Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 96 of 182
Found at i:29061878 original size:44 final size:45
Alignment explanation
Indices: 29061815--29061930 Score: 162
Period size: 44 Copynumber: 2.6 Consensus size: 45
29061805 TATATTACAT
* *
29061815 AGTTTGTTCTAACACATCTCATTTAAAACTAGAAAGTTTGTTC-A
1 AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
* *
29061859 AGTTTTTTCCAACACATCTCATTTAAAATTACAAAGTTTGTTCAA
1 AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
* * *
29061904 AATTTGTTCCAATACTTCTCATTTAAA
1 AGTTTGTTCCAACACATCTCATTTAAA
29061931 TTTCAAAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 39 0.62
45 24 0.38
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (45 bp):
AGTTTGTTCCAACACATCTCATTTAAAACTACAAAGTTTGTTCAA
Found at i:29065473 original size:13 final size:14
Alignment explanation
Indices: 29065430--29065477 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
29065420 GGAGTAGGAT
29065430 TCTGTATATCTGT-
1 TCTGTATATCTGTA
*
29065443 TATGTATATCTG-A
1 TCTGTATATCTGTA
29065456 TTCTG-ATATCTGTA
1 -TCTGTATATCTGTA
29065470 TCTG-ATAT
1 TCTGTATAT
29065478 GGACTTAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 26 0.87
14 4 0.13
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TCTGTATATCTGTA
Found at i:29067113 original size:31 final size:30
Alignment explanation
Indices: 29067064--29067173 Score: 98
Period size: 31 Copynumber: 3.5 Consensus size: 30
29067054 TTTGATCTTT
*
29067064 TTAAACCTTTTTTAAACCCTAAATAAAGCCC
1 TTAATCCTTTTTT-AACCCTAAATAAAGCCC
* *
29067095 TCTAATCCTTTTTTAACCCTAAACAAAACACC
1 T-TAATCCTTTTTTAACCCTAAATAAAGC-CC
*
29067127 TTAATCC-TTTTTAGACCCT-AATCATAGCCC
1 TTAATCCTTTTTTA-ACCCTAAAT-AAAGCCC
29067157 TTTAATCACTCTTTTTA
1 -TTAATC-CT-TTTTTA
29067174 TTCAAACACT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
30 10 0.15
31 34 0.52
32 15 0.23
34 6 0.09
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (30 bp):
TTAATCCTTTTTTAACCCTAAATAAAGCCC
Found at i:29067210 original size:32 final size:33
Alignment explanation
Indices: 29067169--29067230 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
29067159 TAATCACTCT
* *
29067169 TTTTATTCAAACACTAAA-CTCTAACAAAACCC
1 TTTTATTCAAACACCAAATCCCTAACAAAACCC
* *
29067201 TTTTCTTCAAACCCCAAATCCCTAACAAAA
1 TTTTATTCAAACACCAAATCCCTAACAAAA
29067231 TCTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 15 0.60
33 10 0.40
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (33 bp):
TTTTATTCAAACACCAAATCCCTAACAAAACCC
Found at i:29067628 original size:11 final size:11
Alignment explanation
Indices: 29067608--29067641 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
29067598 TTTCTATTTC
*
29067608 TATTTTTTTTG
1 TATTTGTTTTG
29067619 TATTTGTTTTG
1 TATTTGTTTTG
29067630 TATTTGTATTTG
1 TATTTGT-TTTG
29067642 GGTTTTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (11 bp):
TATTTGTTTTG
Found at i:29069438 original size:17 final size:16
Alignment explanation
Indices: 29069403--29069452 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
29069393 TTAATTTTTT
*
29069403 TTAAATATTAAATAAAA
1 TTAAAAATT-AATAAAA
29069420 TTCAAAAAGTTAA-AAAA
1 TT-AAAAA-TTAATAAAA
29069437 TTAAAAATTAATAAAA
1 TTAAAAATTAATAAAA
29069453 AGCATTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 4 0.14
16 9 0.31
17 8 0.28
18 6 0.21
19 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TTAAAAATTAATAAAA
Found at i:29069453 original size:17 final size:16
Alignment explanation
Indices: 29069403--29069453 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
29069393 TTAATTTTTT
*
29069403 TTAAATATTAAATAAAA
1 TTAAAAATTAAA-AAAA
29069420 TTCAAAAAGTT-AAAAAA
1 TT-AAAAA-TTAAAAAAA
29069437 TTAAAAATTAATAAAAA
1 TTAAAAATTAA-AAAAA
29069454 GCATTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 6 0.21
17 13 0.45
18 6 0.21
19 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
TTAAAAATTAAAAAAA
Found at i:29069602 original size:18 final size:18
Alignment explanation
Indices: 29069581--29069615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29069571 TATATAAAAT
29069581 TTTTAAAAAATTATTAAA
1 TTTTAAAAAATTATTAAA
* *
29069599 TTTTATAAAATTTTTAA
1 TTTTAAAAAATTATTAA
29069616 TAAAATATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAAATTATTAAA
Found at i:29069939 original size:21 final size:22
Alignment explanation
Indices: 29069902--29069944 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
29069892 GAATTTTACT
*
29069902 TAATATTTATATAATTT-TTAA
1 TAATATTTATACAATTTATTAA
29069923 TAATATTT-TACAGATTTATTAA
1 TAATATTTATACA-ATTTATTAA
29069945 AAAATCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATATTTATACAATTTATTAA
Found at i:29071186 original size:3 final size:3
Alignment explanation
Indices: 29071178--29071202 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
29071168 CTCCATTGAT
29071178 GTA GTA GTA GTA GTA GTA GTA GTA G
1 GTA GTA GTA GTA GTA GTA GTA GTA G
29071203 AGGCAACGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GTA
Found at i:29074200 original size:31 final size:29
Alignment explanation
Indices: 29074134--29074200 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
29074124 ATGGATATGA
*
29074134 TTTTTAACAAAAGGATCAATTTGCTCTTT
1 TTTTTAACAAAAGGATCAATTTGCACTTT
**
29074163 AATTTAACATATAAGGA-CTAATTTGCACTTT
1 TTTTTAACA-A-AAGGATC-AATTTGCACTTT
29074194 TTTTTAA
1 TTTTTAA
29074201 TAAAGGGTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 7 0.23
30 2 0.07
31 21 0.70
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (29 bp):
TTTTTAACAAAAGGATCAATTTGCACTTT
Found at i:29076356 original size:13 final size:13
Alignment explanation
Indices: 29076338--29076389 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
29076328 AGTCATTTTC
29076338 TCAATAAGAAAGA
1 TCAATAAGAAAGA
*
29076351 TCAATAAGAAA-T
1 TCAATAAGAAAGA
29076363 TCCAA-ATA-AAAGA
1 T-CAATA-AGAAAGA
29076376 TCAATAAGAAAGA
1 TCAATAAGAAAGA
29076389 T
1 T
29076390 ATTGTAATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (13 bp):
TCAATAAGAAAGA
Found at i:29076826 original size:18 final size:18
Alignment explanation
Indices: 29076782--29076826 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
29076772 CATTCGTTTC
*
29076782 CAAAACATTATTCATTTA
1 CAAAACGTTATTCATTTA
*
29076800 CAAATCGTTATTCAATTT-
1 CAAAACGTTATTC-ATTTA
29076818 CAAAACGTT
1 CAAAACGTT
29076827 TTCTTCTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAAAACGTTATTCATTTA
Found at i:29079668 original size:11 final size:11
Alignment explanation
Indices: 29079654--29079697 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
29079644 AGATAAATAT
29079654 TATTTTATTAA
1 TATTTTATTAA
*
29079665 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
29079678 TATTTTATTAT
1 TATTTTATTAA
29079689 TATTTTATT
1 TATTTTATT
29079698 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:29081509 original size:2 final size:2
Alignment explanation
Indices: 29081502--29081562 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
29081492 ATGGATATTA
29081502 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
29081544 TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG T
29081563 TCTATTGTTA
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:29081785 original size:33 final size:32
Alignment explanation
Indices: 29081741--29081866 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 32
29081731 CAGTGTTTAT
29081741 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * **
29081773 ATGATAAGACCATAACTGGGTTATGGCATTACAA
1 ATG-TAAGACCATAGCTGGGCTATGGCATT-CTG
* * *
29081807 ATGTAAGACCATGGCAGGG-TCATGGCAATGCATG
1 ATGTAAGACCATAGCTGGGCT-ATGGC-ATTC-TG
* *
29081841 -TGTAAGACCATAGTTGGACTATGGCA
1 ATGTAAGACCATAGCTGGGCTATGGCA
29081867 CAAAAAGAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
32 5 0.07
33 62 0.84
34 7 0.09
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTG
Found at i:29083032 original size:25 final size:25
Alignment explanation
Indices: 29083003--29083058 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
29082993 TTCAAATTCC
*
29083003 AAAAAGTCATTAAGAAAT-ATCAATA
1 AAAAAGTC-TAAAGAAATGATCAATA
* * *
29083028 AAAAATTCTAAATAAATGATCGATA
1 AAAAAGTCTAAAGAAATGATCAATA
29083053 AAAAAG
1 AAAAAG
29083059 ATATCGACTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.23
Consensus pattern (25 bp):
AAAAAGTCTAAAGAAATGATCAATA
Found at i:29083420 original size:207 final size:206
Alignment explanation
Indices: 29082858--29083421 Score: 912
Period size: 206 Copynumber: 2.8 Consensus size: 206
29082848 GGGGTGTTAC
* * *
29082858 AGATATTGACTACACATGTTGAGAAATTATGTTAGAATATGACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
*
29082923 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGTATGTAATGTGTGCTTTG
66 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
* * *
29082988 AAAAATTCAAATTCCAAAAAG-------TCATTAAGAAATATCAATAAAAAATTCTAAATAAATG
131 AAAAATTCAAATTCCAAAAAGTCATTTTTCATTAAGAAAGATCAATAAAAAATTCCAAATAAAAG
*
29083046 ATCGATAAAAA
196 ATCAATAAAAA
* *
29083057 AGATATCGACTCCACATGTTGAGAAATTACGTGAGAATATAACTAATCAAAGGAAATTGGTGAAT
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
29083122 GAAATTG-TTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
66 GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
* *
29083186 AAAAATTCAAATTCCAAAAAGTCATTTTCTCATTAAGAAAGATTAATAAGAAATTCCAAATAAAA
131 AAAAATTCAAATTCCAAAAAGTCATTTT-TCATTAAGAAAGATCAATAAAAAATTCCAAATAAAA
*
29083251 GATCAATAAGAA
