Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003570.1 Hibiscus syriacus cultivar Beakdansim tig00007536_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 90909
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6436 original size:18 final size:18
Alignment explanation
Indices: 6409--6448 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6399 CGTTGTTGCT
*
6409 GAAGATGAAGAAGAAGAG
1 GAAGAGGAAGAAGAAGAG
* *
6427 GAAGAGGAAGATGAAGTG
1 GAAGAGGAAGAAGAAGAG
6445 GAAG
1 GAAG
6449 GAGATGAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.07
Consensus pattern (18 bp):
GAAGAGGAAGAAGAAGAG
Found at i:6447 original size:12 final size:12
Alignment explanation
Indices: 6409--6448 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
6399 CGTTGTTGCT
*
6409 GAAGATGAAGAA
1 GAAGATGAAGAG
*
6421 GAAGAGGAAGAG
1 GAAGATGAAGAG
*
6433 GAAGATGAAGTG
1 GAAGATGAAGAG
6445 GAAG
1 GAAG
6449 GAGATGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.42, T:0.07
Consensus pattern (12 bp):
GAAGATGAAGAG
Found at i:10755 original size:2 final size:2
Alignment explanation
Indices: 10748--10820 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
10738 ATAAATGCAT
10748 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10790 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10821 AGGTATATTC
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14540 original size:15 final size:15
Alignment explanation
Indices: 14516--14560 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
14506 AATTGGTTTT
*
14516 CTGGAGTTTGAATTA
1 CTGGAATTTGAATTA
14531 CTGGAATTTGAATT-
1 CTGGAATTTGAATTA
**
14545 CTGGAAAATGAATTA
1 CTGGAATTTGAATTA
14560 C
1 C
14561 ATTTCTGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (15 bp):
CTGGAATTTGAATTA
Found at i:14584 original size:14 final size:14
Alignment explanation
Indices: 14562--14602 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
14552 ATGAATTACA
*
14562 TTTCTGGAAAATGT
1 TTTCCGGAAAATGT
*
14576 TTTCCGGAAAATAT
1 TTTCCGGAAAATGT
*
14590 TTTCCGTAAAATG
1 TTTCCGGAAAATG
14603 AATTACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:14987 original size:26 final size:25
Alignment explanation
Indices: 14958--15006 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
14948 ATTATTAGAT
*
14958 TATTATTAATATTAATATATAAATAA
1 TATTATTAATATAAATATA-AAATAA
*
14984 TATTATTCATATAAATATAAAAT
1 TATTATTAATATAAATATAAAAT
15007 TTTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTATTAATATAAATATAAAATAA
Found at i:14990 original size:20 final size:20
Alignment explanation
Indices: 14967--15016 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
14957 TTATTATTAA
*
14967 TATTAATATATAA-ATAATAT
1 TATT-ATATATAATATAAAAT
14987 TATTCATATA-AATATAAAAT
1 TATT-ATATATAATATAAAAT
15007 T-TTATATATA
1 TATTATATATA
15017 TTTATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 16 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTATATATAATATAAAAT
Found at i:15093 original size:22 final size:22
Alignment explanation
Indices: 15063--15111 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
15053 TATAATTTAT
*
15063 TATTTTATTATAATATTAAAAA
1 TATTATATTATAATATTAAAAA
* *
15085 TATTATATTATATTATTATAAA
1 TATTATATTATAATATTAAAAA
15107 TATTA
1 TATTA
15112 ATAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTATAATATTAAAAA
Found at i:15101 original size:30 final size:32
Alignment explanation
Indices: 15044--15119 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 32
15034 ATAATATCTT
*
15044 ATATT-ATAATATAATT-TATTATTTTATTAT-A
1 ATATTAATAA-AT-ATTATATTATATTATTATAA
15075 ATATTAA-AAATATTATATTATATTATTATAA
1 ATATTAATAAATATTATATTATATTATTATAA
15106 ATATTAATAAATAT
1 ATATTAATAAATAT
15120 ATTTTAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 3 0.08
30 15 0.38
31 15 0.38
32 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATTAATAAATATTATATTATATTATTATAA
Found at i:15119 original size:22 final size:21
Alignment explanation
Indices: 15075--15131 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
15065 TTTTATTATA
* *
15075 ATATTAAAAATATTATATTAT
1 ATATTATAAATATTATATAAT
15096 ATTATTATAAATATTA-ATAAAT
1 A-TATTATAAATATTATAT-AAT
*
15118 ATATTTTAAATATT
1 ATATTATAAATATT
15132 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTATAAATATTATATAAT
Found at i:15429 original size:42 final size:42
Alignment explanation
Indices: 15340--15432 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
15330 TTCCTCCAAC
* * * *
15340 CAAACACTGGAAAATATTTTTCGGAAAATGAATTACGTAAAA
1 CAAACACGGGAAAATATTTTTCGAAAAACGAATTACATAAAA
* *
15382 CAAACACGGGAAAATATTTTTCGAAAAACGAATTATATGAAA
1 CAAACACGGGAAAATATTTTTCGAAAAACGAATTACATAAAA
*
15424 TAAACACGG
1 CAAACACGG
15433 AATTTCGGGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (42 bp):
CAAACACGGGAAAATATTTTTCGAAAAACGAATTACATAAAA
Found at i:15830 original size:21 final size:21
Alignment explanation
Indices: 15804--15851 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
15794 TGGTTTAAAA
*
15804 AGTTTTCTTATAGAAATCTCT
1 AGTTTTCTTATAGAAATCTAT
15825 AGTTTTCTTATAGAAATCTAT
1 AGTTTTCTTATAGAAATCTAT
15846 AGTTTT
1 AGTTTT
15852 ATTAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
AGTTTTCTTATAGAAATCTAT
Found at i:24909 original size:30 final size:30
Alignment explanation
Indices: 24875--24931 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
24865 AGCAGAAAAA
* *
24875 TAAATGTTGGAATCTTAAAGGACTGAACTG
1 TAAATGCTAGAATCTTAAAGGACTGAACTG
*
24905 TAAATGCTAGAATTTTAAAGGACTGAA
1 TAAATGCTAGAATCTTAAAGGACTGAA
24932 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (30 bp):
TAAATGCTAGAATCTTAAAGGACTGAACTG
Found at i:25322 original size:4 final size:4
Alignment explanation
Indices: 25313--25338 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
25303 CATATATTCA
25313 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
