Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015370.1 Kokia drynarioides strain JFW-HI SEQ_130417, 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: 443270
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1022 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:5068 original size:59 final size:59
Alignment explanation
Indices: 4997--5115 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
4987 ACAGCTATAA
*
4997 ATATAAAATTAAAAATTCCTAAAAGGGGTCCCCACTTTAAAATGTTCGAAAAAGTCTGC
1 ATATAAAATTAAAAATTCCTAAAAGGGGTCCCCACTTTAAAATGGTCGAAAAAGTCTGC
*
5056 ATATAAAATTAAAAATTTCTAAAAGGGGTCCCCACTTTAAAATGGTCGAAAAAGTCTGC
1 ATATAAAATTAAAAATTCCTAAAAGGGGTCCCCACTTTAAAATGGTCGAAAAAGTCTGC
5115 A
1 A
5116 GCATTGTCTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (59 bp):
ATATAAAATTAAAAATTCCTAAAAGGGGTCCCCACTTTAAAATGGTCGAAAAAGTCTGC
Found at i:12117 original size:21 final size:21
Alignment explanation
Indices: 12093--12165 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
12083 ATAAGTAATA
12093 CAATGTAAGATAATGTATATT
1 CAATGTAAGATAATGTATATT
* * * *
12114 CAATGTAA-CTATTCGTATCCTCA
1 CAATGTAAGATAAT-GTAT-AT-T
*
12137 CAATGTAAGATAATGAATATT
1 CAATGTAAGATAATGTATATT
12158 CAATGTAA
1 CAATGTAA
12166 CTATTCGTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
20 3 0.08
21 20 0.51
22 2 0.05
23 11 0.28
24 3 0.08
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
CAATGTAAGATAATGTATATT
Found at i:12142 original size:44 final size:44
Alignment explanation
Indices: 12092--12179 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
12082 AATAAGTAAT
*
12092 ACAATGTAAGATAATGTATATTCAATGTAACTATTCGTATCCTC
1 ACAATGTAAGATAATGAATATTCAATGTAACTATTCGTATCCTC
12136 ACAATGTAAGATAATGAATATTCAATGTAACTATTCGTATCCTC
1 ACAATGTAAGATAATGAATATTCAATGTAACTATTCGTATCCTC
12180 TCTAAATTCG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (44 bp):
ACAATGTAAGATAATGAATATTCAATGTAACTATTCGTATCCTC
Found at i:12581 original size:6 final size:6
Alignment explanation
Indices: 12570--12595 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12560 TGCCGCGAAA
12570 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
12596 ACGTCCTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:21385 original size:16 final size:16
Alignment explanation
Indices: 21361--21398 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
21351 TCATTCTCTC
21361 TTTTT-TTTTT-ACATA
1 TTTTTATTTTTGA-ATA
21376 TTTTTATTTTTGAATA
1 TTTTTATTTTTGAATA
21392 TTTTTAT
1 TTTTTAT
21399 AATTTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.24
16 15 0.71
17 1 0.05
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTATTTTTGAATA
Found at i:30567 original size:20 final size:21
Alignment explanation
Indices: 30516--30566 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 21
30506 TTTATATTTT
30516 TATAATTTTTAAAAGATTAAA
1 TATAATTTTTAAAAGATTAAA
30537 TCA-AATTTTTAAAAG-TTAAAA
1 T-ATAATTTTTAAAAGATT-AAA
30558 TATAATTTT
1 TATAATTTT
30567 ACCATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 3 0.11
21 23 0.85
22 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (21 bp):
TATAATTTTTAAAAGATTAAA
Found at i:31989 original size:5 final size:6
Alignment explanation
Indices: 31963--31996 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31953 GATGGTTGGC
**
31963 TTTTAT TTTTAT TTAAAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
31997 GTGGAGAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:34354 original size:47 final size:47
Alignment explanation
Indices: 34292--34382 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
34282 GTATTACCAA
* *
34292 GTCTATTTTTAGTAAATGCCAAAGAGCTTCTTAAATTTATTCATGTT