195 GATCAATAAAAA
* *
29083263 AGATATCGACTCCACATATTGAGAAATTATGTGAGAATATGACTAATCGAAA-GAAATTAGTGAA
1 AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATC-AAAGGAAATTGGTGAA
29083327 TGAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTT
65 TGAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTT
29083392 GAAAAATTCAAATTCCAAAAAGTCATTTTT
130 GAAAAATTCAAATTCCAAAAAGTCATTTTT
29083422 GTACCATTCT
Statistics
Matches: 338, Mismatches: 17, Indels: 13
0.92 0.05 0.04
Matches are distributed among these distances:
198 77 0.23
199 67 0.20
206 106 0.31
207 88 0.26
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (206 bp):
AGATATCGACTCCACATGTTGAGAAATTATGTGAGAATATGACTAATCAAAGGAAATTGGTGAAT
GAAATTGTTTTTTTTCTCATTCTCAATACATTATTTTAGATGCAATGGATGTAATGTGTGCTTTG
AAAAATTCAAATTCCAAAAAGTCATTTTTCATTAAGAAAGATCAATAAAAAATTCCAAATAAAAG
ATCAATAAAAA
Found at i:29089552 original size:464 final size:464
Alignment explanation
Indices: 29088684--29089611 Score: 1811
Period size: 464 Copynumber: 2.0 Consensus size: 464
29088674 CTAGCAGTGG
29088684 TAACCCCTTGAGCAAGCGATCGAATACAACAATTCACTTTGGGAATCATCCCACCGCCTACCTTC
1 TAACCCCTTGAGCAAGCGATCGAATACAACAATTCACTTTGGGAATCATCCCACCGCCTACCTTC
29088749 CCTTCCTCAATCATTTTCTTCACTCCCTTTATATCAATCTCTTTCACCAAGCTTCCAGGGTCCTC
66 CCTTCCTCAATCATTTTCTTCACTCCCTTTATATCAATCTCTTTCACCAAGCTTCCAGGGTCCTC
29088814 TCGGTTTCTCAGAATCCCTGCGACGTCGGTCAACAGAATCAGTTTCTCAGCCCCCAATGCCGCCG
131 TCGGTTTCTCAGAATCCCTGCGACGTCGGTCAACAGAATCAGTTTCTCAGCCCCCAATGCCGCCG
29088879 CCACCTCACCAGCTACCGTGTCTGCATTGATGTTGTAAGGCTGACCATACTCATCCGCCGCCACT
196 CCACCTCACCAGCTACCGTGTCTGCATTGATGTTGTAAGGCTGACCATACTCATCCGCCGCCACT
29088944 GAAGCAATCACCGGGATGCTTCCGTTGTCCACGATCGTTTGGAGGACTGTGGGGTCCACTCTCGC
261 GAAGCAATCACCGGGATGCTTCCGTTGTCCACGATCGTTTGGAGGACTGTGGGGTCCACTCTCGC
* *
29089009 AACCTCTCCGACAAACCCCAACTGTGCAGCGTTTGGGCTGGGCCTGGCAACTAAAAGGCGGCCGT
326 AACCTCTCCCACAAACCCCAACTGTGCAGCGTTTGGGCTGGGCCGGGCAACTAAAAGGCGGCCGT
*
29089074 CCATGCCAGAAAGGCCCACGGCGGTGGCTCCAGCGTAATTGATACGAGAAACCAGGTCTTTGTTA
391 CCATGCCAGAAAGGCCCACAGCGGTGGCTCCAGCGTAATTGATACGAGAAACCAGGTCTTTGTTA
29089139 ACTTTTCCA
456 ACTTTTCCA
29089148 TAACCCCTTGAGCAAGCGATCGAATACAACAATTCACTTTGGGAATCATCCCACCGCCTACCTTC
1 TAACCCCTTGAGCAAGCGATCGAATACAACAATTCACTTTGGGAATCATCCCACCGCCTACCTTC
29089213 CCTTCCTCAATCATTTTCTTCACTCCCTTTATATCAATCTCTTTCACCAAGCTTCCAGGGTCCTC
66 CCTTCCTCAATCATTTTCTTCACTCCCTTTATATCAATCTCTTTCACCAAGCTTCCAGGGTCCTC
29089278 TCGGTTTCTCAGAATCCCTGCGACGTCGGTCAACAGAATCAGTTTCTCAGCCCCCAATGCCGCCG
131 TCGGTTTCTCAGAATCCCTGCGACGTCGGTCAACAGAATCAGTTTCTCAGCCCCCAATGCCGCCG
*
29089343 CCACCTCACCGGCTACCGTGTCTGCATTGATGTTGTAAGGCTGACCATACTCATCCGCCGCCACT
196 CCACCTCACCAGCTACCGTGTCTGCATTGATGTTGTAAGGCTGACCATACTCATCCGCCGCCACT
29089408 GAAGCAATCACCGGGATGCTTCCGTTGTCCACGATCGTTTGGAGGACTGTGGGGTCCACTCTCGC
261 GAAGCAATCACCGGGATGCTTCCGTTGTCCACGATCGTTTGGAGGACTGTGGGGTCCACTCTCGC
*
29089473 AACTTCTCCCACAAACCCCAACTGTGCAGCGTTTGGGCTGGGCCGGGCAACTAAAAGGCGGCCGT
326 AACCTCTCCCACAAACCCCAACTGTGCAGCGTTTGGGCTGGGCCGGGCAACTAAAAGGCGGCCGT
29089538 CCATGCCAGAAAGGCCCACAGCGGTGGCTCCAGCGTAATTGATACGAGAAACCAGGTCTTTGTTA
391 CCATGCCAGAAAGGCCCACAGCGGTGGCTCCAGCGTAATTGATACGAGAAACCAGGTCTTTGTTA
29089603 ACTTTTCCA
456 ACTTTTCCA
29089612 ACAAGGACCA
Statistics
Matches: 459, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
464 459 1.00
ACGTcount: A:0.22, C:0.33, G:0.20, T:0.25
Consensus pattern (464 bp):
TAACCCCTTGAGCAAGCGATCGAATACAACAATTCACTTTGGGAATCATCCCACCGCCTACCTTC
CCTTCCTCAATCATTTTCTTCACTCCCTTTATATCAATCTCTTTCACCAAGCTTCCAGGGTCCTC
TCGGTTTCTCAGAATCCCTGCGACGTCGGTCAACAGAATCAGTTTCTCAGCCCCCAATGCCGCCG
CCACCTCACCAGCTACCGTGTCTGCATTGATGTTGTAAGGCTGACCATACTCATCCGCCGCCACT
GAAGCAATCACCGGGATGCTTCCGTTGTCCACGATCGTTTGGAGGACTGTGGGGTCCACTCTCGC
AACCTCTCCCACAAACCCCAACTGTGCAGCGTTTGGGCTGGGCCGGGCAACTAAAAGGCGGCCGT
CCATGCCAGAAAGGCCCACAGCGGTGGCTCCAGCGTAATTGATACGAGAAACCAGGTCTTTGTTA
ACTTTTCCA
Found at i:29099295 original size:40 final size:40
Alignment explanation
Indices: 29099236--29099376 Score: 228
Period size: 40 Copynumber: 3.5 Consensus size: 40
29099226 AGGCTTGTGC
* *
29099236 CTAGCAGGCTTAATGCCGGTGAAATATTCAAACTACACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
29099276 CTAGCAGGCTTAATACCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
29099316 CTAGCAGGCTTAATGCCAGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
29099356 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
29099377 TACGGAATCA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 93 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:29099657 original size:2 final size:2
Alignment explanation
Indices: 29099650--29099680 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29099640 AACGAAGGCT
*
29099650 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29099681 GGATGAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:29100547 original size:2 final size:2
Alignment explanation
Indices: 29100540--29100570 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29100530 CATCCGCATG
*
29100540 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29100571 ATGGTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29100816 original size:14 final size:14
Alignment explanation
Indices: 29100797--29100827 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29100787 AGTAAATATC
*
29100797 ATATATATATTTAT
1 ATATATATATTCAT
29100811 ATATATATATTCAT
1 ATATATATATTCAT
29100825 ATA
1 ATA
29100828 GAACGTCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATATTCAT
Found at i:29101027 original size:273 final size:274
Alignment explanation
Indices: 29100614--29101159 Score: 1049
Period size: 273 Copynumber: 2.0 Consensus size: 274
29100604 TGGGGTGGTT
29100614 GTTGTTAAATAATGAACTTTGCTTAAAAGTATATTTGACTTGTTAAATATATAATATGAGAATAA
1 GTTGTTAAATAATGAACTTTGCTTAAAAGTATATTTGACTTGTTAAATATATAATATGAGAATAA
29100679 TAAAGTTGAAAGTATATATGCAGTTAGTGAGTAGAGAATATTAAATTATTGAGTTATAAATTTAT
66 TAAAGTTGAAAGTATATATGCAGTTAGTGAGTAGAGAATATTAAATTATTGAGTTATAAATTTAT
29100744 GCAAAGGTTGAATAAAAAAAATGCTATGTACTGGACCTGTATTAGTAAATATCATATATATATTT
131 GCAAAGGTTGAATAAAAAAAATGCTATGTACTGGACCTGTATTAGTAAATATCATATATATATTT
29100809 ATATATATATATTCATATAGAACGTCTTGAAATTTGTTTGATTCAAGTATATAGGTGATAAGAAA
196 ATATATATATATTCATATAGAACGTCTTGAAATTTGTTTGATTCAAGTATATAGGTGATAAGAAA
29100874 TATAATTATGTATG
261 TATAATTATGTATG
*
29100888 GTTGTTAAATAATGAACTTTGCTTAAAAGTATATTTGACTTGTTATAT-TATAATATGAGAATAA
1 GTTGTTAAATAATGAACTTTGCTTAAAAGTATATTTGACTTGTTAAATATATAATATGAGAATAA
29100952 TAAAGTTGAAAGTATATATGCAGTTAGTGAGTAGAGAATATTAAATTATTGAGTTATAAATTTAT
66 TAAAGTTGAAAGTATATATGCAGTTAGTGAGTAGAGAATATTAAATTATTGAGTTATAAATTTAT
*
29101017 GCAAAGGTTGAATAAAAAAAATGCTATGTACTGGACCTGTATTAGTAAATATTATATATATATTT
131 GCAAAGGTTGAATAAAAAAAATGCTATGTACTGGACCTGTATTAGTAAATATCATATATATATTT
* *
29101082 GTATATATATATTCATATAGAATGTCTTGAAATTTGTTTGATTCAAGTATATAGGTGATAAGAAA
196 ATATATATATATTCATATAGAACGTCTTGAAATTTGTTTGATTCAAGTATATAGGTGATAAGAAA
29101147 TATAATTATGTAT
261 TATAATTATGTAT
29101160 ATAAGATTTG
Statistics
Matches: 268, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
273 221 0.82
274 47 0.18
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (274 bp):
GTTGTTAAATAATGAACTTTGCTTAAAAGTATATTTGACTTGTTAAATATATAATATGAGAATAA
TAAAGTTGAAAGTATATATGCAGTTAGTGAGTAGAGAATATTAAATTATTGAGTTATAAATTTAT
GCAAAGGTTGAATAAAAAAAATGCTATGTACTGGACCTGTATTAGTAAATATCATATATATATTT
ATATATATATATTCATATAGAACGTCTTGAAATTTGTTTGATTCAAGTATATAGGTGATAAGAAA
TATAATTATGTATG
Found at i:29101711 original size:30 final size:32
Alignment explanation
Indices: 29101648--29101712 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
29101638 ATAAAAATGG
29101648 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
*
29101680 TGAAAATGGAGAAATG-GAAA-CATTTGGAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAA
29101710 TGA
1 TGA
29101713 TTATGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 12 0.38
31 4 0.12
32 16 0.50
ACGTcount: A:0.51, C:0.03, G:0.25, T:0.22
Consensus pattern (32 bp):
TGAAAATGGAGAAATGAGAAATCATTTGAAAA
Found at i:29101743 original size:57 final size:57
Alignment explanation
Indices: 29101674--29101799 Score: 193
Period size: 57 Copynumber: 2.2 Consensus size: 57
29101664 AGAAATCATT
* *
29101674 TGAAAATGAAAATGGAGAAATGGAAA-CATTTGGAAA-TGATTATGATTTTCTCCAAAA
1 TGAAAATGAAAATAGAGAAAT-GAAATCATTTAGAAATTGA-TATGATTTTCTCCAAAA
29101731 TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
1 TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
*
29101788 TGAAAATAAAAA
1 TGAAAATGAAAA
29101800 ATTAAAATGA
Statistics
Matches: 64, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 4 0.06
57 57 0.89
58 3 0.05
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (57 bp):
TGAAAATGAAAATAGAGAAATGAAATCATTTAGAAATTGATATGATTTTCTCCAAAA
Found at i:29106804 original size:11 final size:11
Alignment explanation
Indices: 29106786--29106815 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29106776 ACTAGATTAC
29106786 AAATATTTTAA
1 AAATATTTTAA
*
29106797 ATATATTTTAA
1 AAATATTTTAA
29106808 AAATATTT
1 AAATATTT
29106816 GTCCAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:29109214 original size:18 final size:18
Alignment explanation
Indices: 29109191--29109236 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
29109181 TAAATAGTTT
29109191 GAGTTATTCGAATTAATC
1 GAGTTATTCGAATTAATC
*
29109209 GAGTTATTCAAATTAATC
1 GAGTTATTCGAATTAATC
*
29109227 AAGTTATTCG
1 GAGTTATTCG