25339 GCAATTCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29108 original size:112 final size:112
Alignment explanation
Indices: 28906--29368 Score: 773
Period size: 112 Copynumber: 4.1 Consensus size: 112
28896 TTGTCGGTTT
*
28906 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
28971 GATTTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAA
* **
29018 GTGTTGATACTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
29083 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAA
* * *
29130 GTGTCGATACTTTATAAAAATGTATCGATCTATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
29195 GGTCTATAAATGACAAAACAGGTAAATCGCTACAGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAA
* *
29242 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
29307 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAA
29354 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
29369 TATAAGTATC
Statistics
Matches: 332, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 332 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATATTGAAA
Found at i:29546 original size:182 final size:182
Alignment explanation
Indices: 29239--29876 Score: 1064
Period size: 182 Copynumber: 3.5 Consensus size: 182
29229 GGATATATTG
29239 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAACAA-ATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAA-AATATGACAA
** * *
29303 AACCGGTCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATGTTGATAGTGTCGATACTTTA
65 AACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACAGGATATGTTGAAAGTGTCGATACTTTA
29368 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
*
29421 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
29486 ATCGGTCTCGAAATGACAAAACCGGTAAAGCGCTATAAGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACAGGATATGTTGAAAGTGTCGATACTTTAT
* * *
29551 TATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
29603 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * **
29668 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTAAATACTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACAGGATATGTTGAAAGTGTCGATACTTTAT
* *
29733 TATAACTATAGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-TCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCT-AAT
* *
29785 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTATAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
29850 ATCGGTCTCGAAATGACAAAACCGGTA
66 ACCGGTCTCGAAATGACAAAACCGGTA
29877 GTAAAAAAGT
Statistics
Matches: 427, Mismatches: 27, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
181 2 0.00
182 425 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACAGGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:30498 original size:23 final size:23
Alignment explanation
Indices: 30472--30519 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
30462 AAATAGGTTA
* *
30472 ATATAAACGTTACCTATTACATT
1 ATATAAACGCTACCTAATACATT
* *
30495 ATATAAGCGCTACCTAATATATT
1 ATATAAACGCTACCTAATACATT
30518 AT
1 AT
30520 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
ATATAAACGCTACCTAATACATT
Found at i:33097 original size:13 final size:14
Alignment explanation
Indices: 33079--33108 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
33069 CTTCATTTTC
33079 TTTTTCCT-TTAAT
1 TTTTTCCTGTTAAT
33092 TTTTTCCTGTTAAT
1 TTTTTCCTGTTAAT
33106 TTT
1 TTT
33109 GTTATTGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTTTCCTGTTAAT
Found at i:33398 original size:942 final size:940
Alignment explanation
Indices: 30812--33441 Score: 4492
Period size: 934 Copynumber: 2.8 Consensus size: 940
30802 TTTTCCCCGG
* * * *
30812 CCAAAAAGGATGAATCACAACATGTTTTTACCGATCTTTCTTCATTTTCGGTTGAATTTCAAGAT
1 CCAAAAAGGATGAATCACAACATGATTTTACTGATATTTCTTCGTTTTCGGTTGAATTTCAAGAT
* * *
30877 GTTTTACACAAGGCTTTGATGTTCATTCTCAAGAAGCAGAAAAGGTAGCAACATTTTTTATTTTT
66 GGTTTACACAAGGCTTTGATGTTCATTCTCAAGAAGCAGAAAATGTAGCAACATTTTGTATTTTT
* * * *
30942 AATGAAGATTTTAGTTCGTTTTTCTTTTATTTTCAGAAAACAACTTGCAAAAAGGAAGATCCGTC
131 AATGGAGATTTTACTTCGTTTTTCTTTTATTTTCAGAAAATAGCTTGCAAAAAGGAAGATCCGTC
*
31007 TAAAACACAACTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCAG
196 TAAAACACAGCTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCAG
* *
31072 AAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGTATATTTTACATTATTTTTTTATCAA
261 AAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTATTTTTTTATCAG
31137 AAAATGA-AGGGTAAAAAGGAAGAGCCACCTCAAGCACAATAGGTTTTGATCGATATCTTTATTT
326 AAAATGACA-GGTAAAAAGGAAGAGCCACCTCAAGCACAATAGGTTTTGATCGATATCTTTATTT
*
31201 TCTTTTTCCTTTAATCTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
390 TCTTTTTCCTTTAATTTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
* *
31266 ACATGAAAATGATACTTTGGGATTTTACTTCATATTTTAAAAAATATTATCGATCATAAACTAGC
455 ACAAGAAAATGATACTTTGGGATTTTACTTCAT-TTTTAAAAAATATTATCGATCATAAACTAGT
* * *
31331 AAAAAATGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATATTTTTCTTATGTTTTCTAT
519 AAAAAAGGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATCTTTTTCTTCTGTTTTCTAT
*
31396 CCGGGTTAAGAAAATTTTGGTGTT------CAGAAAAAGGAAGAAAATTAACTACATATTGAGAC
584 CCGGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAAGGAAGAAAATGAACTACATATTGAGAC
* * *
31455 TTGAGTTAGCGTATATTTTATATTAATTCTTTTATATTTTCTGGATCACCTAACAGAAAGTAAGA
649 TTGAGTTAGCGTATATTTTACATTAATTCTTTTATATTTTCTGGATCGCCTAACAGAAAGGAAGA
*
31520 ATTGTGTTAAGCACAACAAGTTTTGATTTGTTTTCTCTCTCTTTTCACACTATGTTCGTTTCAAA
714 ATTGTGTTAAGCACAACAAGTTTTGATTTGTTTTCTCTCTCTTTTCACACTATGTTAGTTTCAAA
*
31585 GGGTTATTTCGGTTTGAATCTAAGTGTTTGCTTGTTTAAATGTTGTGAATGAGAGGCATTTACCG
779 GGGTTATTTCGGTTTGAATCTAAGTGTTTGCTTGTTTAAATATTGTGAATGAGAGGCATTTACCG
31650 AGATTGATGAGTGAAAGGTCGGTGCTGTTTGTTGATTTTGTGATCCGTTTGGGATGTGATTTTTT
844 AGATTGATGAGTGAAAGGTCGGTGCTGTTTGTTGATTTTGTGATCCGTTTGGGATGTGATTTTTT
*
31715 TAATTCCGAAAGATCAAGGATTATTATGGCTA
909 GAATTCCGAAAGATCAAGGATTATTATGGCTA