1 GTCTATTATTAGTAAATGCCAAAGAGCTTCATAAATTTATTCATGTT
* * *
34339 GTCTATTATTGGTAAATGTCAAAGAGCTTCATAAGTTTATTCAT
1 GTCTATTATTAGTAAATGCCAAAGAGCTTCATAAATTTATTCAT
34383 TTTAGAAACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (47 bp):
GTCTATTATTAGTAAATGCCAAAGAGCTTCATAAATTTATTCATGTT
Found at i:42481 original size:311 final size:310
Alignment explanation
Indices: 41906--42512 Score: 1036
Period size: 311 Copynumber: 2.0 Consensus size: 310
41896 TAATAACACT
41906 CTCTTGTAATTACCAAGAATTGTAATTCTCTAGATGTATTTGGCTGACAAAATGTAATCACATCG
1 CTCTTGTAATTACCAAGAATTGTAATTCTCTAGATGTATTTGGCTGACAAAATGTAATCACATCG
41971 TTAATATATTATATTTGTTAGGTTGTGCACTCTTTAATGTTTAACGTATGCTCTTTATCATCATC
66 TTAATATATTATATTTGTTAGGTTGTGCACTCTTTAATGTTTAACGTATGCTCTTTATCATCATC
* *
42036 ATTTGAATTTGAATTTGCATAATTAAGATTATGAAGATCTTCTTCTAAGTACTCTTTGAAGAATG
131 ATTTGAATTTGAATTTGCATAATTAAGATTATGAAGATCTCCTTCCAAGTACTCTTTGAAGAATG
* * * * * * *
42101 AATCATTTCAATTTTACTTATGATTGAAGTTATGAATTATACAATATGTTAATACGATCTAAGTT
196 AATCATTCCAATTCTACTTATGATTGAAGTTATGAAATATACAACATGCTAATACAATCTAAATT
*
42166 TTTTTTATGCTATATTAAGATGATGTTAATAAGAGATTTTTTTTACAACA
261 TTTTTTATGCTATACTAAGATGATGTTAATAAGAGATTTTTTTTACAACA
*
42216 CTCTTGTAATTACCAAGAATTGTAATTCTCTAGATGTGTTTGGCTGACAAAATGTAATCACATC-
1 CTCTTGTAATTACCAAGAATTGTAATTCTCTAGATGTATTTGGCTGACAAAATGTAATCACATCG
* *
42280 TCTAATATATTATATTTGTTAGGTTGTGCACTCTTTAATATTTTAATGTATGCTCTTTATCATCA
66 T-TAATATATTATATTTGTTAGGTTGTGCACTCTTTAAT-GTTTAACGTATGCTCTTTATCATCA
* * * *
42345 TCATTTGAATTTGAATTTGCATCATTAAGATTATGAAGATCTCCTTCCACGTATTCTTTGAAGCA
129 TCATTTGAATTTGAATTTGCATAATTAAGATTATGAAGATCTCCTTCCAAGTACTCTTTGAAGAA
42410 TGAATCATTCCAATTCTACTTATGATTGAAGTTATGAAATATACAACATGCTAATACAATCTAAA
194 TGAATCATTCCAATTCTACTTATGATTGAAGTTATGAAATATACAACATGCTAATACAATCTAAA
42475 TTTTTTTTATGCTATACTAAGATGATGTTAATAAGAGA
259 TTTTTTTTATGCTATACTAAGATGATGTTAATAAGAGA
42513 AATATTTTTT
Statistics
Matches: 278, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
309 1 0.00
310 100 0.36
311 177 0.64
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (310 bp):
CTCTTGTAATTACCAAGAATTGTAATTCTCTAGATGTATTTGGCTGACAAAATGTAATCACATCG
TTAATATATTATATTTGTTAGGTTGTGCACTCTTTAATGTTTAACGTATGCTCTTTATCATCATC
ATTTGAATTTGAATTTGCATAATTAAGATTATGAAGATCTCCTTCCAAGTACTCTTTGAAGAATG
AATCATTCCAATTCTACTTATGATTGAAGTTATGAAATATACAACATGCTAATACAATCTAAATT
TTTTTTATGCTATACTAAGATGATGTTAATAAGAGATTTTTTTTACAACA
Found at i:47736 original size:22 final size:22
Alignment explanation
Indices: 47687--47737 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
47677 AACTGGATTG
*
47687 AGATTTTTAAATAAAAAATTTA
1 AGATTTTTAAATAAAAAATTCA
* *
47709 AGATTTTTAAGTACAAAATCTCA
1 AGATTTTTAAATAAAAAAT-TCA
47732 A-ATTTT
1 AGATTTT
47738 AACAAAATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (22 bp):
AGATTTTTAAATAAAAAATTCA
Found at i:54533 original size:104 final size:104
Alignment explanation
Indices: 54346--54554 Score: 373
Period size: 104 Copynumber: 2.0 Consensus size: 104
54336 TTAATATTTA
*
54346 ATCTGTTTAATACCAGAGCACATACGTGTATGCATGCTTTCTGCTGTGAATGAAATTGTTTAGAA
1 ATCTGTTTAATACCAGAGCACAGACGTGTATGCATGCTTTCTGCTGTGAATGAAATTGTTTAGAA
* *
54411 ATACAAAATGGAGTTGTGGTGTTATACACACACATATAT
66 AGACAAAATGGAGCTGTGGTGTTATACACACACATATAT
* *
54450 ATCTTTTTAATACCAGAGCACAGACGTGTATGCATGCTTTCTTCTGTGAATGAAATTGTTTAGAA
1 ATCTGTTTAATACCAGAGCACAGACGTGTATGCATGCTTTCTGCTGTGAATGAAATTGTTTAGAA
54515 AGACAAAATGGAGCTGTGGTGTTATACACACACATATAT
66 AGACAAAATGGAGCTGTGGTGTTATACACACACATATAT
54554 A
1 A
54555 CATATACTGT
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (104 bp):
ATCTGTTTAATACCAGAGCACAGACGTGTATGCATGCTTTCTGCTGTGAATGAAATTGTTTAGAA
AGACAAAATGGAGCTGTGGTGTTATACACACACATATAT
Found at i:60514 original size:13 final size:13