29109237 GATCAACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (18 bp):
GAGTTATTCGAATTAATC
Found at i:29114898 original size:62 final size:63
Alignment explanation
Indices: 29114832--29114995 Score: 219
Period size: 62 Copynumber: 2.7 Consensus size: 63
29114822 ACGCAGTAAA
*
29114832 TTACACGGCCTGGGCACACAC-CAGTGTCCCTGGCTGTGTGGTCTTGTACCAAAAATAATGAG
1 TTACACGGCCTAGGCACACACGCAGTGTCCCTGGCTGTGTGGTCTTGTACCAAAAATAATGAG
* * *
29114894 TTACACGGCCTAGGCA-A-ACGCATGTGTCCCTGGCCGTGTGGTCTTGTACCACAAATAGTGAG
1 TTACACGGCCTAGGCACACACGCA-GTGTCCCTGGCTGTGTGGTCTTGTACCAAAAATAATGAG
* * * *
29114956 TTACACAGCCTAGGCACACGCTC-GTGGCCCTGGCTGTGTG
1 TTACACGGCCTAGGCACACACGCAGTGTCCCTGGCTGTGTG
29114996 AACTCTTCAC
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
60 2 0.02
61 3 0.03
62 81 0.91
63 1 0.01
64 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (63 bp):
TTACACGGCCTAGGCACACACGCAGTGTCCCTGGCTGTGTGGTCTTGTACCAAAAATAATGAG
Found at i:29121854 original size:62 final size:62
Alignment explanation
Indices: 29121786--29121928 Score: 200
Period size: 62 Copynumber: 2.3 Consensus size: 62
29121776 TTACATGGCT
29121786 TGGGCACACGCTCGTGTCCCT-GTC-CATGTTGTCTTGTACCACAAACAGTGAGTTACACAGCC
1 TGGGCACACGCTCGTGTCCCTAGTCGCATG--GTCTTGTACCACAAACAGTGAGTTACACAGCC
* * * *
29121848 TGGGCACACGCTTGTGTCCCTAGTCGTATGGTCTTGTACCACAAATAGTGAGTTACACGGCC
1 TGGGCACACGCTCGTGTCCCTAGTCGCATGGTCTTGTACCACAAACAGTGAGTTACACAGCC
* *
29121910 TAGGCACACGCACGTGTCC
1 TGGGCACACGCTCGTGTCC
29121929 TTGGACGTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
62 66 0.92
63 3 0.04
64 3 0.04
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.25
Consensus pattern (62 bp):
TGGGCACACGCTCGTGTCCCTAGTCGCATGGTCTTGTACCACAAACAGTGAGTTACACAGCC
Found at i:29125045 original size:18 final size:20
Alignment explanation
Indices: 29125016--29125061 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
29125006 TATGATTTAT
29125016 AGGTTGAATTGAA-TACTTG
1 AGGTTGAATTGAAGTACTTG
29125035 AGGTT-AATTGAAGTACTT-
1 AGGTTGAATTGAAGTACTTG
29125053 A-GTTGAATT
1 AGGTTGAATT
29125062 AAATTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 12 0.48
19 10 0.40
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (20 bp):
AGGTTGAATTGAAGTACTTG
Found at i:29126657 original size:54 final size:54
Alignment explanation
Indices: 29126575--29126691 Score: 146
Period size: 54 Copynumber: 2.2 Consensus size: 54
29126565 CAATTCAGTG
* * *
29126575 AGTTACACAGTCTAGCACACGGCCTGCGACACGACTGTGTGTCAC-AAATTAGAA
1 AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGAC-CTAAATTAGAA
* * * **
29126629 AGTTACACGGTCTGGCACATGGCCTGCGATACGACCGTGTGACCTAAATTAGGG
1 AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGACCTAAATTAGAA
29126683 AGTTACACG
1 AGTTACACG
29126692 ATTTAAGACA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (54 bp):
AGTTACACGGTCTAGCACACGGCCTGCGACACGACCGTGTGACCTAAATTAGAA
Found at i:29127771 original size:2 final size:2
Alignment explanation
Indices: 29127764--29127799 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29127754 CGAGTTTAGG
29127764 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29127800 ATGTCCATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29128778 original size:3 final size:3
Alignment explanation
Indices: 29128770--29128801 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29128760 TTTTCTCTTA
29128770 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29128802 CCTTATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29133135 original size:21 final size:22
Alignment explanation
Indices: 29133086--29133135 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
29133076 TAAAAATATT
* *
29133086 TATAACATTATTTTTATGAATA
1 TATAATATTATATTTATGAATA
29133108 -AGT-ATATTATATTTAT-AATA
1 TA-TAATATTATATTTATGAATA
29133128 TATAATAT
1 TATAATAT
29133136 ATACACATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 7
0.72 0.06 0.22
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TATAATATTATATTTATGAATA
Found at i:29134535 original size:33 final size:32
Alignment explanation
Indices: 29134397--29134557 Score: 124
Period size: 33 Copynumber: 4.8 Consensus size: 32
29134387 ACATTCGTAG
*
29134397 TGCCATAACCCAGGTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTA-CATCAGAA
* * * *
29134430 TACCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGCCATAACCCAGCTATGGTCTTACAT-CAGA-A
*** * * * * *
29134464 CTGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 -TGCCATAACCCAGCTATGGTCTTAC-ATCAGAA
* *
29134498 TGCCATAACCAAGTTATGGTCTTATCATCAGAA
1 TGCCATAACCCAGCTATGGTCTTA-CATCAGAA
*
29134531 TGCCATAGCCCAGCTATGGTCTTACAT
1 TGCCATAACCCAGCTATGGTCTTACAT
29134558 ATAAACACTG
Statistics
Matches: 96, Mismatches: 27, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
32 6 0.06
33 65 0.68
34 2 0.02
35 22 0.23
36 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (32 bp):
TGCCATAACCCAGCTATGGTCTTACATCAGAA
Found at i:29137307 original size:8 final size:8
Alignment explanation
Indices: 29137294--29137336 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
29137284 TAAAAATTAT
29137294 AATTAAAA
1 AATTAAAA
29137302 AATTAAAA
1 AATTAAAA
*
29137310 AGTTCAAAA
1 AATT-AAAA
29137319 AA-TAATAA
1 AATTAA-AA
29137327 AATTAAAA
1 AATTAAAA
29137335 AA
1 AA
29137337 ATTACAATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 2 0.07
8 20 0.67
9 8 0.27
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (8 bp):
AATTAAAA
Found at i:29137320 original size:17 final size:18
Alignment explanation
Indices: 29137294--29137340 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
29137284 TAAAAATTAT
29137294 AATT-AAAAAATTAA-AA
1 AATTAAAAAAATTAATAA
* *
29137310 AGTTCAAAAAA-TAATAA
1 AATTAAAAAAATTAATAA
29137327 AATTAAAAAAATTA
1 AATTAAAAAAATTA
29137341 CAATTCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 6 0.24
17 17 0.68
18 2 0.08
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AATTAAAAAAATTAATAA
Found at i:29137345 original size:15 final size:15
Alignment explanation
Indices: 29137285--29137355 Score: 54
Period size: 15 Copynumber: 4.5 Consensus size: 15
29137275 TAAATAATCT
*
29137285 AAAAATTATAATT-A
1 AAAAATTAAAATTAA
29137299 AAAAATTAAAAAGTTCAA
1 AAAAATT-AAAA-TT-AA
*
29137317 AAAATAATAAAATTAA
1 AAAA-ATTAAAATTAA
* **
29137333 AAAAATTACAATTCC
1 AAAAATTAAAATTAA
29137348 AAAAATTA
1 AAAAATTA
29137356 TAAAAATGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 7 0.15
15 18 0.39
16 8 0.17
17 2 0.04
18 9 0.20
19 2 0.04
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAATTAA
Found at i:29137394 original size:21 final size:20
Alignment explanation
Indices: 29137348--29137412 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
29137338 TTACAATTCC
* *
29137348 AAAAATTATAAAAATGTAAA
1 AAAAATTATAAAATTTTAAA
*
29137368 ACAAAATTATAAAATTTTCCAA
1 A-AAAATTATAAAATTTT-AAA
*
29137390 AAAAATTCTAAAATTTTAGAA
1 AAAAATTATAAAATTTTA-AA
29137411 AA
1 AA
29137413 TAGGAATACA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 33 0.89
22 3 0.08
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAATTTTAAA
Found at i:29137488 original size:3 final size:3
Alignment explanation
Indices: 29137480--29137512 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29137470 AAAATGTTTT
29137480 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29137513 CCTAAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:29139138 original size:27 final size:29
Alignment explanation
Indices: 29139108--29139165 Score: 77
Period size: 26 Copynumber: 2.1 Consensus size: 29
29139098 TAGATTGTTA
*
29139108 AAATTCTTTTAAAAGA-A-AACTC-AAGAG
1 AAATTC-TTTAAAAAACATAACTCAAAGAG
29139135 AAATTCTTTAAAAAACATAACTCAAAGAG
1 AAATTCTTTAAAAAACATAACTCAAAGAG
29139164 AA
1 AA
29139166 TTTTATTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 8 0.30
27 7 0.26
28 5 0.19
29 7 0.26
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (29 bp):
AAATTCTTTAAAAAACATAACTCAAAGAG
Found at i:29145335 original size:112 final size:111
Alignment explanation
Indices: 29145077--29145401 Score: 421
Period size: 112 Copynumber: 3.0 Consensus size: 111
29145067 AAAATTCAAG
* * * * *
29145077 AGGATATTTGGCAATATGGTTAAACGAG--AAATCGAAACCCAGCACATTA-GGACACG-TTCCT
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGA-ACGTTTTCT
* * **
29145138 TGAATTTCCAAACGCAAAACATTACCTTATTTTGAAA--TTTTTGGA
65 CGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAA
*
29145183 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
29145248 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTT-AAA
* *
29145295 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCAAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
* * * ** *
29145360 GAATTTTCAAAAGC-TAATGTTGCCTTATTTAGAAATTTTTTT
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTT
29145402 TGAAGTATGG
Statistics
Matches: 193, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
106 24 0.12
108 24 0.12
109 41 0.21
111 29 0.15
112 75 0.39
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (111 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGAACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTTTAAA
Found at i:29145459 original size:20 final size:20
Alignment explanation
Indices: 29145423--29145460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29145413 GTTAATATAC
*
29145423 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
29145443 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