* *
31747 CAAAAAAGGATGAATCACAACAGGATTTTACTGATATTTCTTCGTTTTCGGTTGAATTTCAAGAT
1 CCAAAAAGGATGAATCACAACATGATTTTACTGATATTTCTTCGTTTTCGGTTGAATTTCAAGAT
31812 GGTTTACACAAGG-TTTGATGTTCATTCTCAAGAAGCAG-AAATGGTAGCAACATTTTGTATTTT
66 GGTTTACACAAGGCTTTGATGTTCATTCTCAAGAAGCAGAAAAT-GTAGCAACATTTTGTATTTT
* * *
31875 TAATGGAGGTTTTACTTCGTTTTTCTTTTCTTTTCAGAAAATAGCTTGCAAAAAGGAAGACCCGT
130 TAATGGAGATTTTACTTCGTTTTTCTTTTATTTTCAGAAAATAGCTTGCAAAAAGGAAGATCCGT
* *
31940 CTAAAACACAGTTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTTA
195 CTAAAACACAGCTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCA
32005 GAAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTATTTTTTTATCA
260 GAAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTATTTTTTTATCA
* * *
32070 GAAAATGACGGGTAAAAAGGAATAGCCACCTCGAGCACAATAGGTTTTGATCGATATCTTTATTT
325 GAAAATGACAGGTAAAAAGGAAGAGCCACCTCAAGCACAATAGGTTTTGATCGATATCTTTATTT
*
32135 TCTTTTTCCTTTAATTTTTTCTTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
390 TCTTTTTCCTTTAATTTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
* * * *
32200 ACAGGAAAATTATACTTTGGGTTTTTACTTCATTTTAAAAAAAATATTATCGATCATAAACTA-T
455 ACAAGAAAATGATACTTTGGGATTTTACTTCATTTT-TAAAAAATATTATCGATCATAAACTAGT
*
32264 CAAAAAAGGAAGAGCCTTGTGAAACACCACTGGTTTTTATACATATCTTTTTCTTCTGTTTTCTA
519 -AAAAAAGGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATCTTTTTCTTCTGTTTTCTA
*
32329 TCCGGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAATGAAGAAAATGAACTACATATTGAGA
583 TCCGGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAAGGAAGAAAATGAACTACATATTGAGA
** * *
32394 CTTGAAATAGCGTATATTTTACATTAATTCTCTTATATTTTCTGTATCGCCTAACAGAAAGGAAG
648 CTTGAGTTAGCGTATATTTTACATTAATTCTTTTATATTTTCTGGATCGCCTAACAGAAAGGAAG
* *
32459 AATTGTGTTAAGCACAATAAGTTTTGACTTGTTTTCTCTCTCTTTTCACACTATGTTAGTTTCAA
713 AATTGTGTTAAGCACAACAAGTTTTGATTTGTTTTCTCTCTCTTTTCACACTATGTTAGTTTCAA
*
32524 AGGGTTATTTCGGTTTGAATCTAAGTGTTTGCTTGTTTAAATATTGTGAATGAGCGGCA-TTACC
778 AGGGTTATTTCGGTTTGAATCTAAGTGTTTGCTTGTTTAAATATTGTGAATGAGAGGCATTTACC
32588 GAGATTGATGAGTGAAAGGTCGGTGCTGTTTGTTGATTTTGTGATCCGTTTGGGATGTGAATTTT
843 GAGATTGATGAGTGAAAGGTCGGTGCTGTTTGTTGATTTTGTGATCCGTTTGGGATGTG-ATTTT
32653 TTGAATTCCGAAAGATCAAGGATTATTATGGCTA
907 TTGAATTCCGAAAGATCAAGGATTATTATGGCTA
*
32687 CCAAAAAGGATGAATCACAACATGATTTTACTGATTTTTCTTCGTTTTCGGTTGAATTTCAAGAT
1 CCAAAAAGGATGAATCACAACATGATTTTACTGATATTTCTTCGTTTTCGGTTGAATTTCAAGAT
* *
32752 GGTTTACACAAGGCTTTGATGTTCATTCTCGAGAAGCAGAAAATGTAGCAAAATTTTGTATTTTT
66 GGTTTACACAAGGCTTTGATGTTCATTCTCAAGAAGCAGAAAATGTAGCAACATTTTGTATTTTT
* *
32817 AATGGAGATTTTACTTTGTTTTTCTTTTATTTTCAGAAAATAGCTTGCAAAAAGGAAGATTCGTC
131 AATGGAGATTTTACTTCGTTTTTCTTTTATTTTCAGAAAATAGCTTGCAAAAAGGAAGATCCGTC
32882 TAAAACACAGCTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCAG
196 TAAAACACAGCTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCAG
* *
32947 AAACATAATATATTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTATTTTTTTTATCA
261 AAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTA-TTTTTTTATCA
* * *
33012 GAAAATGACAGGTAAAAAGGAAGAGTCATCTCAAGCACAATAGGTTTTGATCGATATCTTCATTT
325 GAAAATGACAGGTAAAAAGGAAGAGCCACCTCAAGCACAATAGGTTTTGATCGATATCTTTATTT
33077 TCTTTTTCCTTTAATTTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
390 TCTTTTTCCTTTAATTTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAA
*
33142 ACAAGAAAATGATACTTTGGGATTTTACTTCATTTTTTAAAAATATTATCGATCATAAACTAGTA
455 ACAAGAAAATGATACTTTGGGATTTTACTTCATTTTTAAAAAATATTATCGATCATAAACTAGTA
*
33207 AAAACGGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATCTTTTTTCTTCTGTTTTCTAT
520 AAAAAGGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATC-TTTTTCTTCTGTTTTCTAT
33272 CCGGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAAGGAAGACAAA-GAACTACATATTGAGA
584 CCGGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAAGGAAGA-AAATGAACTACATATTGAGA
*
33336 CTTTAGTTAGCGTATATTTTACATTAATTCTTTTATATTTTCTGGATCGCCTAACAGAAAGGAAG
648 CTTGAGTTAGCGTATATTTTACATTAATTCTTTTATATTTTCTGGATCGCCTAACAGAAAGGAAG
* * *
33401 AATTATGTTATGCACTACAAGTTTTGATTTGTTTTCTCTCT
713 AATTGTGTTAAGCACAACAAGTTTTGATTTGTTTTCTCTCT
33442 TTTCTGTTAA
Statistics
Matches: 1589, Mismatches: 89, Indels: 27
0.93 0.05 0.02
Matches are distributed among these distances:
933 6 0.00
934 491 0.31
935 71 0.04
939 64 0.04
940 322 0.20
941 286 0.18
942 346 0.22
943 3 0.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (940 bp):
CCAAAAAGGATGAATCACAACATGATTTTACTGATATTTCTTCGTTTTCGGTTGAATTTCAAGAT
GGTTTACACAAGGCTTTGATGTTCATTCTCAAGAAGCAGAAAATGTAGCAACATTTTGTATTTTT
AATGGAGATTTTACTTCGTTTTTCTTTTATTTTCAGAAAATAGCTTGCAAAAAGGAAGATCCGTC
TAAAACACAGCTGGTTTGATTTTCTCTTTTATCCTAATTCGGTTTTAGGAGAATTTGGTGTTCAG
AAACAGAATATGTTTTAAAAACTACAATGTGATTTAATGGATATTTTACATTATTTTTTTATCAG
AAAATGACAGGTAAAAAGGAAGAGCCACCTCAAGCACAATAGGTTTTGATCGATATCTTTATTTT
CTTTTTCCTTTAATTTTTTCCTGTTAATTTTGTTATTGTTTTCAGAAGATTTTGTTGGTAAGAAA
CAAGAAAATGATACTTTGGGATTTTACTTCATTTTTAAAAAATATTATCGATCATAAACTAGTAA
AAAAGGAAGAGCCTTGTGAAGCACCACTGGTTTTTATACATATCTTTTTCTTCTGTTTTCTATCC
GGGTTAAGAAAATTTTGGTGTTCAGAAACAGAAAAAGGAAGAAAATGAACTACATATTGAGACTT
GAGTTAGCGTATATTTTACATTAATTCTTTTATATTTTCTGGATCGCCTAACAGAAAGGAAGAAT
TGTGTTAAGCACAACAAGTTTTGATTTGTTTTCTCTCTCTTTTCACACTATGTTAGTTTCAAAGG
GTTATTTCGGTTTGAATCTAAGTGTTTGCTTGTTTAAATATTGTGAATGAGAGGCATTTACCGAG
ATTGATGAGTGAAAGGTCGGTGCTGTTTGTTGATTTTGTGATCCGTTTGGGATGTGATTTTTTGA
ATTCCGAAAGATCAAGGATTATTATGGCTA
Found at i:35336 original size:25 final size:25
Alignment explanation
Indices: 35302--35356 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
35292 GGAGAAAAGG
35302 TGGTTCATTCTAACACATACTTCAT
1 TGGTTCATTCTAACACATACTTCAT
35327 TGGTTCATTCTAACACATACTTCAT
1 TGGTTCATTCTAACACATACTTCAT
35352 TGGTT
1 TGGTT
35357 TTCTTTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (25 bp):
TGGTTCATTCTAACACATACTTCAT
Found at i:36178 original size:123 final size:122
