGACGTTAAACACAAGGATA
*
38603288 GTCCGATGGGACGTTAAACACGA-GATA
1 GTCCGATGGGACGTTAAACACAAGGATA
* * *
38603315 GTCCGACGGGAAGTT-AA-ACATGGCATA
1 GTCCGATGGGACGTTAAACACAAGG-ATA
*
38603342 GTCTGATGGGACGTTAAACACAAGG-TA
1 GTCCGATGGGACGTTAAACACAAGGATA
38603369 GTCCG
1 GTCCG
38603374 TTAGGACAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
25 2 0.03
26 3 0.04
27 57 0.83
28 2 0.03
29 5 0.07
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (28 bp):
GTCCGATGGGACGTTAAACACAAGGATA
Found at i:38604568 original size:13 final size:12
Alignment explanation
Indices: 38604539--38604587 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 12
38604529 AGACAAAAAT
38604539 AAAAAC-ACAAG
1 AAAAACTACAAG
38604550 -AAAACTACAGAG
1 AAAAACTACA-AG
38604562 AAAAACTA-AAG
1 AAAAACTACAAG
*
38604573 AAAACCTA-AAG
1 AAAAACTACAAG
38604584 AAAA
1 AAAA
38604588 TGAAAACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 5 0.15
11 19 0.56
12 3 0.09
13 7 0.21
ACGTcount: A:0.69, C:0.14, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAACTACAAG
Found at i:38606532 original size:9 final size:10
Alignment explanation
Indices: 38606512--38606540 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
38606502 CATTTATGTT
38606512 TTTCTATTCA
1 TTTCTATTCA
38606522 TTTCT-TTCA
1 TTTCTATTCA
38606531 TTTCTATTCA
1 TTTCTATTCA
38606541 AACACGCAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:38608327 original size:31 final size:31
Alignment explanation
Indices: 38608280--38608400 Score: 152
Period size: 31 Copynumber: 3.9 Consensus size: 31
38608270 TATGTGATAG
* * *
38608280 TACATGGTATACATATGCAATTATGAATTAT
1 TACAGGGTATAAATATGCAATTATGAATGAT
* * *
38608311 TACAGGGTATAAATATGTAGTTATGAATGGT
1 TACAGGGTATAAATATGCAATTATGAATGAT
* *
38608342 TGCAGGGTATAAATATACAATTATGAATGAT
1 TACAGGGTATAAATATGCAATTATGAATGAT
* *
38608373 TACAGGGTATGAATATGCAAATATGAAT
1 TACAGGGTATAAATATGCAATTATGAAT
38608401 AGTTGATGGC
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.34
Consensus pattern (31 bp):
TACAGGGTATAAATATGCAATTATGAATGAT
Found at i:38608398 original size:62 final size:62
Alignment explanation
Indices: 38608285--38608405 Score: 170
Period size: 62 Copynumber: 2.0 Consensus size: 62
38608275 GATAGTACAT
* * * * ** *
38608285 GGTATACATATGCAATTATGAATTATTACAGGGTATAAATATGTAGTTATGAATGGTTGCAG
1 GGTATAAATATACAATTATGAATGATTACAGGGTATAAATATGCAAATATGAATAGTTGCAG
*
38608347 GGTATAAATATACAATTATGAATGATTACAGGGTATGAATATGCAAATATGAATAGTTG
1 GGTATAAATATACAATTATGAATGATTACAGGGTATAAATATGCAAATATGAATAGTTG
38608406 ATGGCCATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (62 bp):
GGTATAAATATACAATTATGAATGATTACAGGGTATAAATATGCAAATATGAATAGTTGCAG
Found at i:38610949 original size:9 final size:9
Alignment explanation
Indices: 38610935--38610971 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
38610925 CAACTAATTA
38610935 TAACAATAT
1 TAACAATAT
*
38610944 TAACAACATT
1 TAACAATA-T
38610954 TAACAATAT
1 TAACAATAT
38610963 TAACAATAT
1 TAACAATAT
38610972 CACTAACTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (9 bp):
TAACAATAT
Found at i:38612804 original size:24 final size:23
Alignment explanation
Indices: 38612777--38612821 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
38612767 TTACAAATAG
*
38612777 AAAATAAAGTTAAGTAAGAAATGA
1 AAAATAAAATTAAGTAA-AAATGA
38612801 AAAATAAAATTAAGTAAAAAT
1 AAAATAAAATTAAGTAAAAAT
38612822 TGTCCATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (23 bp):
AAAATAAAATTAAGTAAAAATGA
Found at i:38615722 original size:21 final size:20
Alignment explanation
Indices: 38615691--38615747 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
38615681 TTCTCAATCC
38615691 AATATACATTTCAATATCACAAT
1 AATAT-CATTTCAAT-TCA-AAT
38615714 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATTCAAAT
*
38615732 CATATCATTTGCAATT
1 AATATCATTT-CAATT
38615748 TCCATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 3 0.10
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
AATATCATTTCAATTCAAAT
Found at i:38617365 original size:51 final size:50
Alignment explanation
Indices: 38617292--38617484 Score: 210
Period size: 51 Copynumber: 3.8 Consensus size: 50
38617282 CAATGATGTT
* * *
38617292 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACTATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACTA-TACCATC
** ** * * *
38617343 CACTACACGTAGTAGCAAGCACATAGTACTACACACGTGATCAAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CTATACCATC
* * * *
38617394 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTAT--CATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CTATACCATC
38617443 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 C-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGAC
38617485 CATCACTTTC
Statistics
Matches: 114, Mismatches: 26, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 5 0.04
50 35 0.31
51 72 0.63
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACTATACCATC
Found at i:38617483 original size:101 final size:101
Alignment explanation
Indices: 38617299--38617483 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 101
38617289 GTTCGGTTCA
*
38617299 CATAGTAGCCTGCACATAGTACTACACATGTGACTATTACCATCCACTACACGTAGTAGCAAGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACTATTA-CATCCACTACACGTAGTAGCAAGCA
38617364 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
** **
38617401 CATAGTAGCCTGCACATAGTACTACACATGCGACCTA-T-CATCCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGTACTACACATGCGA-CTATTACATCC-ACTACACGTAGTAGCAAGC
38617464 ACATAGTACTACACACGTGA
64 ACATAGTACTACACACGTGA
38617484 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 5 0.07
101 35 0.46
102 33 0.43
103 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACTATTACATCCACTACACGTAGTAGCAAGCAC
ATAGTACTACACACGTGATCAAAACTATCCGGTACG
Found at i:38619825 original size:20 final size:20
Alignment explanation
Indices: 38619798--38619839 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
38619788 TAAAATTTAA
*
38619798 ATTTAACCCTTA-AAAATGC
1 ATTTAACCCTCATAAAATGC
38619817 ATTTCAACCCTCATAAAATGC
1 ATTT-AACCCTCATAAAATGC
38619838 AT
1 AT
38619840 AACTTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 7 0.35
21 9 0.45
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTAACCCTCATAAAATGC
Found at i:38634421 original size:21 final size:21
Alignment explanation
Indices: 38634375--38634421 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
38634365 AATTTTCAAT
*
38634375 ATTATTAAATATATATTTATA
1 ATTAATAAATATATATTTATA
* *
38634396 TTTAATAAATTATGTATTT-TA
1 ATTAATAAA-TATATATTTATA
38634417 ATTAA
1 ATTAA
38634422 ATCATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTAATAAATATATATTTATA
Found at i:38634464 original size:16 final size:18
Alignment explanation
Indices: 38634443--38634479 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
38634433 TACTAATATT
38634443 ATTAATAA-T-TTTTAAA
1 ATTAATAATTATTTTAAA
38634459 ATTAATAATTATTTTAAA
1 ATTAATAATTATTTTAAA
38634477 ATT
1 ATT
38634480 TAAATAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 1 0.05
18 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATAATTATTTTAAA
Found at i:38634487 original size:20 final size:18
Alignment explanation
Indices: 38634444--38634500 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
38634434 ACTAATATTA
38634444 TTAATAAT-TTTTAAAA-
1 TTAATAATATTTTAAAAT
38634460 TTAATAATTATTTTAAAAT
1 TTAATAA-TATTTTAAAAT
*
38634479 TTAAATAATATTCTTAATAT
1 TT-AATAATATT-TTAAAAT
38634499 TT
1 TT
38634501 TATATTAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
16 7 0.20
17 1 0.03
18 8 0.23
19 6 0.17
20 13 0.37
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATAATATTTTAAAAT
Found at i:38635413 original size:17 final size:17
Alignment explanation
Indices: 38635374--38635414 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
38635364 CCTTTTAATT
38635374 TTAAAGTTAATTAAAAAA
1 TTAAA-TTAATTAAAAAA
38635392 TTAAATTAA-TAAAAAA
1 TTAAATTAATTAAAAAA
38635408 TATAAAT
1 T-TAAAT
38635415 ATGAAAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 9 0.41
18 5 0.23
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TTAAATTAATTAAAAAA