Alignment explanation
Indices: 60496--60523 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
60486 AATTATGACA
60496 TAGTAAACATTAG
1 TAGTAAACATTAG
60509 TAGTAAACATTAG
1 TAGTAAACATTAG
60522 TA
1 TA
60524 ATCAGCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.32
Consensus pattern (13 bp):
TAGTAAACATTAG
Found at i:60998 original size:58 final size:58
Alignment explanation
Indices: 60908--61018 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
60898 AAATAATATG
** *
60908 ACAGAATAAACATTAGTGATTCAAGAATGTAAACATTGATGCAGCTTCTATAAGTACA
1 ACAGAATAAACATTAGTGATTCAAGAATGTAAACATCAATGAAGCTTCTATAAGTACA
* * *
60966 ACAGAGTAAACATTAGTGATT-AGCGGATGTAAACATCAATGAAGCTTCTATAA
1 ACAGAATAAACATTAGTGATTCA-AGAATGTAAACATCAATGAAGCTTCTATAA
61019 TTAACTAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 1 0.02
58 45 0.98
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (58 bp):
ACAGAATAAACATTAGTGATTCAAGAATGTAAACATCAATGAAGCTTCTATAAGTACA
Found at i:61275 original size:58 final size:58
Alignment explanation
Indices: 61192--61301 Score: 195
Period size: 58 Copynumber: 1.9 Consensus size: 58
61182 AAATTATGAA
*
61192 AGTAAACATTAGTGATTCAAGGATGTAAACATTGATGCAGCTTCTATAATTATAACAG
1 AGTAAACATTAGTGATTCAAGGATGTAAACATCGATGCAGCTTCTATAATTATAACAG
61250 AGTAAACATTAGTGATTCACA-GATGTAAACATCGATGCAGCTTCTATAATTA
1 AGTAAACATTAGTGATTCA-AGGATGTAAACATCGATGCAGCTTCTATAATTA
61302 ACTAAAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
58 49 0.98
59 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (58 bp):
AGTAAACATTAGTGATTCAAGGATGTAAACATCGATGCAGCTTCTATAATTATAACAG
Found at i:61306 original size:280 final size:284
Alignment explanation
Indices: 60801--61377 Score: 916
Period size: 280 Copynumber: 2.0 Consensus size: 284
60791 GAGTCAATGG
60801 ATAGTAAACATTAATGATTCATAATCATAAACATTGATATCTAACAAAAGAATTAAAGACCAACA
1 ATAGTAAACATTAATGATTCATAATCATAAACATTGATATCTAACAAAAGAATTAAAGACCAACA
* *
60866 AAACAAGCAAATTGGTTTTCGTAAATATTCTCAAATAATATGACAGAATAAACATTAGTGATTCA
66 AAACAAGCAAATTGGATTTCATAAATATTCTCAAATAATATGACAGAATAAACATTAGTGATTCA
*
60931 AGAATGTAAACATTGATGCAGCTTCTATAAGTACAACAGAGTAAACATTAGTGATTAGCGGATGT
131 AGAATGTAAACATTGATGCAGCTTCTATAAGTACAACAGAGTAAACATTAGTGATTAGCAGATGT
*
60996 AAACATCAATGAAGCTTCTATAATTAACTAAAGAATCATATGTAATAGGACAACAAGCGGATAGG
196 AAACATCAATGAAGCTTCTATAATTAACTAAAGAATCATATGTAATAGGACAACAAGCAGATAGG
* *
61061 ACACAAATATTCTCAAATTATGAC
261 ACACAAATACTATCAAATTATGAC
* * *
61085 ATAGTAAACATTAATGATTCATAATCATAAACATTGATATCTAACAAAGGATTTAAA-AGCCAAG
1 ATAGTAAACATTAATGATTCATAATCATAAACATTGATATCTAACAAAAGAATTAAAGA-CCAAC
* *
61149 AAAACAAGCAAATTGGATTTCATAAATATTC-CAAA-ATTATGA-A-AGTAAACATTAGTGATTC
65 AAAACAAGCAAATTGGATTTCATAAATATTCTCAAATAATATGACAGAATAAACATTAGTGATTC
* * *
61210 AAGGATGTAAACATTGATGCAGCTTCTATAATTATAACAGAGTAAACATTAGTGATTCA-CAGAT
130 AAGAATGTAAACATTGATGCAGCTTCTATAAGTACAACAGAGTAAACATTAGTGATT-AGCAGAT
* * *
61274 GTAAACATCGATGCAGCTTCTATAATTAACTAAAGAATCATATGTAGTAGGACAACAAGCAGATA
194 GTAAACATCAATGAAGCTTCTATAATTAACTAAAGAATCATATGTAATAGGACAACAAGCAGATA
*
61339 GGACACAAATACTATCATATTATGAC
259 GGACACAAATACTATCAAATTATGAC
61365 ATAAG-AAACATTA
1 AT-AGTAAACATTA
61378 GTGAATCGCG
Statistics
Matches: 272, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
280 169 0.62
281 4 0.01
282 6 0.02
283 5 0.02
284 88 0.32
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (284 bp):
ATAGTAAACATTAATGATTCATAATCATAAACATTGATATCTAACAAAAGAATTAAAGACCAACA
AAACAAGCAAATTGGATTTCATAAATATTCTCAAATAATATGACAGAATAAACATTAGTGATTCA
AGAATGTAAACATTGATGCAGCTTCTATAAGTACAACAGAGTAAACATTAGTGATTAGCAGATGT
AAACATCAATGAAGCTTCTATAATTAACTAAAGAATCATATGTAATAGGACAACAAGCAGATAGG
ACACAAATACTATCAAATTATGAC