29145461 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:29145624 original size:4 final size:4
Alignment explanation
Indices: 29145528--29145613 Score: 61
Period size: 4 Copynumber: 20.8 Consensus size: 4
29145518 ACAAACAAAC
* *
29145528 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA- ACAT AAA- AAAGG ACATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAA-T A-A-AT
* *
29145578 AAAT AAAT ACAT AAAT GAACAT AAA- AAAA AAAT AAA
1 AAAT AAAT AAAT AAAT -AA-AT AAAT AAAT AAAT AAA
29145614 GGAAAATAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
3 8 0.12
4 44 0.66
5 10 0.15
6 4 0.06
7 1 0.01
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:29145747 original size:17 final size:18
Alignment explanation
Indices: 29145727--29145760 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29145717 TATATGTTTT
29145727 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
29145744 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
29145761 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:29145772 original size:84 final size:88
Alignment explanation
Indices: 29145680--29145849 Score: 233
Period size: 90 Copynumber: 2.0 Consensus size: 88
29145670 ATATATATGT
*
29145680 ATGTATATACATAAAATTATAAAAATAT-G-AAAATA-TATATATG-TTTTAAGGA-TATTAAAT
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAA-AATTATTAAAT
29145740 ATAAAAGGTTATGTAAATATATAC
65 ATAAAAGGTTATGTAAATATATAC
* * *
29145764 ATGTATATATATATAATTATGAAAATATGGAAAAATATGTATATATGTATTTTAAAATTATTAAA
1 ATGTATATACATAAAATTATAAAAATATGGAAAAATA-GTATATATG-ATTTTAAAATTATTAAA
*
29145829 TATAAAAGTTTATGTAAATAT
64 TATAAAAGGTTATGTAAATAT
29145850 GTATATGCAC
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
84 25 0.34
85 1 0.01
86 6 0.08
88 8 0.11
89 1 0.01
90 33 0.45
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.39
Consensus pattern (88 bp):
ATGTATATACATAAAATTATAAAAATATGGAAAAATAGTATATATGATTTTAAAATTATTAAATA
TAAAAGGTTATGTAAATATATAC
Found at i:29146953 original size:12 final size:12
Alignment explanation
Indices: 29146914--29146954 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
29146904 TGCAGGTGCA
*
29146914 GGTGGCAGAGTT
1 GGTGGCTGAGTT
*
29146926 GGTAGCTGAGTT
1 GGTGGCTGAGTT
29146938 GGTGGCTGAGTT
1 GGTGGCTGAGTT
29146950 GGTGG
1 GGTGG
29146955 TGGCAGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.12, C:0.07, G:0.51, T:0.29
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:29147567 original size:44 final size:44
Alignment explanation
Indices: 29147506--29148126 Score: 242
Period size: 44 Copynumber: 13.7 Consensus size: 44
29147496 ACCTGATGCG
*
29147506 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
* * * * *
29147550 ATCCACTCCACTGTAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGA-T-C---CTT-TAT-T--T-TA
* * *
29147604 ATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
* * * * *
29147648 ATCCACTCCACTGTAACTTCAGAGAGTTAGGATTACTAGCTTCAATCTGATGTG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGA-T-C---CTT-TAT-T--T-TA
* * *
29147702 ATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
* * * * * *
29147746 ATCCACTCCACTGTAACTTCAGAGAGTTAGGAT--TACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCT-TTA-TTTTA
* * *** *
29147790 ATCTACTCTA-TGGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCA
1 ATCTACTCCACT-GTAACT-TCAGAGAGATAAGATCCT-TTATTTTA
* * * ** *
29147834 ATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCT
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCT-TTATT-TT-A
* * * * *
29147880 GTCTACTCCACTGTAACCTCAGGGAGATAAGA-CC-TGA-TTCA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
** *
29147921 ATCTACTCTGCTGTAACTTCAGAGAGATGAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
** * * * ** * * **
29147965 ATCCGCTCAACTGTAACTTCAGGGAGATAGGATAGTGT-CTTGG
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
* * *** *
29148008 ATCTGCTCCACTGTAA-TCTCAGGGAGATAAGAT-CTCTGGCTTCA
1 ATCTACTCCACTGTAACT-TCAGAGAGATAAGATCCT-TTATTTTA
* * * **
29148052 ATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGTGGTTTTA
1 ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTA
** *
29148096 ATCCGCTCCACTGCAACTTCAGGAAGAGATA
1 ATCTACTCCACTGTAACTTCA-G-AGAGATA
29148127 TGATTACTTC
Statistics
Matches: 437, Mismatches: 101, Indels: 76
0.71 0.16 0.12
Matches are distributed among these distances:
41 26 0.06
42 6 0.01
43 37 0.08
44 237 0.54
45 8 0.02
46 39 0.09
47 2 0.00
48 4 0.01
49 12 0.03
50 4 0.01
51 2 0.00
52 2 0.00
53 4 0.01
54 54 0.12
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
ATCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
Found at i:29147667 original size:98 final size:98
Alignment explanation
Indices: 29147498--29147793 Score: 565
Period size: 98 Copynumber: 3.0 Consensus size: 98
29147488 GAGATAAGAC
* * *
29147498 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
29147563 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
66 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
29147596 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
29147661 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
66 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
29147694 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
1 CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
29147759 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
66 TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
29147792 CT
1 CT
29147794 ACTCTATGGT
Statistics
Matches: 195, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 195 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (98 bp):
CTGATGTGATCTACTCTATTATAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTG
TAACTTCAGAGAGTTAGGATTACTAGCTTCAAT
Found at i:29147978 original size:131 final size:128
Alignment explanation
Indices: 29147786--29148259 Score: 433
Period size: 131 Copynumber: 3.6 Consensus size: 128
29147776 GATTACTAGC
* * *** * *
29147786 TTCAATCTACTCTA-TGGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTA
1 TTCAATCTACTCTACT-GTAACT-TCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTA
* *
29147849 ACCTCAGGGAGATAAGATCTGAAATTCTTCTGTCTACTCCACTGTAACCTCAGGGAGATAAGACC
64 ACTTCAGGGAGATAAGAT-T--AATTCTT-TGTCTGCTCCACTGTAACCTCAGGGAGATAAGACC
29147914 T-GA
125 TGGA
* * *
29147917 TTCAATCTACTCTGCTGTAACTTCAGAGAGATGAGATCCT-TTATTTTAATCCGCTCAACTGTAA
1 TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGAT-CTATTATTTTAATCCGCTCCACTGTAA
* * * *
29147981 CTTCAGGGAGATAGGA-TAGTGTCTTGGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT
65 CTTCAGGGAGATAAGATTAAT-TCTTTG-TCTGCTCCACTGTAACCTCAGGGAGATAAGA-C-CT
*
29148045 GGC
126 GGA
* * * * * ** *
29148048 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCAAC
1 TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAAC
* * * * *
29148113 TTCAGGAAGAGATATGATTACTTCTTTCGTCTGCTCCACTGCAACTTCAGGAAGATAAGA-CTGG
66 TTCAGG--GAGATAAGATTAATTCTTT-GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGG
29148177 A
128 A
* * * * *
29148178 TACGATCTACTCTACTGCT-ACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCTCTGCAA
1 TTCAATCTACTCTACTG-TAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAA
*
29148242 CTTCAGGGA-ATAGGATTA
65 CTTCAGGGAGATAAGATTA
29148260 TCTGCTTCAA
Statistics
Matches: 283, Mismatches: 46, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
127 11 0.04
128 35 0.12
129 2 0.01
130 66 0.23
131 122 0.43
132 4 0.01
133 39 0.14
134 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (128 bp):
TTCAATCTACTCTACTGTAACTTCAGAGAGATAAGATCTATTATTTTAATCCGCTCCACTGTAAC
TTCAGGGAGATAAGATTAATTCTTTGTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGGA
Found at i:29148022 original size:43 final size:44
Alignment explanation
Indices: 29147715--29148172 Score: 269
Period size: 44 Copynumber: 10.4 Consensus size: 44
29147705 TACTCTATTA
* * * * **
29147715 TAACTTCAGAGAGATAAGATC-CTTTATTTTAATCCACTCCACTG
1 TAACTTCAGGGAGATAAGATCACTGT-CTTCAATCTGCTCCACTG
* * * * * *
29147759 TAACTTCAGAGAGTTAGGATTACTAG-CTTCAATCTACTCTA-TGG
1 TAACTTCAGGGAGATAAGATCACT-GTCTTCAATCTGCTCCACT-G
* *
29147803 TAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
1 TAACT-TCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* * ** *
29147847 TAACCTCAGGGAGATAAGATCTGAAAT-TCTTCTGTCTACTCCACTG
1 TAACTTCAGGGAGATAAGATC---ACTGTCTTCAATCTGCTCCACTG
* * * **
29147893 TAACCTCAGGGAGATAAGA-C-CTG-ATTCAATCTACTCTGCTG
1 TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* * * * * * *
29147934 TAACTTCAGAGAGATGAGATC-CTTTATTTTAATCCGCTCAACTG
1 TAACTTCAGGGAGATAAGATCACTGT-CTTCAATCTGCTCCACTG
* * **
29147978 TAACTTCAGGGAGATAGGAT-AGTGTCTTGGATCTGCTCCACTG
1 TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* *
29148021 TAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTG
1 TAACT-TCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
* ** * *
29148065 TAACCTCAGGGAGATAAGATCTGTGGT-TTTAATCCGCTCCACTG
1 TAACTTCAGGGAGATAAGATCACT-GTCTTCAATCTGCTCCACTG
* * * *
29148109 CAACTTCAGGAAGAGATATGATTACT-TCTTTC-GTCTGCTCCACTG
1 TAACTTCAGG--GAGATAAGATCACTGTC-TTCAATCTGCTCCACTG
* *
29148154 CAACTTCAGGAAGATAAGA
1 TAACTTCAGGGAGATAAGA
29148173 CTGGATACGA
Statistics
Matches: 321, Mismatches: 70, Indels: 47
0.73 0.16 0.11
Matches are distributed among these distances:
41 30 0.09
42 4 0.01
43 40 0.12
44 174 0.54
45 26 0.08
46 46 0.14
47 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