Found at i:38639076 original size:65 final size:65
Alignment explanation
Indices: 38638996--38639126 Score: 262
Period size: 65 Copynumber: 2.0 Consensus size: 65
38638986 CGACCATGAG
38638996 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
1 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
38639061 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
1 TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
38639126 T
1 T
38639127 GTTAAACTCC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (65 bp):
TAAGCTTCTTCATCCACTTATTCATCCAAAATAGTTATGGTATCATGTAAATTTCCACCCTTTTT
Found at i:38641254 original size:41 final size:40
Alignment explanation
Indices: 38641209--38641291 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 40
38641199 ATTTTTTTGT
**
38641209 TTAGGGTTTTGTTAAAATAATTTAGGTTTAGGG-TTGTAGGG
1 TTAGGGTTTCATTAAAATAATTTAGGTTT-GGGATT-TAGGG
38641250 TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
1 TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
38641290 TT
1 TT
38641292 TAAGAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (40 bp):
TTAGGGTTTCATTAAAATAATTTAGGTTTGGGATTTAGGG
Found at i:38641431 original size:30 final size:32
Alignment explanation
Indices: 38641362--38641442 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 32
38641352 GTTTTAAGGG
* *
38641362 TTTTAAATAAATTAATTAATTTAAGGTTTAGA
1 TTTTAAAAAAATTAATTAAATTAAGGTTTAGA
* *
38641394 GTTTTTAAGAAAATTAATTAAATTAGGGTTTA-A
1 --TTTTAAAAAAATTAATTAAATTAAGGTTTAGA
*
38641427 -TTTAAAAAAAATAATT
1 TTTTAAAAAAATTAATT
38641443 TTGTGTTTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 14 0.34
33 1 0.02
34 26 0.63
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (32 bp):
TTTTAAAAAAATTAATTAAATTAAGGTTTAGA
Found at i:38641524 original size:16 final size:16
Alignment explanation
Indices: 38641503--38641557 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
38641493 CTCTGGTTCA
*
38641503 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
38641519 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
38641535 CTGTAATGAAATAGAG
1 CTGTAATGGAATAGAG
*
38641551 CTATAAT
1 CTGTAAT
38641558 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:38641716 original size:6 final size:6
Alignment explanation
Indices: 38641705--38641733 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
38641695 AGGTAGATGA
38641705 TTATTG TTATTG TTATTG TTATTG TTATT
1 TTATTG TTATTG TTATTG TTATTG TTATT
38641734 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:38644449 original size:126 final size:126
Alignment explanation
Indices: 38644226--38644460 Score: 312
Period size: 126 Copynumber: 1.9 Consensus size: 126
38644216 TTTTCTCTAC
* *
38644226 AGTAGTTTTAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAGATAATATAAAAAACGCTTCAA
1 AGTAGTTTTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCAA
* * * *
38644291 ACAGGATGCACTGTCAGTAAAATTACTAAAAAAAGCTCTCACGTAGACATTTTTTTTATAT
66 ACAAGATGCACTGTCAGCAAAATTACTAAAAAAAACTCCCACGTAGACATTTTTTTTATAT
* * * * *
38644352 AGTAGTTCTT-GAAAAAATAATTTTGAGAAGACGGTTTTGAAAAAATAGTGTCAAAAATGCTTCA
1 AGTAGTT-TTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCA
* * *
38644416 AGCAAGATGCACTGTTAGCAAAATTGA-TGAAAAAAACTCCCACGT
65 AACAAGATGCACTGTCAGCAAAATT-ACTAAAAAAAACTCCCACGT
38644461 GGATGCTCTT
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
126 90 0.97
127 3 0.03
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (126 bp):
AGTAGTTTTAGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAATATAAAAAACGCTTCAA
ACAAGATGCACTGTCAGCAAAATTACTAAAAAAAACTCCCACGTAGACATTTTTTTTATAT
Found at i:38647573 original size:24 final size:23
Alignment explanation
Indices: 38647517--38647573 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
38647507 AAGAACTTCT
*
38647517 ATTTTATTAAAAATATAAAAATA
1 ATTTTATTAAAAATATAAAAACA
38647540 ATTTACTATT-AAAATATTAAAAACA
1 ATTT--TATTAAAAATA-TAAAAACA
38647565 ACTTTTATT
1 A-TTTTATT
38647574 TTATTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 12 0.41
26 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTTTATTAAAAATATAAAAACA
Found at i:38647837 original size:24 final size:24
Alignment explanation
Indices: 38647800--38647853 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
38647790 AAATGCGGAA
*
38647800 GTGTTTGCAACACCCACAGTGGAG
1 GTGTTTACAACACCCACAGTGGAG
* *
38647824 GTGTTTACATCACCCACGGTGGAG
1 GTGTTTACAACACCCACAGTGGAG
38647848 GTGTTT
1 GTGTTT
38647854 GAATCTCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (24 bp):
GTGTTTACAACACCCACAGTGGAG
Found at i:38648045 original size:18 final size:18
Alignment explanation
Indices: 38648022--38648059 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38648012 AGAAAATGAA
* *
38648022 ACATATAAGGGTTAGGAT
1 ACATATAAAGGCTAGGAT
38648040 ACATATAAAGGCTAGGAT
1 ACATATAAAGGCTAGGAT
38648058 AC
1 AC
38648060 GCAGTTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (18 bp):
ACATATAAAGGCTAGGAT
Found at i:38649845 original size:32 final size:32
Alignment explanation
Indices: 38649809--38649869 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
38649799 ATTTAATTAA
*
38649809 AGAGA-GCTTTGAGAAATTTAGGGAGAAATTTG
1 AGAGATGCTTTGAGAAATTT-GGAAGAAATTTG
**
38649841 AGAGATTTTTTGAGAAATTTGGAAGAAAT
1 AGAGATGCTTTGAGAAATTTGGAAGAAAT
38649870 GTTGTGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 13 0.52
33 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.28, T:0.31
Consensus pattern (32 bp):
AGAGATGCTTTGAGAAATTTGGAAGAAATTTG
Found at i:38658573 original size:18 final size:19
Alignment explanation
Indices: 38658545--38658580 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38658535 ATTCAAACAA
*
38658545 AAAAAATCAAAATCAAAAT
1 AAAAAATCAAAAACAAAAT
38658564 AAAAAA-CAAAAACAAAA
1 AAAAAATCAAAAACAAAA
38658581 AAAGAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.81, C:0.11, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAAAATCAAAAACAAAAT
Found at i:38658653 original size:7 final size:7
Alignment explanation
Indices: 38658643--38658673 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
38658633 AGAAGAGAAA
38658643 AAAAAAG
1 AAAAAAG
38658650 -AAAAAG
1 AAAAAAG
38658656 AAAAAAG
1 AAAAAAG
38658663 AAAAAAG
1 AAAAAAG
38658670 AAAA
1 AAAA
38658674 GGAGAGGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:38658655 original size:6 final size:6
Alignment explanation
Indices: 38658613--38658673 Score: 52
Period size: 6 Copynumber: 9.7 Consensus size: 6
38658603 AATCAATGTC
* * *
38658613 AAAATG AAAATG AAAAAG AGAGAAG AGAAAA- AAAAAG AAAAAG AAAAAAG
1 AAAAAG AAAAAG AAAAAG A-AAAAG A-AAAAG AAAAAG AAAAAG -AAAAAG
38658663 AAAAAAG AAAA
1 -AAAAAG AAAA
38658674 GGAGAGGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
5 4 0.08
6 23 0.47
7 22 0.45
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:38658659 original size:14 final size:15
Alignment explanation
Indices: 38658642--38658673 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
38658632 GAGAAGAGAA
38658642 AAAAAAAG-AAAAAG
1 AAAAAAAGAAAAAAG
38658656 -AAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
38658670 AAAA
1 AAAA
38658674 GGAGAGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.44
14 6 0.38
15 3 0.19
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:38658673 original size:25 final size:26
Alignment explanation
Indices: 38658613--38658674 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
38658603 AATCAATGTC
* * *
38658613 AAAATGAAAATGAAAAAGAGAGAAGAG
1 AAAAAGAAAA-GAAAAAGAAAAAAGAG
38658640 AAAAA-AAAAGAAAAAGAAAAAAGA-
1 AAAAAGAAAAGAAAAAGAAAAAAGAG
38658664 AAAAAGAAAAG
1 AAAAAGAAAAG
38658675 GAGAGGCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 18 0.58
26 4 0.13
27 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (26 bp):
AAAAAGAAAAGAAAAAGAAAAAAGAG
Found at i:38659544 original size:7 final size:7
Alignment explanation
Indices: 38659532--38659572 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
38659522 AAAAAGGGGG
38659532 ATGAAAA
1 ATGAAAA
38659539 ATGAAAA
1 ATGAAAA
*
38659546 ATGAAAC
1 ATGAAAA
38659553 ATG-AAA