Alignment explanation
Indices: 35944--36190 Score: 361
Period size: 123 Copynumber: 2.0 Consensus size: 122
35934 AGACTAGTGG
** * *
35944 ACATGGTATTTCGAGAGCTTCACCTCGAAGAGTAATATATTAAAATGATTTAACTATTGTTCCGG
1 ACATGGTATTTCGAGAGCTTCACCTCGAAGAGTAATATAGAAAAAGGATTTAACTATTGTTCCAG
* * *
36009 CTGAGGAAAGGATTTGGGCTAGAATATTGGAGAAGAACTGGAGTATGCTATATTTTT
66 CTGAAGAAAGGATTTGGGCTAGAATATTGGAGAAGAACTGGAGTATGATATAATTTT
* * * *
36066 ACATGGTATATTTGATAGCTTCACCTTGAAGAGTAGTATAGAAAAAGGATTTAACTATTGATT-C
1 ACATGGTAT-TTCGAGAGCTTCACCTCGAAGAGTAATATAGAAAAAGGATTTAACTATTG-TTCC
*
36130 AGCTGAAGAAAGGATTTGGGCTAGAATATTGGGGAAGAACTGGAGTATGATATAATTTT
64 AGCTGAAGAAAGGATTTGGGCTAGAATATTGGAGAAGAACTGGAGTATGATATAATTTT
36189 AC
1 AC
36191 TAGATGCGTT
Statistics
Matches: 111, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
122 9 0.08
123 100 0.90
124 2 0.02
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (122 bp):
ACATGGTATTTCGAGAGCTTCACCTCGAAGAGTAATATAGAAAAAGGATTTAACTATTGTTCCAG
CTGAAGAAAGGATTTGGGCTAGAATATTGGAGAAGAACTGGAGTATGATATAATTTT
Found at i:44435 original size:13 final size:13
Alignment explanation
Indices: 44417--44441 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44407 ATATTTGAAT
44417 AGTCTTCATATAC
1 AGTCTTCATATAC
44430 AGTCTTCATATA
1 AGTCTTCATATA
44442 GGCGTCTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
AGTCTTCATATAC
Found at i:44480 original size:14 final size:15
Alignment explanation
Indices: 44461--44490 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
44451 AATAGGAAGT
44461 AATCCCTGC-TAATA
1 AATCCCTGCATAATA
44475 AATCCCTGCATAATA
1 AATCCCTGCATAATA
44490 A
1 A
44491 TCTCTACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.27, G:0.07, T:0.27
Consensus pattern (15 bp):
AATCCCTGCATAATA
Found at i:46423 original size:45 final size:45
Alignment explanation
Indices: 46356--46441 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
46346 AAGCTCCTCA
* * ** *
46356 GATAAAGGCAAAGGAGTGGAACCTATCAAA-ACTGTTAAAAAAAAG
1 GATAAAGGAAAAAGAGCAGAACCAATCAAATA-TGTTAAAAAAAAG
46401 GATAAAGGAAAAAGAGCAGAACCAATCAAATATGTTAAAAA
1 GATAAAGGAAAAAGAGCAGAACCAATCAAATATGTTAAAAA
46442 TCCAGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
45 34 0.97
46 1 0.03
ACGTcount: A:0.55, C:0.10, G:0.20, T:0.15
Consensus pattern (45 bp):
GATAAAGGAAAAAGAGCAGAACCAATCAAATATGTTAAAAAAAAG
Found at i:48239 original size:3 final size:3
Alignment explanation
Indices: 48231--48263 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
48221 AACTGGCATG
*
48231 TAA TAA TAA T-T TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
48264 GAAAAAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 26 0.96
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:48605 original size:116 final size:115
Alignment explanation
Indices: 48374--48799 Score: 563
Period size: 116 Copynumber: 3.7 Consensus size: 115
48364 GATGGAAATG
* * * *
48374 TTGAAAACATTATGC-CTAG-AGGTCTTATGAATGACCCTGAGGTCTTATCATGTTGCACTGTAT
1 TTGAAAACATTCTGCACT-GTAGGTCTTATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAG
* *
48437 GTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTACTAAAGACTTT
65 GTCTTACAGATGACCCG-AGGCTTTAAATATCAAAAAGCTCCTAAAGGCTTT
* *
48489 TTGTAAACATTCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGG
1 TTGAAAACATTCTGCACTGTAGGTCTTATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAGG
* * **
48554 TCTTACAGATGACCCAGAGGTTTTAAATATCAAAAAACTCCCGAAGGCTTT
66 TCTTACAGATGACCC-GAGGCTTTAAATATCAAAAAGCTCCTAAAGGCTTT
* * *
48605 TTGAAAACA-TCTTGCATTGTAGGTCTTATGGATGGCCCTAAGGTCTTATCATCTTGCACTGTAG
1 TTGAAAACATTC-TGCACTGTAGGTCTTATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAG
*
48669 GTCTTACAAATGACCCGGAGGCTTTAAATATCAAAAAGCTCCTAAAGGCTTT
65 GTCTTACAGATGACCC-GAGGCTTTAAATATCAAAAAGCTCCTAAAGGCTTT
* * * *
48721 TTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGGAGG-CTTTAAAAACATCATGCACTG
1 TTGAAAACATTCTGCACTGTAGGTCTTATGGATGACCCTGAGGTC-TT---ATCATCTTGCACTG
48785 TAGGTCTTACAGATG
62 TAGGTCTTACAGATG
48800 TGGGAAATAG
Statistics
Matches: 273, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
115 17 0.06
116 228 0.84
117 2 0.01
119 26 0.10
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (115 bp):
TTGAAAACATTCTGCACTGTAGGTCTTATGGATGACCCTGAGGTCTTATCATCTTGCACTGTAGG
TCTTACAGATGACCCGAGGCTTTAAATATCAAAAAGCTCCTAAAGGCTTT
Found at i:49575 original size:22 final size:22
Alignment explanation
Indices: 49454--49576 Score: 133
Period size: 22 Copynumber: 5.6 Consensus size: 22
49444 AATTAATTTT
*
49454 TCATCTTTGAAAAGAAAATCTA
1 TCATCTTTGAAGAGAAAATCTA
* *
49476 TCATATTTGAAGAGAAAACCTA
1 TCATCTTTGAAGAGAAAATCTA
*
49498 TCATTTTTGAAGA-AAGAATCTA
1 TCATCTTTGAAGAGAA-AATCTA
* *
49520 TTATCTTTGAAGA-AAGAATATA
1 TCATCTTTGAAGAGAA-AATCTA
* * *
49542 TCATCTTTGAAGTGATAATTTA
1 TCATCTTTGAAGAGAAAATCTA
49564 TCATCTTTGAAGA
1 TCATCTTTGAAGA
49577 ATGTAGATGT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
21 2 0.02
22 83 0.97
23 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAGAGAAAATCTA
Found at i:49997 original size:54 final size:54
Alignment explanation
Indices: 49938--50092 Score: 213
Period size: 54 Copynumber: 2.9 Consensus size: 54
49928 CCATAACTGA
* *
49938 TTCGTAAAACATTTGGCAATACATTCATTCTTTCATGTGGTTTCTGCAAAGATG
1 TTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGTTTCTGCAAAGATG
* * **
49992 TTCGTAAAACATTTAACAACACATTCA-TCATTTCCTGTGGTTTCTGCCCAGATG
1 TTCGTAAAACATTTGACAACACATTCATTC-TTTCATGTGGTTTCTGCAAAGATG
* * *
50046 TTCGTAAAATATTTGACAACACATTCATCCTTTCATGTGGCTTCTGC
1 TTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGTTTCTGC
50093 TCGGATTTCT
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.02
54 85 0.97
55 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (54 bp):
TTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGTTTCTGCAAAGATG
Found at i:53225 original size:133 final size:133
Alignment explanation