TAACTTCAGGGAGATAAGATCACTGTCTTCAATCTGCTCCACTG
Found at i:29154621 original size:112 final size:112
Alignment explanation
Indices: 29154184--29154589 Score: 639
Period size: 112 Copynumber: 3.7 Consensus size: 112
29154174 AAAATTCAAG
* * * * *
29154184 AGGATATTTGGCAATATGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGACACGTTCCTT-
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTT--TTC
* * **
29154246 A--AATTTCCAAACGCAAAACATTACCTTATTTTG-AA-ATTTTT-GGA
64 ACGAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
29154290 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
29154355 GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
66 GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
29154402 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
29154467 GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
66 GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
*
29154514 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
*
29154579 GAATTTTCAAA
66 GAATTTCCAAA
29154590 AGCTAATGTT
Statistics
Matches: 281, Mismatches: 11, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
106 26 0.09
107 1 0.00
108 29 0.10
109 30 0.11
110 2 0.01
111 6 0.02
112 187 0.67
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (112 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCAC
GAATTTCCAAACGCCAAACATTTCCTTATTTTGAAATATTTTTAAAA
Found at i:29154678 original size:20 final size:20
Alignment explanation
Indices: 29154642--29154679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29154632 GTTAATATAC
*
29154642 ATAATGGAATAATAAATATG
1 ATAATGGAACAATAAATATG
29154662 ATAATGTGAACAA-AAATA
1 ATAATG-GAACAATAAATA
29154680 ATATGAGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (20 bp):
ATAATGGAACAATAAATATG
Found at i:29154829 original size:22 final size:21
Alignment explanation
Indices: 29154780--29154829 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
29154770 AGGACATATA
* *
29154780 AATAAATACATAAATGAACAT
1 AATAAAAACATAAATGAAAAT
*
29154801 AAAAAAAACAATAAATGAAAAT
1 AATAAAAAC-ATAAATGAAAAT
*
29154823 TATAAAA
1 AATAAAA
29154830 TATGAACATG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (21 bp):
AATAAAAACATAAATGAAAAT
Found at i:29154937 original size:17 final size:18
Alignment explanation
Indices: 29154917--29154950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29154907 TATATGTTTT
29154917 AAGGATAT-TAAATATAA
1 AAGGATATGTAAATATAA
*
29154934 AAGGTTATGTAAATATA
1 AAGGATATGTAAATATA
29154951 TACATGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (18 bp):
AAGGATATGTAAATATAA
Found at i:29155614 original size:30 final size:30
Alignment explanation
Indices: 29155578--29155636 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
29155568 GGCCCATTTT
29155578 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAG
*
29155608 TATTTTAAAAATATTTTAAAATTAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAA
29155637 TTAAAAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAG
Found at i:29155617 original size:11 final size:10
Alignment explanation
Indices: 29155578--29155629 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
29155568 GGCCCATTTT
29155578 TATTTTAAAA
1 TATTTTAAAA
29155588 -ATTTTAAAA
1 TATTTTAAAA
* **
29155597 AATTAAAAAA
1 TATTTTAAAA
29155607 GTATTTTAAAAA
1 -TATTTT-AAAA
29155619 TATTTTAAAA
1 TATTTTAAAA
29155629 T
1 T
29155630 TAAAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 9 0.26
10 12 0.35
11 9 0.26
12 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:29155638 original size:38 final size:38
Alignment explanation
Indices: 29155591--29155674 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 38
29155581 TTTAAAAATT
* *
29155591 TTAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
29155629 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
29155667 TTAAAAAA
1 TTAAAAAA
29155675 AAAAATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (38 bp):
TTAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
Found at i:29156521 original size:12 final size:12
Alignment explanation
Indices: 29156490--29156530 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29156480 TGCACGTACA
* *
29156490 GGTGGCAGATTT
1 GGTGGCTGAGTT
*
29156502 GGTAGCTGAGTT
1 GGTGGCTGAGTT
29156514 GGTGGCTGAGTT
1 GGTGGCTGAGTT
29156526 GGTGG
1 GGTGG
29156531 TGGCAGAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.49, T:0.32
Consensus pattern (12 bp):
GGTGGCTGAGTT
Found at i:29157738 original size:2 final size:2
Alignment explanation
Indices: 29157731--29157758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29157721 CCTACTATGC
29157731 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
29157759 CTCAACCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29162010 original size:29 final size:29
Alignment explanation
Indices: 29161977--29162035 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
29161967 ACTACTATGC
29161977 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
29162006 AAGTAGTATCAGCTATCACCACTAATGTA
1 AAGTAGTATCAGCTATCACCACTAATGTA
29162035 A
1 A
29162036 CGTAAGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (29 bp):
AAGTAGTATCAGCTATCACCACTAATGTA
Found at i:29162063 original size:29 final size:29
Alignment explanation
Indices: 29162031--29162088 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29162021 TCACCACTAA
29162031 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
29162060 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
1 TGTAACGTAAGCAAGGTAAGTCTTAGTAC
29162089 AGTAGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (29 bp):
TGTAACGTAAGCAAGGTAAGTCTTAGTAC
Found at i:29165794 original size:34 final size:35
Alignment explanation
Indices: 29165754--29165822 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
29165744 CCTTCTTCAC
29165754 CCCTGCCCT-AAAATCACATTATTATAATAAGTCA
1 CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
***
29165788 CCCTGCCCTAAAAATTTTATTATTATAATAAGTCA
1 CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
29165823 AGTTTCATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (35 bp):
CCCTGCCCTAAAAATCACATTATTATAATAAGTCA
Found at i:29175355 original size:23 final size:24
Alignment explanation
Indices: 29175310--29175355 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
29175300 AAAAAAAGAA
* *
29175310 ACATTTGTATTTTTCAATTCTCAC
1 ACATTTGTATTTCTCAATACTCAC
29175334 ACATTTGT-TTTCTCAATACTCA
1 ACATTTGTATTTCTCAATACTCA
29175356 TATGTTAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (24 bp):
ACATTTGTATTTCTCAATACTCAC
Found at i:29175793 original size:21 final size:21
Alignment explanation
Indices: 29175767--29175878 Score: 81
Period size: 21 Copynumber: 5.5 Consensus size: 21
29175757 ATTTTTGGTA
29175767 AGTTGGGGCAGCTTGTTGATG
1 AGTTGGGGCAGCTTGTTGATG
*
29175788 AGTTGGGGCAGCTTG-TAACTG
1 AGTTGGGGCAGCTTGTTGA-TG
* *
29175809 AGTTAGGGCAGCCTG-T--TG
1 AGTTGGGGCAGCTTGTTGATG
* * *
29175827 AGTTGGGGTA-CTCTCTTGCTG
1 AGTTGGGGCAGCT-TGTTGATG
* * * *
29175848 ATTTGGGGTAGCCTGTTGCTG
1 AGTTGGGGCAGCTTGTTGATG
29175869 AGTTGGGGCA
1 AGTTGGGGCA
29175879 ACCACTTGGT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.01
18 11 0.15
19 1 0.01
20 2 0.03
21 57 0.78
22 1 0.01
ACGTcount: A:0.14, C:0.14, G:0.39, T:0.32
Consensus pattern (21 bp):
AGTTGGGGCAGCTTGTTGATG
Found at i:29176628 original size:26 final size:25
Alignment explanation
Indices: 29176581--29176629 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
29176571 ACATGCATAT
**
29176581 TATTAAAAAATACTTATTGCATGCA
1 TATTAAAAAATACTTACAGCATGCA
*
29176606 TATTAAAAAATAGTTAACAGCATG
1 TATTAAAAAATACTT-ACAGCATG
29176630 TGACCATCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (25 bp):
TATTAAAAAATACTTACAGCATGCA
Found at i:29176694 original size:136 final size:135
Alignment explanation
Indices: 29176540--29176852 Score: 495
Period size: 136 Copynumber: 2.3 Consensus size: 135
29176530 ATCACACACA
* * *
29176540 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTATTAAAAAA-TACTTATTGCATG
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTA-CAAAAAATTACTCACTGCATG
* * *
29176604 CATATTAAAAAATAGTTAACAGCATGTGACCATCCCCACCAACAATTACTGCATGCATATTAAAA
65 CATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAA
29176669 AAACAGT
130 AAA-AGT
* * *
29176676 CACACACACACACTCCTAAATAATAATCACTACATGCATATTACAAAAAATTACTCACTGCATGC
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATGC
29176741 ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
66 ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
29176806 AAAGT
131 AAAGT
* *
29176811 CACACACACACACACCTAAAAAA-AGTCACTGCATACATATTA
1 CACACACACACACACCTAAAAAATAGTCACTACATGCATATTA
29176853 AATAGTTATA
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 16 0.10
135 30 0.19
136 116 0.72
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (135 bp):
CACACACACACACACCTAAAAAATAGTCACTACATGCATATTACAAAAAATTACTCACTGCATGC
ATATTAAAAAATAGTCAACAGCATGTGACCATCCCCACCAACAATCACTACATGCATATTAAAAA
AAAGT
Found at i:29178874 original size:62 final size:62
Alignment explanation
Indices: 29178743--29178880 Score: 204
Period size: 62 Copynumber: 2.2 Consensus size: 62
29178733 CCATTTCTGT
*
29178743 CAGACAATAACCAATACAAAAATAATTTAATACAAACGCAACCATTTAAGTCATGCACATGG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* * ** *
29178805 CAAACAATAACCAATACAAAAATAATTTAATACAAACACAATCATTTCTGTCATGCACATTG