1 ATGAAAA
*
38659559 ATGGAAA
1 ATGAAAA
38659566 ATGAAAA
1 ATGAAAA
38659573 GTAATGACTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:38660641 original size:21 final size:21
Alignment explanation
Indices: 38660615--38660664 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
38660605 CTACAACTTA
* * *
38660615 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAACGAGAG
38660636 AAGCAGAGGCGGCAACGAGAG
1 AAGCAGAGGCGGCAACGAGAG
*
38660657 AAACAGAG
1 AAGCAGAG
38660665 TAGAGCAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:38661067 original size:43 final size:43
Alignment explanation
Indices: 38661011--38661276 Score: 327
Period size: 43 Copynumber: 6.2 Consensus size: 43
38661001 TCACCAAACA
* *
38661011 ATAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAAATCATGATCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
* *
38661054 ATAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGGTCATGATCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
* * *
38661097 ATAGCGGCGTTTGTGAGATAAGCGTCGCTAAAAGTCATGATCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
* * **
38661140 ATAGCGGCGTTTGAGGAAAAATTGCCGCTAAAAGTCATGATCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
* * **
38661183 ATAGCCGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGCCT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
* * * * * *
38661226 TTAGTGGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCCTGAACT
1 ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
*
38661268 TTAGCGGCG
1 ATAGCGGCG
38661277 CTTATTTCTA
Statistics
Matches: 191, Mismatches: 32, Indels: 1
0.85 0.14 0.00
Matches are distributed among these distances:
42 34 0.18
43 157 0.82
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (43 bp):
ATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAAGTCATGATCT
Found at i:38670480 original size:21 final size:21
Alignment explanation
Indices: 38670451--38670491 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38670441 CCTCTGTCAG
* *
38670451 TCAATTCTTGCAACTGCGCTT
1 TCAACTCTTGCAACTCCGCTT
*
38670472 TCAACTCTTGTAACTCCGCT
1 TCAACTCTTGCAACTCCGCT
38670492 AAGGCCATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (21 bp):
TCAACTCTTGCAACTCCGCTT
Found at i:38675455 original size:18 final size:17
Alignment explanation
Indices: 38675434--38675469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38675424 AAATAGATTG
38675434 ATGAGATAAAAATAAATA
1 ATGAGA-AAAAATAAATA
*
38675452 ATGAGAATAAATAAATA
1 ATGAGAAAAAATAAATA
38675469 A
1 A
38675470 GTAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (17 bp):
ATGAGAAAAAATAAATA
Found at i:38678187 original size:19 final size:18
Alignment explanation
Indices: 38678158--38678209 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
38678148 GAATGACACA
*
38678158 TTAACAAATATTAATATTTT
1 TTAA-AAATATTAA-ATTAT
38678178 TTAAAAATATTCAAATTAT
1 TTAAAAATATT-AAATTAT
38678197 TTAAAAA-ATTAAA
1 TTAAAAATATTAAA
38678210 AAGTTATTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 18 0.60
20 6 0.20
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAAAATATTAAATTAT
Found at i:38683573 original size:41 final size:41
Alignment explanation
Indices: 38683528--38683616 Score: 124
Period size: 41 Copynumber: 2.2 Consensus size: 41
38683518 GTCAGGCTCG
* *
38683528 AAGCCTGATGTAACACACCAGCATAAAGCCTACTAGGCACA
1 AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
* * *
38683569 AAGCCTGATATAATACACCAGCACGAAGCCTGCTAGGCACA
1 AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
*
38683610 TAGCCTG
1 AAGCCTG
38683617 CTAGGCGTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.16
Consensus pattern (41 bp):
AAGCCTGATATAACACACCAGCACAAAGCCTACTAGGCACA
Found at i:38685079 original size:3 final size:3
Alignment explanation
Indices: 38685073--38685106 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38685063 CCTCTTATTA
38685073 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
38685107 GATTTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:38707725 original size:22 final size:23
Alignment explanation
Indices: 38707697--38707749 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
38707687 TGAGTTTCTC
* *
38707697 ATTTTTTT-AATGTGGTACCTGT
1 ATTTTTTTCAATGTGATACATGT
38707719 ATTTTTTTCCCAATGTGATACATGT
1 ATTTTTTT--CAATGTGATACATGT
38707744 ATTTTT
1 ATTTTT
38707750 CAAAAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.31
25 18 0.69
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (23 bp):
ATTTTTTTCAATGTGATACATGT
Found at i:38708419 original size:16 final size:16
Alignment explanation
Indices: 38708398--38708428 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
38708388 TGTATTGAAA
38708398 TAGAGGCGTAATGGAT
1 TAGAGGCGTAATGGAT
38708414 TAGAGGCGTAATGGA
1 TAGAGGCGTAATGGA
38708429 ATGGAGACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.39, T:0.23
Consensus pattern (16 bp):
TAGAGGCGTAATGGAT
Found at i:38708439 original size:16 final size:16
Alignment explanation
Indices: 38708396--38708441 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
38708386 GCTGTATTGA
*
38708396 AATAGAGGCGTAATGG
1 AATAGAGACGTAATGG
* *
38708412 ATTAGAGGCGTAATGG
1 AATAGAGACGTAATGG
*
38708428 AATGGAGACGTAAT
1 AATAGAGACGTAAT
38708442 AGCAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.22
Consensus pattern (16 bp):
AATAGAGACGTAATGG
Found at i:38708472 original size:45 final size:44
Alignment explanation
Indices: 38708421--38708510 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
38708411 GATTAGAGGC
**
38708421 GTAATGGAATGGAGACGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAAAGACGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* * *
38708466 GTAATGGAATAAAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAAAGACGTAATAGAAATCATGTGTTTGGTTGAAT
38708510 G
1 G
38708511 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.03
44 18 0.46
45 20 0.51
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAAAGACGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:38708703 original size:17 final size:15
Alignment explanation
Indices: 38708664--38708695 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38708654 TTTAAACATA
*
38708664 ATTATTATTAAATAT
1 ATTATAATTAAATAT
38708679 ATTATAATTAAATAT
1 ATTATAATTAAATAT
38708694 AT
1 AT
38708696 AATTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:38708870 original size:120 final size:120
Alignment explanation
Indices: 38708653--38709188 Score: 916
Period size: 120 Copynumber: 4.5 Consensus size: 120
38708643 ATTTAATCAT
*
38708653 ATTTAAACATAATTATTATTAAATATATTATAATT-AAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
38708717 GTCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
65 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
38708773 AATTAACATAATTATTATTAAATATATTATAATTAAAATCTATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
38708838 TTAATAATCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38708893 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
38708958 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
38709013 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
38709077 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATA
66 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* *
38709132 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
38709189 TAAAATAATT
Statistics
Matches: 399, Mismatches: 15, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
119 140 0.35
120 259 0.65
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAA
TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:38708935 original size:18 final size:17
Alignment explanation
Indices: 38708914--38708948 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38708904 TTATTATTAA
*
38708914 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38708932 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38708949 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:38709055 original size:18 final size:17
Alignment explanation
Indices: 38709034--38709068 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38709024 TTATTATTAA