Indices: 52987--53254 Score: 401
Period size: 133 Copynumber: 2.0 Consensus size: 133
52977 TTCAACTTTA
* * *
52987 TTGACATTAGTCTTAATTAGACTAATTAAACGGTTCAACTCATTACAATGTCTTTGACTTGACAA
1 TTGACATTAGCCTTAATTAGACTAATTAAACGGTTCAACTCATCACAATGTCTTTGACCTGACAA
* * * * *
53052 TCACAGTGGAGCAAACACCGAATTGCCAAATACCCGATCAAGGTCATGTTTTGAATATATGACTT
66 TCACAGTAGAACAAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTT
53117 TTT
131 TTT
* * * * *
53120 TTGACATTAGCCTTCATTGGACTAATTAGAGGGTTCAACTTATCACAATGTCTTTGACCTGACAA
1 TTGACATTAGCCTTAATTAGACTAATTAAACGGTTCAACTCATCACAATGTCTTTGACCTGACAA
* *
53185 TCACATTAGAACAAACACCAAACTGCCAAATACTCGATCAAGGTCATGCTTTGAATATATGACTT
66 TCACAGTAGAACAAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTT
53250 TTT
131 TTT
53253 TT
1 TT
53255 TAAAAGAACT
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
133 120 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.33
Consensus pattern (133 bp):
TTGACATTAGCCTTAATTAGACTAATTAAACGGTTCAACTCATCACAATGTCTTTGACCTGACAA
TCACAGTAGAACAAACACCAAACTGCCAAATACCCGATCAAGGTCATGCTTTGAATATATGACTT
TTT
Found at i:54356 original size:16 final size:16
Alignment explanation
Indices: 54335--54368 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
54325 TGGATTTGCC
54335 AACATTAACACAAAGA
1 AACATTAACACAAAGA
54351 AACATTAACACAAAGA
1 AACATTAACACAAAGA
54367 AA
1 AA
54369 GGAGCGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.65, C:0.18, G:0.06, T:0.12
Consensus pattern (16 bp):
AACATTAACACAAAGA
Found at i:56778 original size:25 final size:25
Alignment explanation
Indices: 56744--56793 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
56734 GTTACTTTCG
*
56744 TTTTTATTTAATTAAGATGTGGTCA
1 TTTTCATTTAATTAAGATGTGGTCA
56769 TTTTCATTTAATTAAGATGTGGTCA
1 TTTTCATTTAATTAAGATGTGGTCA
56794 CCCTGAGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (25 bp):
TTTTCATTTAATTAAGATGTGGTCA
Found at i:56804 original size:25 final size:25
Alignment explanation
Indices: 56751--56804 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
56741 TCGTTTTTAT
*** *
56751 TTAATTAAGATGTGGTCATTTTCAT
1 TTAATTAAGATGTGGTCACCCTCAG
*
56776 TTAATTAAGATGTGGTCACCCTGAG
1 TTAATTAAGATGTGGTCACCCTCAG
56801 TTAA
1 TTAA
56805 CTGCACTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.41
Consensus pattern (25 bp):
TTAATTAAGATGTGGTCACCCTCAG
Found at i:58575 original size:15 final size:17
Alignment explanation
Indices: 58545--58576 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
58535 ATTTATTTTT
58545 ATCTATCTTACAATTTA
1 ATCTATCTTACAATTTA
58562 ATCTA-CTT-CAATTTA
1 ATCTATCTTACAATTTA
58577 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (17 bp):
ATCTATCTTACAATTTA
Found at i:58703 original size:16 final size:16
Alignment explanation
Indices: 58673--58703 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58663 GAAAAGGAAA
*
58673 AAAAAATAACAAAAAC
1 AAAAAATAAAAAAAAC
58689 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
58704 TAACAAAAAA
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:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAAATAAAAAAAAC
Found at i:58711 original size:12 final size:12
Alignment explanation
Indices: 58671--58717 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
58661 AAGAAAAGGA
58671 AAAAAAAATAAC
1 AAAAAAAATAAC
* *
58683 AAAAACAAAAAAT
1 AAAAA-AAATAAC
58696 AAAAAAAATAAC
1 AAAAAAAATAAC
58708 AAAAAAAATA
1 AAAAAAAATA
58718 TATAATATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAAAAATAAC
Found at i:62839 original size:18 final size:17
Alignment explanation
Indices: 62816--62849 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62806 CATAAAAACA
*
62816 TGATATGTATATTAATTT
1 TGATATATAT-TTAATTT
62834 TGATATATATTTAATT
1 TGATATATATTTAATT
62850 AAGTTGTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TGATATATATTTAATTT
Found at i:63096 original size:10 final size:10
Alignment explanation
Indices: 63076--63135 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
63066 AGTTGGAGAA
63076 TTAATTTTATT
1 TTAA-TTTATT
63087 TTAATTTATT
1 TTAATTTATT
*
63097 TTAATTTAAT
1 TTAATTTATT
*
63107 AT-ATTTATT
1 TTAATTTATT
*
63116 TAAATTTATT
1 TTAATTTATT
*
63126 TTAATATATT
1 TTAATTTATT
63136 CATTTTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
9 6 0.15
10 31 0.76
11 4 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTAATTTATT
Found at i:63410 original size:30 final size:31
Alignment explanation
Indices: 63356--63418 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
63346 TGATGGTCAC
*
63356 ATCTTAATTAAATAAAAACTAAAGTAATCAT
1 ATCTTAATTAAATAAAAACAAAAGTAATCAT
*
63387 ATCTTAATTAAAT-AAAACAAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTAATCAT
63417 AT
1 AT
63419 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.54, C:0.10, G:0.05, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTAATCAT
Found at i:64058 original size:21 final size:20
Alignment explanation
Indices: 64027--64065 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
64017 TAAAATTAGA
64027 TTTTTTTATTTTA-AAGTAC
1 TTTTTTTATTTTATAAGTAC
64046 TTTTTTTAAATTTTATAAGT
1 TTTTTTT--ATTTTATAAGT
64066 TTGATATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
21 6 0.35
22 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTTTTATTTTATAAGTAC
Found at i:69776 original size:21 final size:21
Alignment explanation
Indices: 69752--69811 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
69742 ATGTTTAATG
*
69752 AAAAAGATAGCAATTGTTAAC
1 AAAAGGATAGCAATTGTTAAC
69773 AAAAGGATAGCAATTGTTAAC
1 AAAAGGATAGCAATTGTTAAC
*
69794 AAAAGGATACCAATTGTT
1 AAAAGGATAGCAATTGTT
69812 GGAAAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAAGGATAGCAATTGTTAAC
Found at i:72093 original size:28 final size:31
Alignment explanation
Indices: 72037--72107 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
72027 CAAATAAACA