Found at i:62473 original size:18 final size:18
Alignment explanation
Indices: 62452--62493 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
62442 TTTTTAATTT
62452 TAATTATATT-TTATAGAA
1 TAATTATATTATTAT-GAA
* *
62470 TAATAATATTATTATTAA
1 TAATTATATTATTATGAA
62488 TAATTA
1 TAATTA
62494 AAATAACGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TAATTATATTATTATGAA
Found at i:67183 original size:119 final size:119
Alignment explanation
Indices: 66972--67209 Score: 476
Period size: 119 Copynumber: 2.0 Consensus size: 119
66962 CTGATCATTT
66972 ACATCACCATCTCCATTGCAGCTATAAACCAGAAAAAATAATCAGTAAAGAAGGAAATAAACATG
1 ACATCACCATCTCCATTGCAGCTATAAACCAGAAAAAATAATCAGTAAAGAAGGAAATAAACATG
67037 AAATAGGAACCCAATTTCTTTTCCTGATAGGAAAATAAAATGAAAGAAAGTTGA
66 AAATAGGAACCCAATTTCTTTTCCTGATAGGAAAATAAAATGAAAGAAAGTTGA
67091 ACATCACCATCTCCATTGCAGCTATAAACCAGAAAAAATAATCAGTAAAGAAGGAAATAAACATG
1 ACATCACCATCTCCATTGCAGCTATAAACCAGAAAAAATAATCAGTAAAGAAGGAAATAAACATG
67156 AAATAGGAACCCAATTTCTTTTCCTGATAGGAAAATAAAATGAAAGAAAGTTGA
66 AAATAGGAACCCAATTTCTTTTCCTGATAGGAAAATAAAATGAAAGAAAGTTGA
67210 CTTTTATTCA
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (119 bp):
ACATCACCATCTCCATTGCAGCTATAAACCAGAAAAAATAATCAGTAAAGAAGGAAATAAACATG
AAATAGGAACCCAATTTCTTTTCCTGATAGGAAAATAAAATGAAAGAAAGTTGA
Found at i:69647 original size:16 final size:15
Alignment explanation
Indices: 69619--69656 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
69609 AATTATCTAG
69619 AAATATTTTTATTTT
1 AAATATTTTTATTTT
69634 -AATATTTATATATTTT
1 AAATATTT-T-TATTTT
69650 AAATATT
1 AAATATT
69657 GTTAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 7 0.35
15 1 0.05
16 6 0.30
17 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AAATATTTTTATTTT
Found at i:69663 original size:10 final size:9
Alignment explanation
Indices: 69628--69668 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
69618 GAAATATTTT
69628 TATTTT-AA
1 TATTTTAAA
*
69636 TA-TTTATA
1 TATTTTAAA
69644 TATTTTAAA
1 TATTTTAAA
69653 TATTGTTAAA
1 TATT-TTAAA
69663 TATTTT
1 TATTTT
69669 TACAGATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
7 3 0.11
8 5 0.18
9 11 0.39
10 9 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (9 bp):
TATTTTAAA
Found at i:70760 original size:18 final size:20
Alignment explanation
Indices: 70724--70768 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
70714 GATCAAAACA
*
70724 ATTATTA-AAATAACCTTAT
1 ATTATTATAAATAACATTAT
70743 A-TATTATAAATAA-ATTAT
1 ATTATTATAAATAACATTAT
70761 ATTATTAT
1 ATTATTAT
70769 GATAGTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTATTATAAATAACATTAT
Found at i:72274 original size:20 final size:20
Alignment explanation
Indices: 72222--72275 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
72212 TCTATTAAAC
72222 ATTAAATTAATATATAAATTT
1 ATTAAATT-ATATATAAATTT
**
72243 ATTAAAAAATATATAAATTT
1 ATTAAATTATATATAAATTT
72263 -TTGAAATTATATA
1 ATT-AAATTATATA
72276 AGAAAGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.07
20 20 0.71
21 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTAAATTATATATAAATTT
Found at i:79595 original size:23 final size:23
Alignment explanation
Indices: 79569--79620 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
79559 TAAATTAAAT
*
79569 AAATATCCATA-TTTATATTATTA
1 AAATATCAATATTTTATATTA-TA
* *
79592 AAATATTAATATTTTGTATTATA
1 AAATATCAATATTTTATATTATA
79615 AAATAT
1 AAATAT
79621 TTGTTATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATATCAATATTTTATATTATA
Found at i:79859 original size:20 final size:20
Alignment explanation
Indices: 79830--79868 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
79820 AATATTTGAG
*
79830 ATTAATATTTTAATATTAAA