*
38709034 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38709052 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38709069 TCTAATAATC
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:38712648 original size:15 final size:15
Alignment explanation
Indices: 38712628--38712657 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38712618 AAACATGCTC
38712628 TTAATTTTGGCACTT
1 TTAATTTTGGCACTT
38712643 TTAATTTTGGCACTT
1 TTAATTTTGGCACTT
38712658 GGAGATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.13, T:0.53
Consensus pattern (15 bp):
TTAATTTTGGCACTT
Found at i:38713216 original size:28 final size:28
Alignment explanation
Indices: 38713185--38713254 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
38713175 CATACACAGC
* *
38713185 ATAAATAAATAAAATCACAATATAAAAT
1 ATAAATAAATAAAATAACAATAAAAAAT
** *
38713213 ATAAATGAAATTCAATAATAATAAAAAAT
1 ATAAAT-AAATAAAATAACAATAAAAAAT
38713242 -TAAATTAAATAAA
1 ATAAA-TAAATAAA
38713255 TTAAAACCAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (28 bp):
ATAAATAAATAAAATAACAATAAAAAAT
Found at i:38717012 original size:14 final size:14
Alignment explanation
Indices: 38716993--38717026 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
38716983 GTTTAAGCAT
38716993 TTATGTATAATTAA
1 TTATGTATAATTAA
38717007 TTATGTATAATTAA
1 TTATGTATAATTAA
38717021 TTATGT
1 TTATGT
38717027 TTAAATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TTATGTATAATTAA
Found at i:38722999 original size:19 final size:19
Alignment explanation
Indices: 38722975--38723019 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
38722965 GAGATCTGAA
38722975 TTGTGGAAGCATTCAAACT
1 TTGTGGAAGCATTCAAACT
**
38722994 TTGTGGATTCATTCAAACT
1 TTGTGGAAGCATTCAAACT
*
38723013 TTTTGGA
1 TTGTGGA
38723020 TTCGTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGTGGAAGCATTCAAACT
Found at i:38723020 original size:19 final size:19
Alignment explanation
Indices: 38722984--38723022 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
38722974 ATTGTGGAAG
38722984 CATTCAAACTTTGTGGATT
1 CATTCAAACTTTGTGGATT
*
38723003 CATTCAAACTTTTTGGATT
1 CATTCAAACTTTGTGGATT
38723022 C
1 C
38723023 GTAATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (19 bp):
CATTCAAACTTTGTGGATT
Found at i:38747184 original size:26 final size:26
Alignment explanation
Indices: 38747149--38747199 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
38747139 AATGTGAAAG
*
38747149 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
38747175 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
38747200 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:38747211 original size:103 final size:104
Alignment explanation
Indices: 38747071--38747293 Score: 369
Period size: 103 Copynumber: 2.2 Consensus size: 104
38747061 TGTATATAAA
** * *
38747071 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
38747135 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
38747174 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
38747239 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
38747278 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
38747294 GATATCCATT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 90 0.80
104 22 0.20
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:38747345 original size:71 final size:72
Alignment explanation
Indices: 38747212--38747363 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
38747202 TCATTGGTGG
* *
38747212 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
38747277 GAGGGGT
66 GAGGGGT
***
38747284 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
38747348 GAGGGGT
66 GAGGGGT
38747355 TGCTAAGTG
1 TGCTAAGTG
38747364 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:38754640 original size:104 final size:104
Alignment explanation
Indices: 38754460--38754683 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
38754450 TGTATATAAA
** * *
38754460 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
38754525 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
38754564 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
38754628 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
38754668 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
38754684 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:38754748 original size:26 final size:26
Alignment explanation
Indices: 38754713--38754764 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
38754703 AAATGAAAAG
* *
38754713 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
38754739 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
38754765 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:38754751 original size:70 final size:72
Alignment explanation
Indices: 38754602--38754752 Score: 243
Period size: 72 Copynumber: 2.1 Consensus size: 72
38754592 TCATTGGTGG
* *
38754602 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
38754667 GAGGGGT
66 GAGGGGT
***
38754674 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATT-CCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
38754737 GAGGGGT
66 GAGGGGT
38754744 TGCTAAGTG
1 TGCTAAGTG
38754753 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 20 0.27
71 24 0.32
72 30 0.41
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:38760256 original size:88 final size:88
Alignment explanation
Indices: 38760107--38760284 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 88
38760097 TCCTCGGACT
* *
38760107 ACTCACGTACTCCGTTGTAATTATATTACAACTAGGCCTGTATACTTGCTAATACCACCTCATTC
1 ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCTGTATACTTGCTAATACCACCTCATTC
38760172 ATATATCTTTTACTACAGTATTC
66 ATATATCTTTTACTACAGTATTC
* *
38760195 ACTCACCTACTCCGTTGTAACTATATTACAACTCGG-CTCGTATACTTGCTGATACCACCTCATT
1 ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCT-GTATACTTGCTAATACCACCTCATT
*
38760259 GATATATCTTTTACTACAGTATTC
65 CATATATCTTTTACTACAGTATTC
38760283 AC
1 AC
38760285 ATTCTGGACG
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
87 2 0.02
88 82 0.98
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.37
Consensus pattern (88 bp):
ACTCACCTACTCCGTTGTAACTATATTACAACTAGGCCTGTATACTTGCTAATACCACCTCATTC
ATATATCTTTTACTACAGTATTC
Found at i:38764510 original size:10 final size:10
Alignment explanation
Indices: 38764495--38764576 Score: 74
Period size: 10 Copynumber: 7.6 Consensus size: 10
38764485 AGCAACATAC
*
38764495 AAATTATAAT
1 AAATTACAAT
38764505 AAATTACAAT
1 AAATTACAAT
38764515 AAATTAGCCCTTAAAT
1 AAATTA---C---AAT
*
38764531 TAATTACAAT
1 AAATTACAAT
*
38764541 TAATTACAAT
1 AAATTACAAT
*
38764551 TAATTACAAT
1 AAATTACAAT
38764561 AAATTACAAT
1 AAATTACAAT
38764571 AAATTA
1 AAATTA
38764577 GCCCTCAAAG
Statistics
Matches: 63, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
10 53 0.84
13 2 0.03
16 8 0.13
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (10 bp):
AAATTACAAT
Found at i:38767989 original size:23 final size:22
Alignment explanation
Indices: 38767946--38767989 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
38767936 TTCTAAGTCA
38767946 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
38767969 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
38767990 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:38768148 original size:51 final size:50
Alignment explanation
Indices: 38768088--38768273 Score: 230
Period size: 51 Copynumber: 3.7 Consensus size: 50
38768078 TCGGTTCACA
38768088 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACG
* * * * * *
38768139 TTGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGATACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCGATACACG
* * *
38768190 TGGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACG
* * *
38768240 TAGTAGTCTGTACATAATACTACACATGTGACCA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA
38768274 CCACTTTCAC
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 39 0.35
51 70 0.62
52 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACG
Found at i:38768208 original size:102 final size:101
Alignment explanation