72037 AAATAAT-AATAACAAAGTACGAATAATATAT
1 AAATAATAAATAACAAAGTAC-AATAATATAT
*
72068 ATATAATAAATAA-AAAGTA-AAT-ATATAT
1 AAATAATAAATAACAAAGTACAATAATATAT
72096 AAATTAATAAAT
1 AAA-TAATAAAT
72108 TAAATGACGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 8 0.22
29 11 0.31
31 12 0.33
32 5 0.14
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (31 bp):
AAATAATAAATAACAAAGTACAATAATATAT
Found at i:72175 original size:2 final size:2
Alignment explanation
Indices: 72168--72228 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
72158 GATAATTACA
72168 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72210 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
72229 GTAATAATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72640 original size:23 final size:22
Alignment explanation
Indices: 72614--72668 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
72604 ATATATATAT
*
72614 ATAATAAAATAAATAATATAAAA
1 ATAATAAAAT-AATAATACAAAA
* *
72637 ATAATACAAGTAATAATACAAGA
1 ATAATA-AAATAATAATACAAAA
72660 ATAATAAAA
1 ATAATAAAA
72669 AGAAAGAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (22 bp):
ATAATAAAATAATAATACAAAA
Found at i:73386 original size:37 final size:37
Alignment explanation
Indices: 73345--73449 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
73335 GTGCTTGTGG
* *
73345 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
73382 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* *
73419 AACCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
73450 GACGAAAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:74549 original size:106 final size:106
Alignment explanation
Indices: 74179--75659 Score: 2095
Period size: 106 Copynumber: 14.0 Consensus size: 106
74169 GCATTGTTCT
* * **
74179 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* * * * * * *
74243 ATCAGCCGTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
74285 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGAGAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * * *
74344 TCAGCCG-CCTCTTCATCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * * * *
74386 G-GTTCAAGATCATTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
74450 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
74491 GAGTCCAATATCCTACACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
74556 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
74597 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
74662 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
74703 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
74768 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
74809 GAGTCCAATATCCTTCATTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
74874 CCAGCGGTACCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
74915 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* *
74980 CCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
75021 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
75086 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
75127 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
75192 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
75233 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
*
75298 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
75339 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCAT-TGAAATTG-GAAAGTTGTTTATTGAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-TCTGAAATTGAGAAA-TTGTTTGTTGAC
*
75402 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
75445 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
75510 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
75551 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCCGAAATCAAAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
* * * * * *
75615 CCAGCCGTCCCTTTGTTGTGAAGTTAAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
75656 GAGT
1 GAGT
75660 GGCATGATAT
Statistics
Matches: 1257, Mismatches: 103, Indels: 31
0.90 0.07 0.02
Matches are distributed among these distances:
99 2 0.00
100 73 0.06
101 5 0.00
102 5 0.00
104 3 0.00
105 57 0.05
106 1104 0.88
107 8 0.01
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:76513 original size:22 final size:22
Alignment explanation
Indices: 76487--76563 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
76477 TTATGTTTGG
76487 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
76509 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
76531 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
76553 TCAACGGTTTG
1 TCAAAGGTTTG
76564 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:77185 original size:23 final size:22
Alignment explanation
Indices: 77159--77239 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
77149 TGCATGTGCT
77159 TTTTTGTCCTTTTTTCTTTTTG
1 TTTTTGTCCTTTTTTCTTTTTG
* * *
77181 ATTTTTGTTCTTTTTT-TTGTTC
1 -TTTTTGTCCTTTTTTCTTTTTG
*
77203 TTTTT-TGCTTCTTTTCTTTTTTG
1 TTTTTGTCCTT-TTTTC-TTTTTG
*
77226 TTTTTGCCCTTTTT
1 TTTTTGTCCTTTTT
77240 ATTCTGATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 4 0.09
21 9 0.20
22 4 0.09
23 26 0.57
24 3 0.07
ACGTcount: A:0.01, C:0.14, G:0.09, T:0.77
Consensus pattern (22 bp):
TTTTTGTCCTTTTTTCTTTTTG
Found at i:77197 original size:12 final size:12
Alignment explanation
Indices: 77182--77208 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
77172 TTCTTTTTGA
77182 TTTTTGTTCTTT
1 TTTTTGTTCTTT
77194 TTTTTGTTCTTT
1 TTTTTGTTCTTT
77206 TTT
1 TTT
77209 GCTTCTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (12 bp):
TTTTTGTTCTTT
Found at i:77203 original size:28 final size:27
Alignment explanation
Indices: 77168--77229 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
77158 TTTTTTGTCC
*
77168 TTTTTTC-TTTTTGATTTTTGTTCTTTT
1 TTTTTTCTTTTTTGATTCTT-TTCTTTT
*
77195 TTTTGTTCTTTTTTGCTTCTTTTCTTTT
1 TTTT-TTCTTTTTTGATTCTTTTCTTTT