1 ATTAAGATTTTAATATTAAA
*
79850 ATTAAGATTTTATTATTAA
1 ATTAAGATTTTAATATTAA
79869 TATACTAATA
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTAAGATTTTAATATTAAA
Found at i:80150 original size:22 final size:21
Alignment explanation
Indices: 80099--80151 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
80089 AAACAAATTG
*
80099 TTTATCTT-ATTTTATTAATA
1 TTTATTTTCATTTTATTAATA
* *
80119 TATTACTTTCATTTTATTATTTA
1 T-TTATTTTCATTTTATTA-ATA
80142 TTTATTTTCA
1 TTTATTTTCA
80152 GTTGAATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 5 0.19
22 17 0.65
23 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTTTCATTTTATTAATA
Found at i:80692 original size:13 final size:12
Alignment explanation
Indices: 80669--80718 Score: 57
Period size: 13 Copynumber: 4.0 Consensus size: 12
80659 AATTGGAAAG
80669 ATATTAAATTAA
1 ATATTAAATTAA
80681 ATATTGAAATTAA
1 ATATT-AAATTAA
80694 AT-TTAAGTATTAA
1 ATATTAA--ATTAA
*
80707 ATAATAAATTAA
1 ATATTAAATTAA
80719 CCTTTAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 2 0.06
12 12 0.36
13 16 0.48
14 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (12 bp):
ATATTAAATTAA
Found at i:80718 original size:19 final size:18
Alignment explanation
Indices: 80671--80718 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
80661 TTGGAAAGAT
80671 ATTAAATTAAATATTGAA
1 ATTAAATTAAATATTGAA
*
80689 ATTAAATTTAAGTATT-AA
1 ATTAAA-TTAAATATTGAA
80707 ATAATAAATTAA
1 AT--TAAATTAA
80719 CCTTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
ATTAAATTAAATATTGAA
Found at i:83474 original size:199 final size:203
Alignment explanation
Indices: 83125--83702 Score: 567
Period size: 204 Copynumber: 2.9 Consensus size: 203
83115 TTTTCTTTTT
* ** * * * *
83125 TATGCGAAGTATGGTTGTTTTTATTGTTGATTCATGAGTATGTTGACTTAAAATTTTTAACAATA
1 TATGCGAAATATAATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAAA-TTTTAACAATG
* * * * * *
83190 TTGATCTTTGATGGTGACCGGAAGGTTGTTACGTAATTTAATTTT-CAGTTTCAGTTAAATTTGA
65 TTGATCTTTGATGATGGCCGAAAGGTTGTTACGCAATTTAATTTTCCATTTTTAG-TAAATTTGA
* * * *
83254 ATGCTTCGGTTCCCATTTTTTTTTTAC-TCTTAGATGCTTTACATTACAATTTCAAAAATTTTCA
129 ATGCTTCGATTTCCATTTTTTTTTCACTTCTTAGATGCTTTACATTACAATTTCAAAAA-TTTAA
83318 AAAAA-T-A-A
193 AAAAATTCATA
* *
83326 TA-GCGAAATATTATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAAATTTCAACAATGT
1 TATGCGAAATATAATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAAATTTTAACAATGT
* *
83390 TGATCTTTGATGATGGCCGAAATGTT-TTACGCAATATAATTTTTCCATTTTTAG-AGAATTTGA
66 TGATCTTTGATGATGGCCGAAAGGTTGTTACGCAATTTAA-TTTTCCATTTTTAGTA-AATTTGA
* ** * *
83453 ATGCTTCGATTTCCA--TTTTTTTCACTTTTTTTATTCTTTACGTTACAATTTCAAAAATTTAAA
129 ATGCTTCGATTTCCATTTTTTTTTCACTTCTTAGATGCTTTACATTACAATTTCAAAAATTTAAA
*
83516 AAAATTCATTTTT
194 AAAATTCA---TA
* ** * ** **
83529 TATGCGAAGTATAATTGTTTTTGTTCATGATCCACGAATACATTGACTTAAGCTTTTAACAATGT
1 TATGCGAAATATAATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAAATTTTAACAATGT
* * *
83594 TGATCTTTGATGGTTGGCCGAAAGGTTGCTAC-CAAATTTGATTTTCCATTTTATAGTTAAATTT
66 TGATCTTTGAT-GATGGCCGAAAGGTTGTTACGC-AATTTAATTTTCCATTTT-TAG-TAAA-TT
*
83658 TGAATGCTTCGA-TTCTCA---ATTTTTCACTT-TTAGATGCTTTACATT
126 TGAATGCTTCGATTTC-CATTTTTTTTTCACTTCTTAGATGCTTTACATT
83703 TCACTTCCAA
Statistics
Matches: 312, Mismatches: 46, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
197 18 0.06
198 39 0.12
199 57 0.18
200 51 0.16
201 2 0.01
203 2 0.01
204 63 0.20
205 25 0.08
206 23 0.07
207 15 0.05
208 17 0.05
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.45
Consensus pattern (203 bp):
TATGCGAAATATAATTGTTTTTGTTGTTGATCCATGAATATGTTGACTTAAAATTTTAACAATGT
TGATCTTTGATGATGGCCGAAAGGTTGTTACGCAATTTAATTTTCCATTTTTAGTAAATTTGAAT