Indices: 38768084--38768270 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 101
38768074 ATGTTCGGTT
* *
38768084 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCA-TCCGATACACGTTGTAGCCT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACC--TACCATTCCGATACACGTAGTAGCCT
*
38768148 GCACATAGTACTACACACGTGATCAAAACTATCCGATA
64 GCACATAATACTACACACGTGATCAAAACTATCCGATA
* * * *
38768186 CACATGGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGATACACGTAGTAGTCTGT
1 CACATAGTAGCCTGCACATAGTACTACACATGCGACCTACCATTCCGATACACGTAGTAGCCTGC
*
38768251 ACATAATACTACACATGTGA
66 ACATAATACTACACACGTGA
38768271 CCACCACTTT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 4 0.05
101 37 0.49
102 35 0.46
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
CACATAGTAGCCTGCACATAGTACTACACATGCGACCTACCATTCCGATACACGTAGTAGCCTGC
ACATAATACTACACACGTGATCAAAACTATCCGATA
Found at i:38770707 original size:12 final size:13
Alignment explanation
Indices: 38770690--38770718 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38770680 GTTTTATCTG
38770690 CTTCCAC-TTTCC
1 CTTCCACATTTCC
38770702 CTTCCACATTTCC
1 CTTCCACATTTCC
38770715 CTTC
1 CTTC
38770719 TTCTTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.41
Consensus pattern (13 bp):
CTTCCACATTTCC
Found at i:38773993 original size:26 final size:26
Alignment explanation
Indices: 38773954--38774012 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
38773944 TCTTTTCTCG
*
38773954 AAATTTTACTAGGGGCAAAATCATCA
1 AAATTTTACCAGGGGCAAAATCATCA
*
38773980 AAATTTTACCAGGGGTAAAATCATCA
1 AAATTTTACCAGGGGCAAAATCATCA
38774006 AAATTTT
1 AAATTTT
38774013 GTTAAGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (26 bp):
AAATTTTACCAGGGGCAAAATCATCA
Found at i:38774021 original size:26 final size:26
Alignment explanation
Indices: 38773954--38774026 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
38773944 TCTTTTCTCG
* * *
38773954 AAATTTTACTAGGGGCAAAATCATCA
1 AAATTTTACCAAGGGTAAAATCATCA
*
38773980 AAATTTTACCAGGGGTAAAATCATCA
1 AAATTTTACCAAGGGTAAAATCATCA
***
38774006 AAATTTTGTTAAGGGTAAAAT
1 AAATTTTACCAAGGGTAAAAT
38774027 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCATCA
Found at i:38781791 original size:40 final size:39
Alignment explanation
Indices: 38781747--38781881 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
38781737 ACTAGTTTGG
*
38781747 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGGATAATTCAAAGTAATAA-TTGA
* * * * * *
38781787 CACCCAGTGTCTCATTGGCTAAATAAAAGT-A-AATTGG
1 CACCCAGTGCCTCATCGGATAATTCAAAGTAATAATTGA
* * *
38781824 CACCCAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATTCAAAGTAAT-AATTGA
* *
38781865 CACCTAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
38781882 ACTCGAAGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 18 0.25
38 10 0.14
39 1 0.01
40 24 0.33
41 20 0.27
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCAAAGTAATAATTGA
Found at i:38784340 original size:26 final size:26
Alignment explanation
Indices: 38784268--38784343 Score: 82
Period size: 26 Copynumber: 2.9 Consensus size: 26
38784258 ACATATTTTC
* * *
38784268 TCAAAATTTTACCAGGGGCAAAATCA
1 TCAAAATTTTTCTAGGGGTAAAATCA
** *
38784294 TCAAAATTTTTCTAGATGTAAAATCG
1 TCAAAATTTTTCTAGGGGTAAAATCA
38784320 TCAAAATTTTGT-TAGGGGTAAAAT
1 TCAAAATTTT-TCTAGGGGTAAAAT
38784344 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 40 0.98
27 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (26 bp):
TCAAAATTTTTCTAGGGGTAAAATCA
Found at i:38784783 original size:42 final size:42
Alignment explanation
Indices: 38784736--38784825 Score: 153
Period size: 42 Copynumber: 2.1 Consensus size: 42
38784726 CATATATCTT
38784736 TTTTAAATAATAATTCTACCGATTTCTATTAAGAAGAGAGAA
1 TTTTAAATAATAATTCTACCGATTTCTATTAAGAAGAGAGAA
* **
38784778 TTTTAATTTTTAATTCTACCGATTTCTATTAAGAAGAGAGAA
1 TTTTAAATAATAATTCTACCGATTTCTATTAAGAAGAGAGAA
38784820 TTTTAA
1 TTTTAA
38784826 TTTTTACCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (42 bp):
TTTTAAATAATAATTCTACCGATTTCTATTAAGAAGAGAGAA
Found at i:38784826 original size:42 final size:42
Alignment explanation
Indices: 38784746--38784831 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
38784736 TTTTAAATAA
38784746 TAATTCTACCGATTTCTATTAAGAAGAGAGAATTTTAATTTT
1 TAATTCTACCGATTTCTATTAAGAAGAGAGAATTTTAATTTT
38784788 TAATTCTACCGATTTCTATTAAGAAGAGAGAATTTTAATTTT
1 TAATTCTACCGATTTCTATTAAGAAGAGAGAATTTTAATTTT
38784830 TA
1 TA
38784832 CCCTAAAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (42 bp):
TAATTCTACCGATTTCTATTAAGAAGAGAGAATTTTAATTTT
Found at i:38789193 original size:22 final size:22
Alignment explanation
Indices: 38789163--38789205 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
38789153 ACACCAAAAC
*
38789163 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
38789185 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
38789206 AGCGCTGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:38789440 original size:43 final size:43
Alignment explanation
Indices: 38789364--38789465 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
38789354 AAACAAAGAC
* * * **
38789364 CTTTAGCGGCA-CTTTAGTAGAAGCGCCGCTAAAGACCCTGAT
1 CTTTAGCGGCATTTTTAGGAGAACCGCCGCTAAAGACCAGGAT
* * *
38789406 CTTTAGCGGCATTTTTGGGAGAACCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCATTTTTAGGAGAACCGCCGCTAAAGACCAGGAT
*
38789449 CTTTAGCGGCGTTTTTA
1 CTTTAGCGGCATTTTTA
38789466 TCTCAAACGC
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
42 11 0.22
43 38 0.78
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCATTTTTAGGAGAACCGCCGCTAAAGACCAGGAT
Found at i:38789546 original size:43 final size:42
Alignment explanation
Indices: 38789469--38789737 Score: 194
Period size: 42 Copynumber: 6.3 Consensus size: 42
38789459 GTTTTTATCT
* *
38789469 CAAACGCCGC-AATAGAACCTGATCTATAGTGGCGCTTATACCA
1 CAAACGCCACTAA-AGAACCTGATCTATAGCGGCGCTT-TACCA
** * * *
38789512 CAAAAACCACTAAAGAACCT-ATTCTTTAGCGGCGCTTTCCCT
1 CAAACGCCACTAAAGAACCTGA-TCTATAGCGGCGCTTTACCA
* * * *
38789554 GAAACGCCGC-AATAGACCCTGATCTATAGCAGCGCTTTTACCA
1 CAAACGCCACTAA-AGAACCTGATCTATAGCGGCGC-TTTACCA
* * *
38789597 CAAACGCCACTAAAG-ACCT-ATTCTTTAGCGGCGCTTTCCTCT
1 CAAACGCCACTAAAGAACCTGA-TCTATAGCGGCGCTTTAC-CA
* * *
38789639 CAAACGCCGC-AATAG-ACTCTGATCTGTAGCGGCGCTTTATCA
1 CAAACGCCACTAA-AGAAC-CTGATCTATAGCGGCGCTTTACCA
* * *
38789681 CAAACGCCGCTAAA-AACCCTTATCTTTAGCGGCGCTTTGACCA
1 CAAACGCCACTAAAGAA-CCTGATCTATAGCGGCGCTTT-ACCA
*
38789724 AAAACGCCACTAAA
1 CAAACGCCACTAAA
38789738 AAGGCCAACA
Statistics
Matches: 178, Mismatches: 33, Indels: 30
0.74 0.14 0.12
Matches are distributed among these distances:
41 9 0.05
42 86 0.48
43 78 0.44
44 5 0.03
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (42 bp):
CAAACGCCACTAAAGAACCTGATCTATAGCGGCGCTTTACCA
Found at i:38789579 original size:85 final size:85
Alignment explanation
Indices: 38789448--38789718 Score: 361
Period size: 85 Copynumber: 3.2 Consensus size: 85
38789438 AAGATCAGGG
* ** * *
38789448 TCTTTAGCGGCGTTTTTATCTCAAACGCCGCAATAGAACCTGATCTATAGTGGCGCTTATACCAC
1 TCTTTAGCGGCGCTTTCCTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTT-TACCAC
**
38789513 AAAAACCACTAAAGAACCTAT
65 AAACGCCACTAAAGAACCTAT
* *
38789534 TCTTTAGCGGCGCTTTCC-CTGAAACGCCGCAATAGACCCTGATCTATAGCAGCGCTTTTACCAC
1 TCTTTAGCGGCGCTTTCCTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGC-TTTACCAC
38789598 AAACGCCACTAAAG-ACCTAT
65 AAACGCCACTAAAGAACCTAT
* * *
38789618 TCTTTAGCGGCGCTTTCCTCTCAAACGCCGCAATAGACTCTGATCTGTAGCGGCGCTTTATCACA
1 TCTTTAGCGGCGCTTTCCTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTACCACA
*
38789683 AACGCCGCTAAA-AACCCT-T
66 AACGCCACTAAAGAA-CCTAT
38789702 ATCTTTAGCGGCGCTTT
1 -TCTTTAGCGGCGCTTT
38789719 GACCAAAAAC
Statistics
Matches: 165, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
84 45 0.27
85 103 0.62
86 17 0.10
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (85 bp):
TCTTTAGCGGCGCTTTCCTCTCAAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTACCACA
AACGCCACTAAAGAACCTAT
Found at i:38789631 original size:42 final size:42
Alignment explanation
Indices: 38789387--38789737 Score: 223