77223 TTGTTTT
1 TT-TTTT
77230 TGCCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 4 0.13
28 14 0.47
29 12 0.40
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (27 bp):
TTTTTTCTTTTTTGATTCTTTTCTTTT
Found at i:81950 original size:24 final size:23
Alignment explanation
Indices: 81923--81972 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
81913 AAATACGAAT
81923 AATATATATAAAATAAATAAAATA
1 AATATATAT-AAATAAATAAAATA
* *
81947 AATATATATAAATTAATAAATTA
1 AATATATATAAATAAATAAAATA
81970 AAT
1 AAT
81973 GACGAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AATATATATAAATAAATAAAATA
Found at i:82420 original size:26 final size:27
Alignment explanation
Indices: 82229--82428 Score: 84
Period size: 26 Copynumber: 7.5 Consensus size: 27
82219 ATATAACAAC
* *
82229 AATAATATCAATAAAAAGAAAATA-AAT
1 AATAATATAAATATAAA-AAAATATAAT
* *
82256 -ATAATAT-AATGATAATAAAATAT-AG
1 AATAATATAAAT-ATAAAAAAATATAAT
*
82281 AA-AAT-T-AATAGAAAAAAATAT-AT
1 AATAATATAAATATAAAAAAATATAAT
* * *
82304 ATATAATATATAAAAAATAAAAAATATAAA
1 A-ATAATATA-AATATA-AAAAAATATAAT
* *
82334 AATAATACAAGTAATAATATAAGAATAATAA-
1 AATAATATAAAT-ATAA-A-AA-AAT-ATAAT
* * * *
82365 AAGAAGAGAAA-GT-AAAAAATATAAT
1 AATAATATAAATATAAAAAAATATAAT
82390 AATAATA-AAATATAAAAAAATATACAT
1 AATAATATAAATATAAAAAAATATA-AT
82417 -ATAATATAAATA
1 AATAATATAAATA
82429 AGTAGAATAA
Statistics
Matches: 132, Mismatches: 21, Indels: 40
0.68 0.11 0.21
Matches are distributed among these distances:
23 12 0.09
24 12 0.09
25 25 0.19
26 30 0.23
27 8 0.06
28 7 0.05
29 20 0.15
30 4 0.03
31 10 0.08
32 4 0.03
ACGTcount: A:0.68, C:0.01, G:0.05, T:0.26
Consensus pattern (27 bp):
AATAATATAAATATAAAAAAATATAAT
Found at i:82465 original size:74 final size:74
Alignment explanation
Indices: 82308--82480 Score: 175
Period size: 74 Copynumber: 2.4 Consensus size: 74
82298 ATATATATAT
* * *
82308 AATAT-ATAAAA-AATAA-AAAATATAAAAATAATACAAGTAATAATATAAGAATAATAAAAGAA
1 AATATAATAAAATAATAATAAAATATAAAAAAAATACAAGTAATAAAATAAGAAGAATAAAAGAA
**
82370 GAGAAAGTA
66 GAGAAAAAA
* *
82379 AA-A-AATATAATAATAATAAAATATAAAAAAATATACATA-TAATATAAATAAGTAGAATAAAA
1 AATATAATAAAATAATAATAAAATATAAAAAAA-ATACA-AGTAATA-AAATAAGAAGAATAAAA
82441 GAA-A-AAAAAA
63 GAAGAGAAAAAA
* *
82451 AATATAATAAAATAATAGTAATA-ATAAAAA
1 AATATAATAAAATAATAATAAAATATAAAAA
82481 TGCAAAGAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
70 6 0.07
71 7 0.08
72 19 0.23
73 19 0.23
74 33 0.39
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.23
Consensus pattern (74 bp):
AATATAATAAAATAATAATAAAATATAAAAAAAATACAAGTAATAAAATAAGAAGAATAAAAGAA
GAGAAAAAA
Found at i:82472 original size:14 final size:13
Alignment explanation
Indices: 82378--82481 Score: 54
Period size: 14 Copynumber: 7.5 Consensus size: 13
82368 AAGAGAAAGT
82378 AAAAAATATAATA
1 AAAAAATATAATA
82391 ATAATAAA-AT-ATA
1 A-AA-AAATATAATA
82404 AAAAAATATACATA
1 AAAAAATATA-ATA
*
82418 TAATATAAATA-AGTA
1 -AA-A-AAATATAATA
* *
82433 GAATAAAAGA-AAAA
1 -AA-AAAATATAATA
82447 AAAAAATATAATA
1 AAAAAATATAATA
*
82460 AAATAATAGTAATA
1 AAAAAATA-TAATA
82474 ATAAAAAT
1 A-AAAAAT
82482 GCAAAGAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
11 3 0.04
12 9 0.13
13 17 0.24
14 19 0.27
15 16 0.23
16 2 0.03
17 5 0.07
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (13 bp):
AAAAAATATAATA
Found at i:82577 original size:2 final size:2
Alignment explanation
Indices: 82570--82595 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82560 AGCAAGTATG
82570 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
82596 ACTAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83109 original size:37 final size:36
Alignment explanation
Indices: 83032--83130 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 36
83022 GCTTGTGGAT
* * * *
83032 CTATCTTTAGCAGTTTAAATCATAGTAGAACTCTATC
1 CTAT-TTTAGGAGTTTAAATCCTAGTAAAACTCTAAC
*
83069 CTATTTTTAGGAGTTTAAATCCTA-TCAAAATTCTAAC
1 CTA-TTTTAGGAGTTTAAATCCTAGT-AAAACTCTAAC
*
83106 CTA-TTTAGGAGTTTGAATCCTAGTA
1 CTATTTTAGGAGTTTAAATCCTAGTA
83131 GGACGAAAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
35 19 0.36
36 2 0.04
37 31 0.58
38 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (36 bp):
CTATTTTAGGAGTTTAAATCCTAGTAAAACTCTAAC
Found at i:83764 original size:21 final size:21
Alignment explanation
Indices: 83730--83769 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
83720 AGTCATATCT
*
83730 AGCCGTTGGGGAT-GTTTTGG
1 AGCCGTTGGAGATGGTTTTGG
83750 AGCCGTTTGGAGATGGTTTT
1 AGCCG-TTGGAGATGGTTTT
83770 TCTGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGGTTTTGG
Found at i:86907 original size:21 final size:21
Alignment explanation
Indices: 86881--86928 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
86871 CGGTTTCTGA
*
86881 ATCATCTG-GATTATAATCATT
1 ATCATC-GAGATTATAATCATC
86902 ATCATCGAGATTATAATCATC
1 ATCATCGAGATTATAATCATC
86923 ATCATC
1 ATCATC
86929 ATCAGAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (21 bp):
ATCATCGAGATTATAATCATC
Found at i:88847 original size:48 final size:48
Alignment explanation
Indices: 88775--89326 Score: 701
Period size: 48 Copynumber: 11.9 Consensus size: 48
88765 TTGCTTCTTC
*
88775 AGAGAACTTTTACTGGTCTGAATAATATTGTTTGCTTCTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* *
88823 GGAGAACTTTTACTGGTTTGAATAACATTGTTTG---CTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
*
88868 AGAGAACTTTTACTGGTATGAAT-ACATTGTTTGCTTCTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* ** *
88915 AGAGAATTTTTACTAATTTGAATAACATTGTTTGCTTCTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
*
88963 AGAGAACTTTTACTGGTCTGAAT---ATAGTTT--TTCTTCATCAAC-
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* *
89005 --AGAACTTTTACTGGTTTGAATAACATTGTTTGCTGCTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* * * *
89051 GGAGAAC-TTTACTAGTTTGAATAACATTGTTTGCTTTTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