GCTTCGATTTCCATTTTTTTTTCACTTCTTAGATGCTTTACATTACAATTTCAAAAATTTAAAAA
AATTCATA
Found at i:100035 original size:106 final size:106
Alignment explanation
Indices: 99850--100061 Score: 397
Period size: 106 Copynumber: 2.0 Consensus size: 106
99840 CTAATTTGTC
*
99850 GGTACTTGGGAAACCCTGATATATAGGAGTTATTTTATGATACTATTAAAGGTCTTCATATCCTT
1 GGTACTTGGGAAACCATGATATATAGGAGTTATTTTATGATACTATTAAAGGTCTTCATATCCTT
99915 GGACAATTCTAAAATTTTCTTTTCGTTTTACATTTTGACAA
66 GGACAATTCTAAAATTTTCTTTTCGTTTTACATTTTGACAA
*
99956 GGTACTTGGGAAACCATGATATATAGGAGTTATTTTCTGATACTATTAAAGGTCTTCATATCCTT
1 GGTACTTGGGAAACCATGATATATAGGAGTTATTTTATGATACTATTAAAGGTCTTCATATCCTT
*
100021 GGCCAATTCTAAAATTTTCTTTTCGTTTTACATTTTGACAA
66 GGACAATTCTAAAATTTTCTTTTCGTTTTACATTTTGACAA
100062 CAACAAATGT
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 103 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (106 bp):
GGTACTTGGGAAACCATGATATATAGGAGTTATTTTATGATACTATTAAAGGTCTTCATATCCTT
GGACAATTCTAAAATTTTCTTTTCGTTTTACATTTTGACAA
Found at i:101407 original size:218 final size:216
Alignment explanation
Indices: 101029--101662 Score: 878
Period size: 218 Copynumber: 2.9 Consensus size: 216
101019 AGCATGGTGA
* * *
101029 ATCATGATTTGTACATTTTATATGTAGGAATAGTGTGTTTTATTTCATAAAAAGACCTGCAAACT
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCA-CAAAAGACCTGCAAACT
* * * * *
101094 AGTTTAAACTCCTTGGCCTTGGAGGGTTTGTTCTTTGTATTTCTTTTTTGTAAAGTTG-TTTTGT
65 AGTGTAAGCTCCTTGGCCTTGGAAGGTTTGTT-TTTGTAATTCTTTTGTGTAAAGTTGTTTTTGT
* * **
101158 TTTCGATGTGGATGGTAGTTGCATTTGAAACATTTTATGAGGAGAAAGGCCATCATTCATGTATC
129 CTTCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGA-AAAGGCCATCATTCATGTATC
*
101223 TTGTCGTCATCCCTAGTTGAATGC
193 TTGTCGTCATCCCCAGTTGAATGC
* * *
101247 ATCATGATTTGTACATTTTATATGTAGGGATAGTATGTTTTATGTCACAATAGACCTGCAAATTA
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
* **
101312 GTGTAAGCTCCTTGGCCTTGGAAGGTTTGTGTTTTGTAATTCTCTTGCATAAAGTTGTTTTTGTC
66 GTGTAAGCTCCTTGGCCTTGGAAGGTTTGT-TTTTGTAATTCTTTTGTGTAAAGTTGTTTTTGTC
*
101377 TTCGATATGGATGGTAGTTGCATTTGAAACATTTTACAAAGGAAAAGGCCATCATTCATGCATCT
130 TTCGATATGGATGGTAGTTGCATTTGAAACATTTTA-AAAGGAAAAGGCCATCATTCATGTATCT
* *
101442 CGTCTTCATCCCCAGTTGAATGC
194 TGTCGTCATCCCCAGTTGAATGC
*
101465 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGTAAACTA
1 ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
* * *
101530 GTGTAAGCTCCTTGGCCTCT-G-AGTGTTTGCATTTTGTAGTTCTTTTGTGTAAAGTTGTGTTTG
66 GTGTAAGCTCCTTGGCCT-TGGAAG-GTTTG-TTTTTGTAATTCTTTTGTGTAAAGTTGTTTTTG
* * * * * * *
101593 TCTTCAATATGGATGGTAGTAGCATTTAAAACATTCTACAAGGAAAAGTCCATTATTCATGTATC
128 TCTTCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGAAAAGGCCATCATTCATGTATC
101658 TTGTC
193 TTGTC
101663 TTTTGATGTA
Statistics
Matches: 369, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
217 91 0.25
218 273 0.74
219 5 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (216 bp):
ATCATGATTTGTACATTTTATATGTAGGGATAGTGTGTTTTATGTCACAAAAGACCTGCAAACTA
GTGTAAGCTCCTTGGCCTTGGAAGGTTTGTTTTTGTAATTCTTTTGTGTAAAGTTGTTTTTGTCT
TCGATATGGATGGTAGTTGCATTTGAAACATTTTAAAAGGAAAAGGCCATCATTCATGTATCTTG
TCGTCATCCCCAGTTGAATGC
Found at i:105345 original size:152 final size:151
Alignment explanation
Indices: 105056--105363 Score: 535
Period size: 152 Copynumber: 2.0 Consensus size: 151
105046 TTGTAGTTAC
* *
105056 AGTAGAGTTATACAACCGTAGTTCAATCAGTGTTATTCTAGGTCTTGAGCATTGATTCGTTTTGT
1 AGTAGAGCTATACAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGATTCGTTTTGT
*
105121 CTACAACTTATCATCTACAATCATGGAATCCCAATCATTCACAATGGATCAATCCATCTAAATCT
66 CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATCT
105186 CATATTATCATCACTAGACCT
131 CATATTATCATCACTAGACCT