Period size: 43 Copynumber: 8.2 Consensus size: 42
38789377 TTAGTAGAAG
** *** * *
38789387 CGCCGCTAAAGACCCTGATCTTTAGCGGCATTTTTGGGAGAAC
1 CGCCGCTAAAGA-CCTGATCTTTAGCGGCGCTTTTACCACAAA
** * * * *
38789430 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTATCTCAAA
1 CGCCGCTAAAGA-CCTGATCTTTAGCGGCGCTTTTACCACAAA
* * *
38789473 CGCCGC-AATAGAACCTGATCTATAGTGGCGCTTATACCACAAA
1 CGCCGCTAA-AG-ACCTGATCTTTAGCGGCGCTTTTACCACAAA
** * * **
38789516 AACCACTAAAGAACCT-ATTCTTTAGCGGCGC-TTTCCCTGAAA
1 CGCCGCTAAAG-ACCTGA-TCTTTAGCGGCGCTTTTACCACAAA
* *
38789558 CGCCGC-AATAGACCCTGATCTATAGCAGCGCTTTTACCACAAA
1 CGCCGCTAA-AGA-CCTGATCTTTAGCGGCGCTTTTACCACAAA
* * *
38789601 CGCCACTAAAGACCT-ATTCTTTAGCGGCGC-TTTCCTCTCAAA
1 CGCCGCTAAAGACCTGA-TCTTTAGCGGCGCTTTTAC-CACAAA
* *
38789643 CGCCGC-AATAGACTCTGATCTGTAGCGGCGC-TTTATCACAAA
1 CGCCGCTAA-AGAC-CTGATCTTTAGCGGCGCTTTTACCACAAA
* * * *
38789685 CGCCGCTAAAAACCCTTATCTTTAGCGGCGCTTTGACCAAAAA
1 CGCCGCTAAAGA-CCTGATCTTTAGCGGCGCTTTTACCACAAA
*
38789728 CGCCACTAAA
1 CGCCGCTAAA
38789738 AAGGCCAACA
Statistics
Matches: 237, Mismatches: 54, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
41 10 0.04
42 85 0.36
43 136 0.57
44 6 0.03
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (42 bp):
CGCCGCTAAAGACCTGATCTTTAGCGGCGCTTTTACCACAAA
Found at i:38790084 original size:21 final size:21
Alignment explanation
Indices: 38790058--38790150 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
38790048 TTTGACGCTG
*
38790058 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTTCAGC
*
38790079 CTCTGCTTCCCTCTCTTCAGC
1 CTCTGCTTCCCTCGCTTCAGC
*
38790100 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTTCAGC
* * * * *
38790121 CTGTACTTCTCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTTCAGC
38790142 CTCTGCTTC
1 CTCTGCTTC
38790151 TCTTGTTGCC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.04, C:0.44, G:0.15, T:0.37
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTTCAGC
Found at i:38790108 original size:12 final size:10
Alignment explanation
Indices: 38790058--38790112 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
38790048 TTTGACGCTG
38790058 CTCTGCTTCC
1 CTCTGCTTCC
*
38790068 CTC-GCTTTAGC
1 CTCTGC-TT-CC
38790079 CTCTGCTTCC
1 CTCTGCTTCC
38790089 CTCT-CTTCAGC
1 CTCTGCTTC--C
38790100 CTCTGCTTCC
1 CTCTGCTTCC
38790110 CTC
1 CTC
38790113 GCTGCAGCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
9 6 0.16
10 14 0.38
11 11 0.30
12 6 0.16
ACGTcount: A:0.04, C:0.47, G:0.11, T:0.38
Consensus pattern (10 bp):
CTCTGCTTCC
Found at i:38790231 original size:66 final size:66
Alignment explanation
Indices: 38790141--38790287 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
38790131 CTCGCTGCTG
* * * *
38790141 CCTCTGCTTCTCTTGTTGCCGCATCTACTTTAAGCTGCT-GCTGGAGTTGTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
38790204 GAA
64 GAA
* * * *
38790207 CCTCAGCTTCTCTCGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
38790272 A
66 A
38790273 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
38790288 ATGTTGCTCC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:38795736 original size:16 final size:16
Alignment explanation
Indices: 38795715--38795758 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
38795705 ATTAAGCTAC
38795715 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
38795731 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* *
38795747 GAAAATTATGTA
1 GTAAGTTATGTA
38795759 AGTTGTGTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:38795754 original size:25 final size:25
Alignment explanation
Indices: 38795726--38795846 Score: 107
Period size: 25 Copynumber: 4.6 Consensus size: 25
38795716 TAAGTTATGT
38795726 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
38795751 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* * * *
38795776 AGTATGCTATGTAAGTTATGTAAGTCGTATAA
1 ATTATG-TAAGTTATTTAT-T-A-T-G-A-AA
*
38795808 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
*
38795833 ATTAAGTAAGTTAT
1 ATTATGTAAGTTAT
38795847 GTAATTTACG
Statistics
Matches: 74, Mismatches: 15, Indels: 14
0.72 0.15 0.14
Matches are distributed among these distances:
25 42 0.57
26 8 0.11
27 2 0.03
28 2 0.03
29 2 0.03
30 2 0.03
31 10 0.14
32 6 0.08
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:38795795 original size:9 final size:9
Alignment explanation
Indices: 38795783--38795850 Score: 59
Period size: 9 Copynumber: 7.8 Consensus size: 9
38795773 AAAAGTATGC
38795783 TATGTAAGT
1 TATGTAAGT
38795792 TATGTAAGT
1 TATGTAAGT
** *
38795801 CGTATAAGT
1 TATGTAAGT
38795810 TATGTAAGT
1 TATGTAAGT
*
38795819 TAT-TTA-T
1 TATGTAAGT
* *
38795826 TATGAAAAT
1 TATGTAAGT
*
38795835 TAAGTAAGT
1 TATGTAAGT
38795844 TATGTAA
1 TATGTAA
38795851 TTTACGAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
7 4 0.09
8 3 0.07
9 37 0.84
ACGTcount: A:0.38, C:0.01, G:0.18, T:0.43
Consensus pattern (9 bp):
TATGTAAGT
Found at i:38795905 original size:34 final size:34
Alignment explanation
Indices: 38795887--38796165 Score: 134
Period size: 34 Copynumber: 9.6 Consensus size: 34
38795877 TTATGTAAGT
38795887 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
38795921 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
38795952 --T--G---T--ATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
38795977 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
38796008 --T--G---T-T-TAATATT-AATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
38796032 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
38796063 --T--G---T--ATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
* *
38796088 TGTAATTTATGTATAATATT-AAT--GTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
38796119 --T--G---T--ATAATATTAAATAACTAAGTTA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTA
*
38796144 TGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAA
38796166 TGTATGTTAT
Statistics
Matches: 181, Mismatches: 17, Indels: 94
0.62 0.06 0.32
Matches are distributed among these distances:
22 34 0.19
23 10 0.06
24 11 0.06
25 21 0.12
26 1 0.01
27 3 0.02
29 4 0.02
31 29 0.16
32 4 0.02
33 19 0.10
34 45 0.25
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (34 bp):
TGTAAGTTATGTATAATATTAAATAACTAAGTTA
Found at i:38795952 original size:22 final size:22
Alignment explanation
Indices: 38795920--38795964 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
38795910 TAACTAAGTT
*
38795920 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38795942 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38795964 A
1 A
38795965 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:38795954 original size:56 final size:56
Alignment explanation
Indices: 38795887--38796409 Score: 859
Period size: 56 Copynumber: 9.2 Consensus size: 56
38795877 TTATGTAAGT
38795887 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
38795943 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
*
38795999 TGTAAGTTATGTTTAATATT-AATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
38796054 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
38796110 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* *
38796166 TGTATGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
*
38796222 TGTATGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* * **
38796278 TGTATGTTATGTATAATATTAATTAACTAAGTTATGTAATTTATGTATAATACCAA
1 TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
* * * * *
38796334 TGTATGTTATGTAATTTATGTATATTAACTAATTAAGTTATGTAATTTATGTATATTAACTAA
1 TGTAAGTTATGT-A--TA---ATATTAAATAACTAAGTTATGTAATTTATGTATAAT-ATTAA
38796397 TGTAAGTTATGTA
1 TGTAAGTTATGTA
38796410 ATATCTTATA
Statistics
Matches: 446, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
55 54 0.12
56 340 0.76
57 1 0.00
59 2 0.00
62 34 0.08
63 15 0.03
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (56 bp):
TGTAAGTTATGTATAATATTAAATAACTAAGTTATGTAATTTATGTATAATATTAA
Found at i:38796008 original size:22 final size:22
Alignment explanation
Indices: 38795976--38796035 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
38795966 TAACTAAGTT
*
38795976 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