1 CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
* *
29178867 TAGACAATAGCCAA
1 CAGACAATAACCAA
29178881 ACACTTTAAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTAATACAAACACAACCATTTAAGTCATGCACATGG
Found at i:29179194 original size:16 final size:17
Alignment explanation
Indices: 29179175--29179210 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
29179165 ATAAAAATTG
29179175 AAATAACCCTAAAT-CA
1 AAATAACCCTAAATCCA
29179191 AAATAACCCTAAATCCA
1 AAATAACCCTAAATCCA
29179208 AAA
1 AAA
29179211 AATACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAACCCTAAATCCA
Found at i:29179211 original size:40 final size:39
Alignment explanation
Indices: 29179128--29179204 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
29179118 AATAAAACCC
**
29179128 AAAATTGAAATAACCCTAAATCAAAATCAAAGTCAAAATA
1 AAAATTGAAATAACCCTAAATCAAAAT-AAACCCAAAATA
*
29179168 AAAATTGAAATAACCCTAAATCAAAAT-AACCCTAAAT
1 AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAAT
29179205 CCAAAAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 7 0.21
40 27 0.79
ACGTcount: A:0.58, C:0.17, G:0.04, T:0.21
Consensus pattern (39 bp):
AAAATTGAAATAACCCTAAATCAAAATAAACCCAAAATA
Found at i:29179646 original size:21 final size:21
Alignment explanation
Indices: 29179620--29179660 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29179610 CAACATCGTA
* *
29179620 AGTTAACTTTCCATATCAGCT
1 AGTTAACTTGCCACATCAGCT
29179641 AGTTAACTTGCCACATCAGC
1 AGTTAACTTGCCACATCAGC
29179661 AGTCCCGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.32
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:29179737 original size:30 final size:30
Alignment explanation
Indices: 29179697--29179762 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
29179687 TATTAATCAA
* *
29179697 TGACTATTTTGTCACTTTT-TATAACGTT-AG
1 TGACTGTTTTGTAACTTTTCTA-AA-GTTGAG
29179727 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
1 TGACTGTTTTGTAACTTTTCTAAAGTTGAG
29179757 TGACTG
1 TGACTG
29179763 AAATGAAACC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.09
30 27 0.84
31 2 0.06
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (30 bp):
TGACTGTTTTGTAACTTTTCTAAAGTTGAG
Found at i:29180438 original size:29 final size:31
Alignment explanation
Indices: 29180406--29180469 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
29180396 TTAATTTTAT
*
29180406 TATTAAATTT-AAA-TAAAATAATGTATTTC
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
* *
29180435 TATT--TTTTAAAAGGAAAATAATGTATTTT
1 TATTAAATTTAAAAGGAAAATAATGTATTTC
29180464 TATTAA
1 TATTAA
29180470 TAACCAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.11
28 3 0.11
29 22 0.79
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (31 bp):
TATTAAATTTAAAAGGAAAATAATGTATTTC
Found at i:29183361 original size:22 final size:22
Alignment explanation
Indices: 29183322--29183363 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29183312 AGATCAACAC
29183322 AAATATAATCACATACATATTA
1 AAATATAATCACATACATATTA
*
29183344 AAATATCAATCTCA-ACATAT
1 AAATAT-AATCACATACATAT
29183364 CAATCATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAATCACATACATATTA
Found at i:29187869 original size:3 final size:3
Alignment explanation
Indices: 29187863--29187891 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29187853 CCACCACCAT
29187863 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CT
29187892 TGCTCTCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:29195961 original size:42 final size:42
Alignment explanation
Indices: 29195908--29196025 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 42
29195898 TGATATGAGT
* *
29195908 TTCAGATTAACCCTTTTGGGTTTCAGTTTAGCTCTT-TTGAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTT-AGC
* ** * * * *
29195950 TTTAGTTTAACCCTAATGGGCTTCAATTTAGCTATTCTTAGC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
* *
29195992 TTCAAATTAACCCTTATGGGTTTCCGTTCAGCTC
1 TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTC
29196026 CAATGAGCTT
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
42 57 0.97
43 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCAAATTAACCCTTATGGGTTTCAGTTTAGCTCTTCTTAGC
Found at i:29196078 original size:42 final size:42
Alignment explanation
Indices: 29196000--29196103 Score: 95
Period size: 42 Copynumber: 2.5 Consensus size: 42
29195990 GCTTCAAATT
* * * * *
29196000 AACCCTTATGGGTTTCCGTTCAGCTCCAATGAGCTTCCGTTC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
** * *
29196042 AACCCTTACGGGTTTCTGTTTAGCACTTATGTGCTTCTGTGC
1 AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
* *
29196084 -AGCCTT-CGGGCTTCTGTTTA
1 AACCCTTACGGGTTTCTGTTTA
29196104 CGATGTACTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 13 0.25
41 5 0.10
42 33 0.65
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (42 bp):
AACCCTTACGGGTTTCTGTTTAGCACCAATGAGCTTCCGTGC
Found at i:29206951 original size:19 final size:18
Alignment explanation
Indices: 29206927--29206962 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29206917 GCAAATGGAT
*
29206927 CATTTCTCATTTTCATTTC
1 CATTTCT-ATTTCCATTTC
29206946 CATTTCTATTTCCATTT
1 CATTTCTATTTCCATTT
29206963 TTTTAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (18 bp):
CATTTCTATTTCCATTTC
Found at i:29206956 original size:12 final size:12
Alignment explanation
Indices: 29206926--29206963 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
29206916 TGCAAATGGA
29206926 TCATTTCTCATTT
1 TCATTTC-CATTT
29206939 TCATTTCCA-TT
1 TCATTTCCATTT
29206950 TCTATTTCCATTT
1 TC-ATTTCCATTT
29206963 T
1 T
29206964 TTTAAAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 9 0.39
13 10 0.43
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:29213131 original size:33 final size:33
Alignment explanation
Indices: 29213089--29213156 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
29213079 TATTGACGTA
29213089 AATGATGACATGATCTTTTTTAATTGGTATAAT
1 AATGATGACATGATCTTTTTTAATTGGTATAAT
29213122 AATGATGACATGATCTTTTTTAATTGGTATAAT
1 AATGATGACATGATCTTTTTTAATTGGTATAAT
29213155 AA
1 AA
29213157 CACATTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (33 bp):
AATGATGACATGATCTTTTTTAATTGGTATAAT
Found at i:29214881 original size:14 final size:15
Alignment explanation
Indices: 29214864--29214896 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29214854 TCAAAACATC
*
29214864 AAAATCAATTAA-AT
1 AAAATCAAATAATAT
29214878 AAAATCAAATAATAT
1 AAAATCAAATAATAT
29214893 AAAA
1 AAAA
29214897 AATGGAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATCAAATAATAT
Found at i:29216526 original size:21 final size:22
Alignment explanation
Indices: 29216472--29216526 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
29216462 ATATTCTGAG
29216472 TTGACATTAT-TTCATATGAAAT
1 TTGA-ATTATATTCATATGAAAT
*
29216494 TT-AATTATTATT-ATATGATAT
1 TTGAATTA-TATTCATATGAAAT
29216515 TTGAATTATATT
1 TTGAATTATATT
29216527 TTGAGTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 16 0.55
22 9 0.31
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (22 bp):
TTGAATTATATTCATATGAAAT
Found at i:29217085 original size:20 final size:20
Alignment explanation
Indices: 29217062--29217100 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29217052 CTTAAATTAA
*
29217062 TTTTCTTTTAAATTTTAAAT
1 TTTTATTTTAAATTTTAAAT
*
29217082 TTTTATTTTATATTTTAAA
1 TTTTATTTTAAATTTTAAA
29217101 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATTTTAAATTTTAAAT
Found at i:29217124 original size:19 final size:18
Alignment explanation
Indices: 29217098--29217133 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29217088 TTTATATTTT
*
29217098 AAAATTATTTTTAATAAA
1 AAAATTATATTTAATAAA
29217116 AAAATTTATATTTAATAA
1 AAAA-TTATATTTAATAA
29217134 TTATCTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTATATTTAATAAA
Found at i:29219422 original size:49 final size:49
Alignment explanation
Indices: 29219349--29219501 Score: 162
Period size: 49 Copynumber: 3.1 Consensus size: 49
29219339 AAGCTAGCCC
* * * *
29219349 GTGTTGTCCACACAGTCTACCCACATGGTTTGCACGATTTCACACAGTT
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
* * * **
29219398 GTGTGGTCTACACGGGCTACCCACACGGTCTGCACGATTTCAGACAGCC
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
* ** * * * *
29219447 GTGTGGTCCACATGGTTTACCTACATGGTCTGTATGATTTCACACGGTT
1 GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
29219496 GTGTGG
1 GTGTGG
29219502 CACTGGGCAG
Statistics
Matches: 83, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
49 83 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (49 bp):
GTGTGGTCCACACGGGCTACCCACATGGTCTGCACGATTTCACACAGTT
Found at i:29226599 original size:36 final size:36
Alignment explanation
Indices: 29226555--29226626 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
29226545 AGCATAACTT
*
29226555 CACATCTTGGATTTCATTATCTC-AGTTTTCTTATCA
1 CACATCTTGGATTTCATTATCTCGA-TTTTCATATCA
29226591 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
1 CACATCTTGGATTTCATTATCTCGATTTTCATATCA
29226627 TTCTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 33 0.97
37 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (36 bp):
CACATCTTGGATTTCATTATCTCGATTTTCATATCA
Found at i:29227772 original size:13 final size:13
Alignment explanation
Indices: 29227754--29227779 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29227744 TTGGATCCGT
29227754 ACCAAAACAATCA
1 ACCAAAACAATCA
29227767 ACCAAAACAATCA