* * *
105207 AGTAGAGACTATATAACCGTAGTTCAATCGGTCTTATTCTAGGTCTTGAGCATTGGTTCGTTTTG
1 AGTAGAG-CTATACAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGATTCGTTTTG
* *
105272 TCTACAACTTATCATCTACGATCATGGAGTCCCAACCATTCACAATGGATCAATCCATCTAAATC
65 TCTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATC
105337 TCATATTATCATCACTAGACCT
130 TCATATTATCATCACTAGACCT
105359 AGTAG
1 AGTAG
105364 TTTTGGATAC
Statistics
Matches: 148, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
151 7 0.05
152 141 0.95
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (151 bp):
AGTAGAGCTATACAACCGTAGTTCAATCAGTCTTATTCTAGGTCTTGAGCATTGATTCGTTTTGT
CTACAACTTATCATCTACAATCATGGAATCCCAACCATTCACAATGGATCAATCCATCTAAATCT
CATATTATCATCACTAGACCT
Found at i:111065 original size:33 final size:31
Alignment explanation
Indices: 111028--111124 Score: 82
Period size: 33 Copynumber: 3.2 Consensus size: 31
111018 CAAAATAACA
111028 AAGAAATTAAAACTACACATCAAGCCAAAGGGC
1 AAGAAATTAAAACTAC-CATCAAGCCAAA-GGC
**
111061 AAGAAGA--AAAAC--CCA-CAAAACAAA--C
1 AAGAA-ATTAAAACTACCATCAAGCCAAAGGC
111086 AAGAAATTAAAACTACCCATCAAGCCAAAAGGC
1 AAGAAATTAAAACTA-CCATCAAGCC-AAAGGC
111119 AAGAAA
1 AAGAAA
111125 AACCCGCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
24 1 0.02
25 6 0.12
26 5 0.10
28 7 0.14
29 5 0.10
30 5 0.10
31 3 0.06
32 5 0.10
33 12 0.24
34 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (31 bp):
AAGAAATTAAAACTACCATCAAGCCAAAGGC
Found at i:111100 original size:58 final size:57
Alignment explanation
Indices: 110910--111262 Score: 352
Period size: 55 Copynumber: 6.3 Consensus size: 57
110900 CCCTCAAATT
* * * *
110910 AAAC-AAGAAACTAAAACTACCCATCAAGCCAAAAGGC-A-AAATAAACCTACAAAC
1 AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAACCCACAAAA
* * ** *
110964 TAACAAAGAAATTAAAATTACCCATCAAATCAGAAGGCAAGAAAAAAAAGCCCACAAAA
1 AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAG-AAAAAAA-CCCACAAAA
* * *
111023 TAACAAAGAAATTAAAACTACACATCAAGCCAAAGGGCAAGAAGAAAAACCCACAAAA
1 AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAA-AAAAACCCACAAAA
*
111081 CAAAC-AAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAG--AAAAACCCGCAAAA
1 -AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAACCCACAAAA
* * *
111136 TAACAAAGAAATTAACACTA--CATCAAG-CAGAAAGGCAAGAAAAAAATCCACAAAA
1 AAACAAAGAAATTAAAACTACCCATCAAGCCA-AAAGGCAAGAAAAAAACCCACAAAA
* * * * * * *
111191 AAACCAA-AAATTAGATCTACCCATCAAGTCAAAAGGC-A-ACAAAAACTCAAAAAA
1 AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAACCCACAAAA
*
111245 AAAAAAAGAAATTGAAAA
1 AAACAAAGAAATT-AAAA
111263 AAATGAGAAA
Statistics
Matches: 247, Mismatches: 36, Indels: 30
0.79 0.12 0.10
Matches are distributed among these distances:
52 2 0.01
53 16 0.06
54 32 0.13
55 78 0.32
56 16 0.06
57 2 0.01
58 51 0.21
59 50 0.20
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (57 bp):
AAACAAAGAAATTAAAACTACCCATCAAGCCAAAAGGCAAGAAAAAAACCCACAAAA
Found at i:111126 original size:29 final size:29
Alignment explanation
Indices: 111036--111127 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
111026 CAAAGAAATT
* *
111036 AAAACTACACATCAAGCCAAAGGGCAAGA
1 AAAACTACCCATCAAGCCAAAAGGCAAGA
* ** * * **
111065 AGAAA-AACCCA-CAAAACAAACAAGAAATT
1 A-AAACTACCCATCAAGCCAAA-AGGCAAGA
111094 AAAACTACCCATCAAGCCAAAAGGCAAGA
1 AAAACTACCCATCAAGCCAAAAGGCAAGA
111123 AAAAC
1 AAAAC
111128 CCGCAAAATA
Statistics
Matches: 43, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
28 10 0.23
29 23 0.53
30 10 0.23
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.07
Consensus pattern (29 bp):
AAAACTACCCATCAAGCCAAAAGGCAAGA
Found at i:111227 original size:109 final size:112
Alignment explanation