*
38795998 ATGTAAGTTATGTTTAATATTA
1 ATGTAAGTTATGTATAATATTA
*
38796020 ATAACTAAGTTATGTA
1 AT--GTAAGTTATGTA
38796036 ATTTATGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 22 0.69
24 10 0.31
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:38796056 original size:22 final size:22
Alignment explanation
Indices: 38796031--38796075 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
38796021 TAACTAAGTT
*
38796031 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38796053 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38796075 A
1 A
38796076 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:38796112 original size:22 final size:22
Alignment explanation
Indices: 38796087--38796131 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
38796077 TAACTAAGTT
*
38796087 ATGTAATTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38796109 ATGTAAGTTATGTATAATATTA
1 ATGTAAGTTATGTATAATATTA
38796131 A
1 A
38796132 ATAACTAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
ATGTAAGTTATGTATAATATTA
Found at i:38796366 original size:18 final size:18
Alignment explanation
Indices: 38796345--38796397 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
38796335 GTATGTTATG
38796345 TAATTTATGTATATTAAC
1 TAATTTATGTATATTAAC
* *
38796363 TAA-TTAAGT-TA-T--G
1 TAATTTATGTATATTAAC
38796376 TAATTTATGTATATTAAC
1 TAATTTATGTATATTAAC
38796394 TAAT
1 TAAT
38796398 GTAAGTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 10
0.65 0.10 0.25
Matches are distributed among these distances:
13 3 0.12
14 5 0.19
15 3 0.12
16 3 0.12
17 5 0.19
18 7 0.27
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (18 bp):
TAATTTATGTATATTAAC
Found at i:38796421 original size:31 final size:32
Alignment explanation
Indices: 38796137--38796411 Score: 206
Period size: 31 Copynumber: 9.4 Consensus size: 32
38796127 ATTAAATAAC
* *
38796137 TAAGTTATGTAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
38796168 TATGTTATGT-A--TA---ATATTAATTAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* *
38796193 TAAGTTATGTAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
38796224 TATGTTATGT-A--TA---ATATTAAATAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* *
38796249 TAAGTTATGTAATTTATGTATAAT-ATTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* * *
38796280 TATGTTATGT-A--TA---ATATTAATTAA-C
1 TAAGTTATGTAATTTATGTATATTAACTAATG
* *
38796305 TAAGTTATGTAATTTATGTATAAT-ACCAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
*
38796336 TATGTTATGTAATTTATGTATATTAACTAAT-
1 TAAGTTATGTAATTTATGTATATTAACTAATG
38796367 TAAGTTATGTAATTTATGTATATTAACTAATG
1 TAAGTTATGTAATTTATGTATATTAACTAATG
38796399 TAAGTTATGTAAT
1 TAAGTTATGTAAT
38796412 ATCTTATATT
Statistics
Matches: 192, Mismatches: 26, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
25 39 0.20
26 17 0.09
28 12 0.06
30 15 0.08
31 91 0.47
32 18 0.09
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (32 bp):
TAAGTTATGTAATTTATGTATATTAACTAATG
Found at i:38799298 original size:35 final size:35
Alignment explanation
Indices: 38799261--38799331 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
38799251 CAACTTTTAA
*
38799261 TTTGTAATATTATAATATTT-ATTTTTTTGTATAAAT
1 TTTG-AATATTATAATATTTAATTTTATTG-ATAAAT
*
38799297 TTTGAATTTTATAATATTTAATTTTATTGATAAAT
1 TTTGAATATTATAATATTTAATTTTATTGATAAAT
38799332 AAATAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (35 bp):
TTTGAATATTATAATATTTAATTTTATTGATAAAT
Found at i:38799529 original size:16 final size:16
Alignment explanation
Indices: 38799475--38799534 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
38799465 ACCGTTGAAA
38799475 CCCTAAACCCC-AAAT-
1 CCCT-AACCCCTAAATC
* *
38799490 CCATAACCCCTTAA-C
1 CCCTAACCCCTAAATC
* *
38799505 CCCTTACCCTTAAATC
1 CCCTAACCCCTAAATC
38799521 CCCTAACCCCTAAA
1 CCCTAACCCCTAAA
38799535 GCATAACCCT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
14 6 0.18
15 15 0.44
16 13 0.38
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (16 bp):
CCCTAACCCCTAAATC
Found at i:38799694 original size:9 final size:8
Alignment explanation
Indices: 38799644--38799741 Score: 50
Period size: 7 Copynumber: 12.9 Consensus size: 8
38799634 ACTGTTGAAA
38799644 CCCTAAAC
1 CCCTAAAC
*
38799652 CCC-AAAT
1 CCCTAAAC
* *
38799659 CCATAACC
1 CCCTAAAC
38799667 CCCT-AAC
1 CCCTAAAC
*
38799674 CCCT-TAC
1 CCCTAAAC
38799681 CCCTAAATC
1 CCCTAAA-C
38799690 CCCT-AAC
1 CCCTAAAC
38799697 CCCTAAA-
1 CCCTAAAC
* *
38799704 GCAT-AAC
1 CCCTAAAC
*
38799711 CCTTAAA-
1 CCCTAAAC
38799718 CCCTAAATC
1 CCCTAAA-C
38799727 CCACT-AAC
1 CC-CTAAAC
38799735 CCCTAAA
1 CCCTAAA
38799742 GATCAAATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
6 2 0.03
7 34 0.51
8 20 0.30
9 9 0.13
10 2 0.03
ACGTcount: A:0.36, C:0.46, G:0.01, T:0.17
Consensus pattern (8 bp):
CCCTAAAC
Found at i:38799694 original size:169 final size:169
Alignment explanation
Indices: 38799410--38799752 Score: 623
Period size: 169 Copynumber: 2.0 Consensus size: 169
38799400 ATAAGAACAT
*
38799410 ATTTGATATAAAAATTAATAAAACTAATTAATCTAATAACTTAAACTCTAACATAACCGTTGAAA
1 ATTTTATATAAAAATTAATAAAACTAATTAATCTAATAACTTAAACTCTAACATAACCGTTGAAA
* *
38799475 CCCTAAACCCCAAATCCATAACCCCTTAACCCCTTACCCTTAAATCCCCTAACCCCTAAAGCATA
66 CCCTAAACCCCAAATCCATAACCCCCTAACCCCTTACCCCTAAATCCCCTAACCCCTAAAGCATA
* *
38799540 ACCCTTAAACTCTAAATCCCCCTAACCCCTAAACATCAA
131 ACCCTTAAACCCTAAATCCCACTAACCCCTAAACATCAA
*
38799579 ATTTTATATAAAAATTAATAAAACTAATTAATCTAATAACTTAAACTCTAACATAACTGTTGAAA
1 ATTTTATATAAAAATTAATAAAACTAATTAATCTAATAACTTAAACTCTAACATAACCGTTGAAA
38799644 CCCTAAACCCCAAATCCATAACCCCCTAACCCCTTACCCCTAAATCCCCTAACCCCTAAAGCATA
66 CCCTAAACCCCAAATCCATAACCCCCTAACCCCTTACCCCTAAATCCCCTAACCCCTAAAGCATA
*
38799709 ACCCTTAAACCCTAAATCCCACTAACCCCTAAAGATCAA
131 ACCCTTAAACCCTAAATCCCACTAACCCCTAAACATCAA
38799748 ATTTT
1 ATTTT
38799753 CAATTACACA
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.41, C:0.31, G:0.02, T:0.25
Consensus pattern (169 bp):
ATTTTATATAAAAATTAATAAAACTAATTAATCTAATAACTTAAACTCTAACATAACCGTTGAAA
CCCTAAACCCCAAATCCATAACCCCCTAACCCCTTACCCCTAAATCCCCTAACCCCTAAAGCATA
ACCCTTAAACCCTAAATCCCACTAACCCCTAAACATCAA
Found at i:38799740 original size:7 final size:7
Alignment explanation
Indices: 38799666--38799740 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 7
38799656 AATCCATAAC
38799666 CCCCTAA
1 CCCCTAA
*
38799673 CCCCTTA
1 CCCCTAA
38799680 CCCCTAAA
1 CCCCT-AA
38799688 TCCCCTAA
1 -CCCCTAA
38799696 CCCCTAA
1 CCCCTAA
** *
38799703 AGCATAA
1 CCCCTAA
*
38799710 CCCTTAA
1 CCCCTAA
*
38799717 ACCCTAAA
1 CCCCT-AA
38799725 TCCCACTAA
1 -CCC-CTAA
38799734 CCCCTAA
1 CCCCTAA
38799741 AGATCAAATT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
7 33 0.63
8 8 0.15
9 9 0.17
10 2 0.04
ACGTcount: A:0.33, C:0.47, G:0.01, T:0.19
Consensus pattern (7 bp):
CCCCTAA
Found at i:38801070 original size:15 final size:15
Alignment explanation
Indices: 38801050--38801087 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
38801040 TTGAAATTAA
38801050 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
38801065 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
38801080 CCCTAAAT
1 CCCTAAAT
38801088 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:38801810 original size:41 final size:41
Alignment explanation
Indices: 38801562--38801881 Score: 268
Period size: 41 Copynumber: 7.8 Consensus size: 41
38801552 TTTTGTTACT
* * ***
38801562 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTA-AATA-C
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAA-G-ACCCGAGC
* * * ** *
38801603 ATTAGCGGCGCTTAGATACAAACGCCGCTGAAGACAAGAGA
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
* * ** *
38801644 ATTAGTGGCGCTCAGTTAGAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
* * *
38801685 ATTAGCGGCTCATAGACAAAAACGTCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
*
38801726 ATTAGCGGCGCATAGACAAAAACGCCGCTAAAGACCCGAGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
* * * * * *
38801767 ATTAGCGGCGCTTAGACGAAATCGCCACTAAAGATCGGGGC
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
* * ** * * * *