1 ACCAAAACAATCA
29227780 TGAAACATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCA
Found at i:29239283 original size:42 final size:42
Alignment explanation
Indices: 29239170--29239288 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 42
29239160 AAGAAAGCTC
* * * ***
29239170 ATACAATGCCAACGTCCCAAACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAAACATGGTCTTACACAAAATCAA
* * * *
29239212 ATAATGATGCCACTGTCCCATAA-AAGGTCTTACACAAAATCAT
1 AT-ACGATGCCAATGTCCCA-AACATGGTCTTACACAAAATCAA
29239255 ATACGATGCCAATGTCCCAAACATGGTCTTACAC
1 ATACGATGCCAATGTCCCAAACATGGTCTTACAC
29239289 GTAAATCTCA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.03
42 28 0.46
43 29 0.48
44 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.24
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAAACATGGTCTTACACAAAATCAA
Found at i:29240447 original size:15 final size:13
Alignment explanation
Indices: 29240414--29240438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29240404 ACAAACGACA
29240414 AAATTTTCACACG
1 AAATTTTCACACG
29240427 AAATTTTCACAC
1 AAATTTTCACAC
29240439 ATATAATTTG
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:29250391 original size:41 final size:40
Alignment explanation
Indices: 29250339--29250498 Score: 151
Period size: 41 Copynumber: 3.7 Consensus size: 40
29250329 AATATTTTTA
* *
29250339 TTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATATAT
1 TTTTTTAATTTTTTTAATTTTAAAATA-TTTTAAAATATAC
*
29250380 TTTTTTAATTTTTTTAATTTTAAAATTTTTTTAAAATTTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAA-TATTTTAAAA-----T---ATAC
*
29250429 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAA-ATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTAAAATATAC
29250468 TTTTTTAATTTTTGTTTTAATTTTTAAAATA
1 TTTTTTAA--TTT-TTTTAA-TTTTAAAATA
29250499 AATTTTTGGT
Statistics
Matches: 101, Mismatches: 5, Indels: 24
0.78 0.04 0.18
Matches are distributed among these distances:
39 12 0.12
41 35 0.35
42 7 0.07
43 10 0.10
46 1 0.01
48 8 0.08
49 28 0.28
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (40 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTAAAATATAC
Found at i:29250391 original size:49 final size:49
Alignment explanation
Indices: 29250333--29250492 Score: 143
Period size: 49 Copynumber: 3.2 Consensus size: 49
29250323 ATAATAAATA
* *
29250333 TTTTT-ATTTTTTTATTTTTTTAATTTTAAAATACTTTTAAAATATATT
1 TTTTTAATTTTTTTATTTTTATAATTTTAAAATACTTTTTAAATATATT
* * *
29250381 TTTTTAATTTTTTTAATTTTAAAATTTTTTTAAAAT--TTTTTAAA-ATACT
1 TTTTTAATTTTTTTATTTTTATAA---TTTTAAAATACTTTTTAAATATATT
* * *
29250430 TTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAT-T-TT
1 TTTTTAATTTTTTT-ATTTT--TATAATTTTAAAATACTTTTTAAATATATT
29250480 TGTTTTAATTTTT
1 T-TTTTAATTTTT
29250493 AAAATAAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
48 5 0.06
49 42 0.47
50 13 0.14
51 19 0.21
52 11 0.12
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (49 bp):
TTTTTAATTTTTTTATTTTTATAATTTTAAAATACTTTTTAAATATATT
Found at i:29250411 original size:11 final size:11
Alignment explanation
Indices: 29250397--29250445 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
29250387 ATTTTTTTAA
29250397 TTTTAAAATTT
1 TTTTAAAATTT
29250408 TTTTAAAA-TT
1 TTTTAAAATTT
29250418 TTTTAAAATACTT
1 TTTTAAAAT--TT
29250431 TTTT--AATTT
1 TTTTAAAATTT
29250440 TTTTAA
1 TTTTAA
29250446 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
9 6 0.18
10 10 0.30
11 11 0.33
13 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:29250423 original size:21 final size:21
Alignment explanation
Indices: 29250397--29250480 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
29250387 ATTTTTTTAA
29250397 TTTTAAAAT-TTTTTTAAAATT
1 TTTTAAAATATTTTTT-AAATT
29250418 TTTTAAAATACTTTTTT-AATT
1 TTTTAAAATA-TTTTTTAAATT
* *
29250439 TTTT----TAATTTTAAAATAT
1 TTTTAAAATATTTTTTAAAT-T
29250457 TTTTAAAATACTTTTTT-AATT
1 TTTTAAAATA-TTTTTTAAATT
29250478 TTT
1 TTT
29250481 GTTTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 5 0.10
21 21 0.42
22 5 0.10
23 10 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAAATATTTTTTAAATT
Found at i:29250449 original size:8 final size:9
Alignment explanation
Indices: 29250378--29250449 Score: 65
Period size: 9 Copynumber: 7.6 Consensus size: 9
29250368 TTTAAAATAT
29250378 ATTTTTTTA
1 ATTTTTTTA
29250387 ATTTTTTTA
1 ATTTTTTTA
**
29250396 A-TTTTAAA
1 ATTTTTTTA
29250404 ATTTTTTTAAA
1 ATTTTTTT--A
*
29250415 ATTTTTTAAA
1 ATTTTTT-TA
29250425 ATACTTTTTTA
1 AT--TTTTTTA
29250436 ATTTTTTTA
1 ATTTTTTTA
29250445 ATTTT
1 ATTTT
29250450 AAAATATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
8 6 0.12
9 26 0.51
10 3 0.06
11 11 0.22
12 5 0.10
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:29250460 original size:39 final size:42
Alignment explanation
Indices: 29250407--29250498 Score: 147
Period size: 39 Copynumber: 2.3 Consensus size: 42
29250397 TTTTAAAATT
29250407 TTTTTAAAAT-TTTTTAAAATACTTTTTTAA-TTT-TTTTAA
1 TTTTTAAAATATTTTTAAAATACTTTTTTAATTTTGTTTTAA
29250446 -TTTTAAAATATTTTTAAAATACTTTTTTAATTTTTGTTTTAA
1 TTTTTAAAATATTTTTAAAATACTTTTTTAA-TTTTGTTTTAA
29250488 TTTTTAAAATA
1 TTTTTAAAATA
29250499 AATTTTTGGT
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 9 0.19
39 20 0.42
41 3 0.06
42 6 0.12
43 10 0.21
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (42 bp):
TTTTTAAAATATTTTTAAAATACTTTTTTAATTTTGTTTTAA
Found at i:29250471 original size:28 final size:28
Alignment explanation
Indices: 29250418--29250471 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
29250408 TTTTAAAATT
* **
29250418 TTTTAAAATACTTTTTTAATTTTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
29250446 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
29250472 TTAATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:29250494 original size:49 final size:49
Alignment explanation
Indices: 29250356--29250492 Score: 161
Period size: 49 Copynumber: 2.7 Consensus size: 49
29250346 ATTTTTTTAA
* *
29250356 TTTTAAAATACTTTTAAAATATATTTTTTTAATTTTTTTAATTTTAAAATTT
1 TTTTAAAATACTTTTTAAAT-T-TTTTTTTAA-TTTTTTAATTTTAAAATAT
**
29250408 TTTTAAAAT--TTTTTAAAATACTTTTTTAATTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTT-AAATTTTTTTTTAA-TTTTTTAATTTTAAAATAT
*
29250457 TTTTAAAATACTTTTTTAATTTTTGTTTTAATTTTT
1 TTTTAAAATACTTTTTAAATTTTT-TTTTAATTTTT
29250493 AAAATAAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
49 36 0.49
50 14 0.19
51 15 0.20
52 9 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (49 bp):
TTTTAAAATACTTTTTAAATTTTTTTTTAATTTTTTAATTTTAAAATAT
Found at i:29251374 original size:25 final size:25
Alignment explanation
Indices: 29251344--29251392 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29251334 TTTCAACTCT
29251344 TATGAGCTTA-CTGTTACTCAGCTCA
1 TATGAGCTTATC-GTTACTCAGCTCA
*
29251369 TATGAGCTTATCGTTATTCAGCTC
1 TATGAGCTTATCGTTACTCAGCTC
29251393 GGAGGAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (25 bp):
TATGAGCTTATCGTTACTCAGCTCA
Found at i:29256520 original size:20 final size:19
Alignment explanation
Indices: 29256487--29256534 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
29256477 TCGTATTCGT
* *
29256487 ATTTT-ATTTTATTTTTAT
1 ATTTTAATTTAATTTTTAC
29256505 ATTTTTAATTTAATTTTTAC
1 A-TTTTAATTTAATTTTTAC
29256525 ATTTTAATTT
1 ATTTTAATTT
29256535 TTCTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTAATTTAATTTTTAC
Found at i:29256530 original size:14 final size:13
Alignment explanation
Indices: 29256493--29256536 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
29256483 TCGTATTTTA
*
29256493 TTTTATTTTTATAT
1 TTTTAATTTTA-AT
29256507 TTTTAA-TTTAAT
1 TTTTAATTTTAAT
29256519 TTTTACATTTTAAT
1 TTTTA-ATTTTAAT
29256533 TTTT
1 TTTT
29256537 CTTTTGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 7 0.26
13 5 0.19
14 15 0.56
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:29260384 original size:3 final size:3
Alignment explanation
Indices: 29260376--29260418 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
29260366 CCTATTCTTT
*
29260376 TTA TTA TTA TTA TTA TTA TT- TTCA TTA TTA TTTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA -TTA TTA TTA TTA
29260419 AATCTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:29262531 original size:50 final size:50
Alignment explanation
Indices: 29262339--29262530 Score: 242
Period size: 50 Copynumber: 3.8 Consensus size: 50
29262329 ATTTGGGTAA
* *
29262339 AGAGGTCCCATGTAAGACCATGTCTGGGACATGTCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
29262389 AGAGGTCCCATGTAAAACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
29262439 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCATCGACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
29262489 AGAACAT-CCATGTAAGACCATGTTTGGGGCATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
29262531 TGTTATTATC
Statistics
Matches: 122, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
50 120 0.98
51 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:29264692 original size:6 final size:6
Alignment explanation
Indices: 29264681--29264738 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
29264671 TTTTCAGCTC
* **
29264681 TATTTT TATTTT TATTATT T-TTAT TATTTT TATTATT T-TAGT TA-TTT
1 TATTTT TATTTT TATT-TT TATTTT TATTTT TATT-TT TATTTT TATTTT
29264728 TATTTT TATTT
1 TATTTT TATTT
29264739 CTTAGACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
5 7 0.17
6 28 0.68