** **
89098 AGAGAACTTTTACCAGTCTGAATAACATTGCCTGCTTCTTCATCAAC-
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* *
89145 AG-GAA--TTTACTGCTCTGAATAACGTTGTTTGCTTCTTCATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* * *
89190 AGAGAACTTTTACCGGTCTGAATAACATTGTTTCCTTCTTTATCAACA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
* * * * *
89238 AGAGGAA-TTTTACTGGTTTGAATAGCATTGCTTGTTTCTTCATCAA-T
1 AGA-GAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
89285 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCA
1 AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCA
89327 GAAGGTAACT
Statistics
Matches: 436, Mismatches: 49, Indels: 39
0.83 0.09 0.07
Matches are distributed among these distances:
40 20 0.05
43 18 0.04
44 43 0.10
45 51 0.12
46 9 0.02
47 109 0.25
48 183 0.42
49 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (48 bp):
AGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCTTCATCAACA
Found at i:88928 original size:92 final size:93
Alignment explanation
Indices: 88633--89322 Score: 752
Period size: 92 Copynumber: 7.5 Consensus size: 93
88623 ACTCTAAAGG
* * * * * * * *
88633 ATCAACAAAAGAACTTTTATTGATCTGAAAAACATT-TTGTGATTCTTCATCAACAGAACTTTTA
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTT-TGCTTCATCAACAAGAGAACTTTTA
* *
88697 CTGGTCTGGATAACATTATTTGCTTCTTC
65 CTGGTCTGAATAACATTGTTTGCTTCTTC
* *
88726 ATCAACAAGAGAAACTTTTACTGGTTTGAATAACATTGTTTGCTTC-T--TC-AGAGAACTTTTA
1 ATCAACAAGAG-AACTTTTACTGGTCTGAATAACATTGTTTGCTTCATCAACAAGAGAACTTTTA
*
88787 CTGGTCTGAATAATATTGTTTGCTTCTTC
65 CTGGTCTGAATAACATTGTTTGCTTCTTC
* *
88816 ATCAACAGGAGAACTTTTACTGGTTTGAATAACATTGTTTGCTTCATCAACAAGAGAACTTTTAC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCATCAACAAGAGAACTTTTAC
*
88881 TGGTATGAAT-ACATTGTTTGCTTCTTC
66 TGGTCTGAATAACATTGTTTGCTTCTTC
* ** *
88908 ATCAACAAGAGAATTTTTACTAATTTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTG---CTTCATCAACAAGAGAACTTT
*
88973 TACTGGTCTGAAT---ATAGTTT--TTCTTC
63 TACTGGTCTGAATAACATTGTTTGCTTCTTC
* *
88999 ATCAAC---AGAACTTTTACTGGTTTGAATAACATTGTTTGCTGCTTCATCAACAGGAGAAC-TT
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTG-TT--TGCTTCATCAACAAGAGAACTTT
* * *
89060 TACTAGTTTGAATAACATTGTTTGCTTTTTC
63 TACTGGTCTGAATAACATTGTTTGCTTCTTC
** ** * * *
89091 ATCAACAAGAGAACTTTTACCAGTCTGAATAACATTGCCTGCTTCTTCATCAACAGGAA--TTTA
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCATCAACAAGA-GAACTTTTA
* *
89154 CTGCTCTGAATAACGTTGTTTGCTTCTTC
65 CTGGTCTGAATAACATTGTTTGCTTCTTC
* *
89183 ATCAACAAGAGAACTTTTACCGGTCTGAATAACATTGTTTCCTTCTTTATCAACAAGAGGAA-TT
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTC---ATCAACAAGA-GAACTT
* * * *
89247 TTACTGGTTTGAATAGCATTGCTTGTTTCTTC
62 TTACTGGTCTGAATAACATTGTTTGCTTCTTC
*
89279 ATCAA-TAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTC
1 ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTC
89323 TTCAGAAGGT
Statistics
Matches: 514, Mismatches: 58, Indels: 48
0.83 0.09 0.08
Matches are distributed among these distances:
87 13 0.03
88 42 0.08
89 36 0.07
90 54 0.11
91 16 0.03
92 146 0.28
93 42 0.08
94 26 0.05
95 107 0.21
96 32 0.06
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (93 bp):
ATCAACAAGAGAACTTTTACTGGTCTGAATAACATTGTTTGCTTCATCAACAAGAGAACTTTTAC
TGGTCTGAATAACATTGTTTGCTTCTTC
Found at i:89124 original size:275 final size:273
Alignment explanation
Indices: 88633--89326 Score: 775
Period size: 275 Copynumber: 2.5 Consensus size: 273
88623 ACTCTAAAGG
* * * *
88633 ATCAACAAAAGAACTTTTATTGATCTGAAAAACATT-TTGTGATTCTTCATCAAC---AGAACTT
1 ATCAACAAGAGAACTTTTACTGATCTGAATAACATTGTT-TGCTTCTTCATCAACAAGAGAACTT
*
88694 TTACTGGTCTGGATAACATTA-TTTGCTTCTTCATCAACAAGAGAAACTTTTACTGGTTTGAATA
65 TTACTGGTCT-G--AATA-TAGTTT--TTCTTCATCAAC---AG-AACTTTTACTGGTTTGAATA
* * *
88758 ACATTG-TT--TGCTTC-TTCAGAGAACTTTTACTGGTCTGAATAATATTGTTTGCTTCTTCATC
120 ACATTGTTTGCTGCTTCATACAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATC
* ** * ** *
88819 AACAGGAGAACTTTTACTGGTTTGAATAACATTGTTTGCTTCATCAACAAGA-GAACTTTTACTG
185 AACAAGAGAACTTTTACCAGTCTGAATAACATTGCCTGCTTCATCAACAACAGGAA--TTTACTG
*
88883 GTATGAAT-ACATTGTTTGCTTCTTC
248 CTATGAATAACATTGTTTGCTTCTTC
* * *
88908 ATCAACAAGAGAATTTTTACTAATTTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
1 ATCAACAAGAGAACTTTTACTGATCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
88973 TACTGGTCTGAATATAGTTTTTCTTCATCAACAGAACTTTTACTGGTTTGAATAACATTGTTTGC
66 TACTGGTCTGAATATAGTTTTTCTTCATCAACAGAACTTTTACTGGTTTGAATAACATTGTTTGC
* *
89038 TGCTTCATCAACAGGAGAAC-TTTACTAGTTTGAATAACATTGTTTGCTTTTTCATCAACAAGAG
131 TGCTTCAT--ACA-GAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAG
* * *
89102 AACTTTTACCAGTCTGAATAACATTGCCTGCTTCTTCATCAACAGGAATTTACTGCTCTGAATAA
193 AACTTTTACCAGTCTGAATAACATTGCCTGCTTCATCAACAACAGGAATTTACTGCTATGAATAA
*
89167 CGTTGTTTGCTTCTTC
258 CATTGTTTGCTTCTTC
* * * *
89183 ATCAACAAGAGAACTTTTACCGGTCTGAATAACATTGTTTCCTTCTTTATCAACAAGAGGAA-TT
1 ATCAACAAGAGAACTTTTACTGATCTGAATAACATTGTTTGCTTCTTCATCAACAAGA-GAACTT
* * * *
89247 TTACTGGTTTGAATAGCATTGCTTGTTTCTTCATCAATAGAGAACTTTTACTGGTCTGAATAACA
65 TTACTGGTCTGAAT---ATAG-TT-TTTCTTCATC-A-ACAGAACTTTTACTGGTTTGAATAACA
*
89312 TTGTTTGCTTCTTCA
123 TTGTTTGCTGCTTCA
89327 GAAGGTAACT
Statistics
Matches: 360, Mismatches: 37, Indels: 37
0.83 0.09 0.09
Matches are distributed among these distances:
269 26 0.07
270 4 0.01
272 6 0.02
273 13 0.04
274 15 0.04
275 209 0.58
276 14 0.04
277 1 0.00
278 20 0.06
279 2 0.01
280 10 0.03
281 1 0.00
282 39 0.11
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (273 bp):
ATCAACAAGAGAACTTTTACTGATCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAACTTT
TACTGGTCTGAATATAGTTTTTCTTCATCAACAGAACTTTTACTGGTTTGAATAACATTGTTTGC
TGCTTCATACAGAGAACTTTTACTAGTCTGAATAACATTGTTTGCTTCTTCATCAACAAGAGAAC
TTTTACCAGTCTGAATAACATTGCCTGCTTCATCAACAACAGGAATTTACTGCTATGAATAACAT
TGTTTGCTTCTTC
Done.