38801808 ATTAGCGGCGTTTTTG-TGAAAGCACCGCTAAAGATCGGAGC
1 ATTAGCGGCG-CTTAGACAAAAACGCCGCTAAAGACCCGAGC
* *
38801849 ATTAGCGGCGCTTACACAAAAATGCCGCTAAAG
1 ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAG
38801882 GTTTAAAAAA
Statistics
Matches: 228, Mismatches: 47, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
39 1 0.00
40 6 0.03
41 218 0.96
42 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.26, T:0.17
Consensus pattern (41 bp):
ATTAGCGGCGCTTAGACAAAAACGCCGCTAAAGACCCGAGC
Found at i:38802024 original size:40 final size:40
Alignment explanation
Indices: 38801944--38802036 Score: 100
Period size: 40 Copynumber: 2.4 Consensus size: 40
38801934 TTATATAAAA
* **
38801944 CGCCGCTAATTC-CTAGTTTTAGCGGCGCTTCCGGATAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGATAAT
* * * *
38801983 CGCTGCTGATGCTCTACCTTTAGCGGCGCTT-TGGCTAAAT
1 CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGAT-AAT
38802023 CGCCGCTAATGCTC
1 CGCCGCTAATGCTC
38802037 GATTTTTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
39 12 0.28
40 31 0.72
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (40 bp):
CGCCGCTAATGCTCTACCTTTAGCGGCGCTTCCGGATAAT
Found at i:38814111 original size:22 final size:23
Alignment explanation
Indices: 38814061--38814105 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
38814051 ATAAAGATAT
* *
38814061 AATTTATAATATATAAAATTTTA
1 AATTAATAATATATAAAATTGTA
38814084 AATTAATAATA-ATAAAATTGTA
1 AATTAATAATATATAAAATTGTA
38814106 CTTTAAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTAATAATATATAAAATTGTA
Found at i:38814178 original size:17 final size:18
Alignment explanation
Indices: 38814153--38814189 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
38814143 TATTTTAAAA
38814153 ATTATAAAT-ATATAAATT
1 ATTATAAATAATA-AAATT
38814171 ATTA-AAATAATAAAATT
1 ATTATAAATAATAAAATT
38814188 AT
1 AT
38814190 ATTTGTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATAAATAATAAAATT
Found at i:38815401 original size:38 final size:36
Alignment explanation
Indices: 38815357--38815458 Score: 102
Period size: 36 Copynumber: 2.8 Consensus size: 36
38815347 ACGTAATCAT
38815357 TTAATTATTTTTTAAAATTAAAAAA-TATAAAAAAAA
1 TTAATTATTTTTTAAAATTAAAAAATTAT-AAAAAAA
* * *
38815393 TTAAAATTA-TTTTAAAAAGTATACAAATTATAAAAAAA
1 TT--AATTATTTTTTAAAATTA-AAAAATTATAAAAAAA
*
38815431 TTAA-TATTTTTTAAATTTTAAAAAATTA
1 TTAATTATTTTTTAAA-ATTAAAAAATTA
38815459 ATTAGATGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
35 2 0.04
36 18 0.34
37 12 0.23
38 18 0.34
39 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATTATTTTTTAAAATTAAAAAATTATAAAAAAA
Found at i:38815430 original size:21 final size:18
Alignment explanation
Indices: 38815370--38815434 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 18
38815360 ATTATTTTTT
*
38815370 AAAATTAAAAAATATAAAA
1 AAAATT-AAAATTATAAAA
**
38815389 AAAATTAAAATTATTTTAA
1 AAAATTAAAATTA-TAAAA
*
38815408 AAAGTATACAAATTAT-AAA
1 AAAAT-TA-AAATTATAAAA
38815427 AAAATTAA
1 AAAATTAA
38815435 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
17 1 0.03
18 8 0.22
19 19 0.51
20 3 0.08
21 6 0.16
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATTAAAATTATAAAA
Found at i:38815443 original size:37 final size:36
Alignment explanation
Indices: 38815357--38815456 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 36
38815347 ACGTAATCAT
38815357 TTAATTATTTTTT-AAAATTAAAAAATATAAAAAAAA
1 TTAA-TATTTTTTAAAAATTAAAAAATATAAAAAAAA
* * *
38815393 TTAAAATTATTTTAAAAAGTATACAAAT-TATAAAAAAA
1 TTAATATT-TTTTAAAAATTA-AAAAATATA-AAAAAAA
**
38815431 TTAATATTTTTTAAATTTTAAAAAAT
1 TTAATATTTTTTAAAAATTAAAAAAT
38815457 TAATTAGATG
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
35 3 0.06
36 13 0.25
37 17 0.33
38 19 0.37
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAATATTTTTTAAAAATTAAAAAATATAAAAAAAA
Found at i:38822725 original size:16 final size:15
Alignment explanation
Indices: 38822704--38822734 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
38822694 TTATAGATTA
38822704 TTGGAAGCTCACTCGG
1 TTGGAAGCTCA-TCGG
38822720 TTGGAAGCTCATCGG
1 TTGGAAGCTCATCGG
38822735 AGACCTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (15 bp):
TTGGAAGCTCATCGG
Found at i:38823893 original size:13 final size:14
Alignment explanation
Indices: 38823870--38823911 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
38823860 TTAAATTTTA
38823870 TTTTAATAATAA-AT
1 TTTTAA-AATAATAT
38823884 TTTTAAAATAATAT
1 TTTTAAAATAATAT
*
38823898 ATTT-AAATAATAT
1 TTTTAAAATAATAT
38823911 T
1 T
38823912 CTTCACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAATAATAT
Found at i:38823909 original size:16 final size:15
Alignment explanation
Indices: 38823868--38823909 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
38823858 ATTTAAATTT
38823868 TATTTTAATAATAAA
1 TATTTTAATAATAAA
38823883 T-TTTTAA-AATAATA
1 TATTTTAATAATAA-A
*
38823897 TATTTAAATAATA
1 TATTTTAATAATA
38823910 TTCTTCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 5 0.22
14 8 0.35
15 6 0.26
16 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTTTAATAATAAA
Found at i:38830864 original size:21 final size:21
Alignment explanation
Indices: 38830850--38830891 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
38830840 AGCCATCGGG
38830850 CCTAGCCGGGTAGCCCAACGA
1 CCTAGCCGGGTAGCCCAACGA
*
38830871 CCTAGCCGGGTAACCCAACGA
1 CCTAGCCGGGTAGCCCAACGA
38830892 ATAATCACCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.38, G:0.26, T:0.10
Consensus pattern (21 bp):
CCTAGCCGGGTAGCCCAACGA
Found at i:38831504 original size:26 final size:26
Alignment explanation
Indices: 38831468--38831519 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38831458 TTACTAAGTT
38831468 TACTTAAACTTATAAGCTTCCTGCTC
1 TACTTAAACTTATAAGCTTCCTGCTC
38831494 TACTTAAACTTATAAGCTTCCTGCTC
1 TACTTAAACTTATAAGCTTCCTGCTC
38831520 AAATTGCAGG
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:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (26 bp):
TACTTAAACTTATAAGCTTCCTGCTC
Found at i:38836128 original size:24 final size:26
Alignment explanation
Indices: 38836104--38836153 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
38836094 ACAACGCATT
38836104 AATTAAAAATATT-TTTAAATAATTAA
1 AATTAAAAATATTATTTAAATAATT-A
* *
38836130 AATTAAAAATTTTATTTTAATAAT
1 AATTAAAAATATTATTTAAATAAT
38836154 ATTACATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTAAAAATATTATTTAAATAATTA
Found at i:38836301 original size:16 final size:16
Alignment explanation
Indices: 38836277--38836307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38836267 GTTATTATGA
*
38836277 TTGATTAAAAAACAAC
1 TTGAGTAAAAAACAAC
38836293 TTGAGTAAAAAACAA
1 TTGAGTAAAAAACAA
38836308 GTATTTGGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (16 bp):
TTGAGTAAAAAACAAC
Found at i:38839618 original size:91 final size:90
Alignment explanation
Indices: 38839492--38839698 Score: 290
Period size: 91 Copynumber: 2.3 Consensus size: 90
38839482 TTGATTTTAG
* *
38839492 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
38839557 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATT-TTTTAAATTATA
* *
38839584 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
38839649 TGTAATAATTATTTTTTAAATTATA
66 TGTAATAATTATTTTTTAAATTATA
* * * *
38839674 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
38839699 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
90 32 0.31
91 53 0.51
92 19 0.18
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (90 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATAATTATTTTTTAAATTATA
Found at i:38839650 original size:28 final size:25
Alignment explanation
Indices: 38839614--38839673 Score: 66
Period size: 28 Copynumber: 2.3 Consensus size: 25
38839604 TATTATCAAG
* *
38839614 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAAT-TATT-TT-TTA
*
38839642 AATTATATGTAATAATTATTTTTTA
1 AATTATATGAAATAATTATTTTTTA
38839667 AATTATA
1 AATTATA
38839674 CAAATTCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 10 0.34
26 2 0.07
27 4 0.14
28 13 0.45
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (25 bp):
AATTATATGAAATAATTATTTTTTA
Done.