7 6 0.15
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TATTTT
Found at i:29264729 original size:9 final size:9
Alignment explanation
Indices: 29264686--29264728 Score: 70
Period size: 9 Copynumber: 4.8 Consensus size: 9
29264676 AGCTCTATTT
29264686 TTATTTTTA
1 TTATTTTTA
29264695 TTATTTTTA
1 TTATTTTTA
29264704 TTATTTTTA
1 TTATTTTTA
29264713 TTA-TTTTA
1 TTATTTTTA
29264721 GTTATTTT
1 -TTATTTT
29264729 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 5 0.16
9 24 0.75
10 3 0.09
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (9 bp):
TTATTTTTA
Found at i:29269681 original size:18 final size:18
Alignment explanation
Indices: 29269660--29269698 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
29269650 AATTCTGTAA
29269660 TTAGTTTAAATTTGATCT
1 TTAGTTTAAATTTGATCT
*
29269678 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTGATCT
29269696 TTA
1 TTA
29269699 AATTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (18 bp):
TTAGTTTAAATTTGATCT
Found at i:29269923 original size:7 final size:7
Alignment explanation
Indices: 29269911--29269946 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
29269901 ACCTTCCAAG
29269911 CCCTTTC
1 CCCTTTC
29269918 CCCTTTC
1 CCCTTTC
*
29269925 CTCTTTC
1 CCCTTTC
29269932 CCCTTTC
1 CCCTTTC
*
29269939 CACTTTC
1 CCCTTTC
29269946 C
1 C
29269947 ATAATTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.03, C:0.53, G:0.00, T:0.44
Consensus pattern (7 bp):
CCCTTTC
Found at i:29273229 original size:142 final size:142
Alignment explanation
Indices: 29272973--29273261 Score: 560
Period size: 142 Copynumber: 2.0 Consensus size: 142
29272963 ATGTTGATTC
29272973 AAATATGTGCTTTATTGGTTTTCAATTCTGGATCATGCCCCAATTGATTGAGACAAAGAATTGAT
1 AAATATGTGCTTTATTGGTTTTCAATTCTGGATCATGCCCCAATTGATTGAGACAAAGAATTGAT
29273038 AATTTGCATTTATTCAGCTGTATTTTTTGCCTATGTTTGTTTTTCATAGGCATGTCTGTCCTGAA
66 AATTTGCATTTATTCAGCTGTATTTTTTGCCTATGTTTGTTTTTCATAGGCATGTCTGTCCTGAA
29273103 ACATTGTCAAAA
131 ACATTGTCAAAA
29273115 AAATATGTGCTTTATTGGTTTTCAATTCTGGATCATGCCCCAATTGATTGAGACAAAGAATTGAT
1 AAATATGTGCTTTATTGGTTTTCAATTCTGGATCATGCCCCAATTGATTGAGACAAAGAATTGAT
*
29273180 AATTTGCATTTATTCAGCTGTATTTTTTGCCTATGTTTGTTTTTCATAGGCATGTTTGTCCTGAA
66 AATTTGCATTTATTCAGCTGTATTTTTTGCCTATGTTTGTTTTTCATAGGCATGTCTGTCCTGAA
29273245 ACATTGTCAAAA
131 ACATTGTCAAAA
*
29273257 CAATA
1 AAATA
29273262 GTGGAACCCA
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 145 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (142 bp):
AAATATGTGCTTTATTGGTTTTCAATTCTGGATCATGCCCCAATTGATTGAGACAAAGAATTGAT
AATTTGCATTTATTCAGCTGTATTTTTTGCCTATGTTTGTTTTTCATAGGCATGTCTGTCCTGAA
ACATTGTCAAAA
Found at i:29273416 original size:77 final size:77
Alignment explanation
Indices: 29273289--29273449 Score: 304
Period size: 77 Copynumber: 2.1 Consensus size: 77
29273279 AAAAATTTAC
*
29273289 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGGTATAAGTATGTGTGTATATCTATA
1 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
*
29273354 CATAGACAATCA
66 AATAGACAATCA
29273366 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
1 TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
29273431 AATAGACAATCA
66 AATAGACAATCA
29273443 TTTTAAT
1 TTTTAAT
29273450 TGTTCTTCCT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (77 bp):
TTTTAATCTAGATGAATCATGACGTTTTGGTTATATATAGCTATAAGTATGTGTGTATATCTATA
AATAGACAATCA
Found at i:29274433 original size:11 final size:11
Alignment explanation
Indices: 29274417--29274454 Score: 76
Period size: 11 Copynumber: 3.5 Consensus size: 11
29274407 TTATAAAATG
29274417 ACAATATCTCA
1 ACAATATCTCA
29274428 ACAATATCTCA
1 ACAATATCTCA
29274439 ACAATATCTCA
1 ACAATATCTCA
29274450 ACAAT
1 ACAAT
29274455 TGATAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (11 bp):
ACAATATCTCA
Found at i:29277165 original size:16 final size:16
Alignment explanation
Indices: 29277144--29277185 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29277134 NNNNNNAATT
*
29277144 ATATATTTTAATTATA
1 ATATATTTTAATAATA
29277160 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
29277175 AT-TATGTTTAA
1 ATATAT-TTTAA
29277186 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:29277575 original size:16 final size:16
Alignment explanation
Indices: 29277554--29277589 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
29277544 GATTTGCTAT
29277554 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29277570 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
29277586 TACA
1 TACA
29277590 ACGAACCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:29280395 original size:25 final size:25
Alignment explanation
Indices: 29280345--29280396 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
29280335 TAACACATCC
* * * *
29280345 TCTGCTTTGTTCTGTTCTGTTCTAT
1 TCTGCTTTGCTCTGCTCTGCTATAT
29280370 TCTGCTTTGCTCTGCTCTGCTATAT
1 TCTGCTTTGCTCTGCTCTGCTATAT
29280395 TC
1 TC
29280397 AGTTCAGTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.06, C:0.25, G:0.15, T:0.54
Consensus pattern (25 bp):
TCTGCTTTGCTCTGCTCTGCTATAT
Found at i:29280968 original size:17 final size:18
Alignment explanation
Indices: 29280935--29280969 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29280925 AAAAGTCTAC
29280935 ATAAAATAAAATATAAAT
1 ATAAAATAAAATATAAAT
*
29280953 ATAAAA-AAATTATAAAT
1 ATAAAATAAAATATAAAT
29280970 TATGCTCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAATAAAATATAAAT
Found at i:29283898 original size:21 final size:20
Alignment explanation
Indices: 29283873--29283935 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
29283863 AATGGGTTTC
*
29283873 CTTTTAGCTCTTTTGAGCTT
1 CTTTTAGCTCTTATGAGCTT
* * *
29283893 CATTTTAACCCTTATGAGTTT
1 C-TTTTAGCTCTTATGAGCTT
*
29283914 CTGTTCAGCTCTTATGAGCTT
1 CT-TTTAGCTCTTATGAGCTT
29283935 C
1 C
29283936 CATTAAACCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (20 bp):
CTTTTAGCTCTTATGAGCTT
Found at i:29283924 original size:42 final size:42
Alignment explanation
Indices: 29283878--29283977 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
29283868 GTTTCCTTTT
* *
29283878 AGCTCTTTTGAGCTT-CATTTTAACCCTTATGAGTTTCTGTTC
1 AGCTCTTATGAGCTTCCA-TTAAACCCTTATGAGTTTCTGTTC
* *
29283920 AGCTCTTATGAGCTTCCATTAAACCCTTATGGGTTTCTGTTT
1 AGCTCTTATGAGCTTCCATTAAACCCTTATGAGTTTCTGTTC
* *
29283962 AGCACTTATGTGCTTC
1 AGCTCTTATGAGCTTC
29283978 TATGCAACCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCCATTAAACCCTTATGAGTTTCTGTTC
Found at i:29287726 original size:32 final size:32
Alignment explanation
Indices: 29287689--29287898 Score: 182
Period size: 32 Copynumber: 6.7 Consensus size: 32
29287679 AATCAAATTA
* *
29287689 GCAATATATAAATACATATACAAATCAATTCG
1 GCAATATATATATACATATACAATTCAATTCG
* ** * *
29287721 CCAATAGGTGTATACTTATACAA-TCAATTCG
1 GCAATATATATATACATATACAATTCAATTCG
*
29287752 GCAATATA-AGTAT--ATATACAATTCAAATCG
1 GCAATATATA-TATACATATACAATTCAATTCG
*
29287782 GCAATATA-AGTATATATATACAATTCAATTCG
1 GCAATATATA-TATACATATACAATTCAATTCG
* * * *
29287814 GCAATATGTGTATACCTATACAATTCAAATCG
1 GCAATATATATATACATATACAATTCAATTCG
* *
29287846 GCAATATA-AGTATATATATACAATTCAATTCA
1 GCAATATATA-TATACATATACAATTCAATTCG
* * *
29287878 ACAGTATATA-AAACATATACA
1 GCAATATATATATACATATACA
29287899 TTTAAATTTA
Statistics
Matches: 143, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
29 7 0.05
30 20 0.14
31 25 0.17
32 90 0.63
33 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (32 bp):
GCAATATATATATACATATACAATTCAATTCG
Found at i:29287849 original size:64 final size:62
Alignment explanation
Indices: 29287737--29287876 Score: 237
Period size: 64 Copynumber: 2.2 Consensus size: 62
29287727 GGTGTATACT
29287737 TATACAA-TCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
1 TATACAATTCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
**
29287798 TATACAATTCAATTCGGCAATATGTGTATACCTATACAATTCAAATCGGCAATATAAGTATATA
1 TATACAATTCAATTCGGCAATATAAGTATA--TATACAATTCAAATCGGCAATATAAGTATATA
29287862 TATACAATTCAATTC
1 TATACAATTCAATTC
29287877 AACAGTATAT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
61 7 0.09
62 20 0.27
64 47 0.64
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (62 bp):
TATACAATTCAATTCGGCAATATAAGTATATATACAATTCAAATCGGCAATATAAGTATATA
Found at i:29305773 original size:43 final size:44
Alignment explanation
Indices: 29305678--29305824 Score: 149
Period size: 43 Copynumber: 3.4 Consensus size: 44
29305668 CAAGATTACG
* * * *
29305678 TGTAAGACCATATCTGGGA-TA-TGGCATCGATATGAGAATTCA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
* *
29305720 TTTAAGACCATGTCTGGGAC-ATTGATATCGATATGTGATTTCA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
* * * * * *
29305763 TGTAATACCATGGCT-TGACTATTGGCATCGATACGTGATTACA
1 TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
*
29305806 TGTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
29305825 TATGGCATTG
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
42 21 0.25
43 60 0.72
44 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACTATTGACATCGATATGTGATTTCA
Found at i:29308631 original size:23 final size:23
Alignment explanation
Indices: 29308605--29308657 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
29308595 ATAAGTGCCA
29308605 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29308628 CACTTGA-ATGTAGCTGAAGCTAC
1 CAC-TGATATGTAGCCGAAGCTAC
29308651 CACTGAT
1 CACTGAT
29308658 CAATAACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Done.