Indices: 110914--111262 Score: 365
Period size: 109 Copynumber: 3.1 Consensus size: 112
110904 CAAATTAAAC
* * * * *
110914 AAGAAACTAAAACTACCCATCAAGCCAAAAGGC-A-AA-ATAAACCTAC-AAACTAACAAAGAAA
1 AAGAAATTAAAACTA-ACATCAAGCCAAAAGGCAAGAAGAAAAACCCACAAAACAAAC-AAGAAA
* * *
110975 TTAAAATTACCCATCAAATCAGAAGGCAAGAAAAAAAAGCCCACAAAATAACA
64 TTAAAACTACCCATCAAGTCAAAAGGCAAG---AAAAA-CCCACAAAATAACA
*
111028 AAGAAATTAAAACTACACATCAAGCCAAAGGGCAAGAAGAAAAACCCACAAAACAAACAAGAAAT
1 AAGAAATTAAAACTA-ACATCAAGCCAAAAGGCAAGAAGAAAAACCCACAAAACAAACAAGAAAT
* *
111093 TAAAACTACCCATCAAGCCAAAAGGCAAGAAAAACCCGCAAAATAACA
65 TAAAACTACCCATCAAGTCAAAAGGCAAGAAAAACCCACAAAATAACA
* *
111141 AAGAAATTAACACT-ACATCAAG-CAGAAAGGCAAGAA-AAAAATCCACAAAA-AAACCAA-AAA
1 AAGAAATTAAAACTAACATCAAGCCA-AAAGGCAAGAAGAAAAACCCACAAAACAAA-CAAGAAA
* * * * * * *
111201 TTAGATCTACCCATCAAGTCAAAAGGCAACAAAAACTCAAAAAAAAAAA
64 TTAAAACTACCCATCAAGTCAAAAGGCAAGAAAAACCCACAAAATAACA
111250 AAGAAATTGAAAA
1 AAGAAATT-AAAA
111263 AAATGAGAAA
Statistics
Matches: 204, Mismatches: 24, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
109 54 0.26
110 21 0.10
111 18 0.09
113 26 0.13
114 35 0.17
115 1 0.00
116 2 0.01
117 40 0.20
118 7 0.03
ACGTcount: A:0.59, C:0.21, G:0.10, T:0.10
Consensus pattern (112 bp):
AAGAAATTAAAACTAACATCAAGCCAAAAGGCAAGAAGAAAAACCCACAAAACAAACAAGAAATT
AAAACTACCCATCAAGTCAAAAGGCAAGAAAAACCCACAAAATAACA
Found at i:113025 original size:19 final size:17
Alignment explanation
Indices: 113010--113081 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 17
113000 AAATTTTATG
113010 ATTATTTTATAATTTTT
1 ATTATTTTATAATTTTT
* *
113027 ATAAATTATATAAATTTTAAT
1 AT-TATTTTAT-AATTTT--T
*
113048 ATTTTTTTATAATTTTT
1 ATTATTTTATAATTTTT
113065 AATTAATTTTATAATTT
1 -ATT-ATTTTATAATTT
113082 ATTAAACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
17 3 0.07
18 9 0.21
19 23 0.53
20 5 0.12
21 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTTTATAATTTTT
Found at i:113028 original size:9 final size:9
Alignment explanation
Indices: 113014--113095 Score: 60
Period size: 9 Copynumber: 8.7 Consensus size: 9
113004 TTTATGATTA
113014 TTTTATAAT
1 TTTTATAAT
*
113023 TTTTATAAA
1 TTTTATAAT
*
113032 TTATATAAAT
1 TTTTAT-AAT
* *
113042 TTTAATATTT
1 TTTTATA-AT
113052 TTTTATAAT
1 TTTTATAAT
113061 TTTTAATTAA-
1 TTTT-A-TAAT
113071 TTTTATAAT
1 TTTTATAAT
113080 TTATTA-AACT
1 TT-TTATAA-T
113090 TTTTAT
1 TTTTAT
113096 TTTATAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.05
9 27 0.47
10 24 0.42
11 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:113056 original size:38 final size:38
Alignment explanation
Indices: 113000--113129 Score: 120
Period size: 38 Copynumber: 3.3 Consensus size: 38
112990 ATTCAATTAA
* *
113000 AAATTTT-ATGATTATTTTATAATTTTTATAAATTATAT
1 AAATTTTAAT-ATTTTTTTATAATTTTTATAAATTTTAT
*
113038 AAATTTTAATATTTTTTTATAATTTTTAATTAATTTTAT
1 AAATTTTAATATTTTTTTATAATTTTT-ATAAATTTTAT
* * * **
113077 AATTTATTAAACTTTTTATTTTATAATATTTA-CGATTTTAT
1 AAATT-TT-AA-TATTT-TTTTATAATTTTTATAAATTTTAT
113118 AAATTTTAATAT
1 AAATTTTAATAT
113130 ATGTATAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
38 25 0.33
39 17 0.22
40 4 0.05
41 13 0.17
42 5 0.07
43 12 0.16
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (38 bp):
AAATTTTAATATTTTTTTATAATTTTTATAAATTTTAT
Found at i:122449 original size:28 final size:28
Alignment explanation
Indices: 122418--122471 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
122408 TAGGGACTAA
* * *
122418 ATCAAATTAGTTCCTCTATTATTAAATG
1 ATCAAATTAATCCCTATATTATTAAATG
*
122446 ATCAATTTAATCCCTATATTATTAAA
1 ATCAAATTAATCCCTATATTATTAAA
122472 AAGAGTTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.43
Consensus pattern (28 bp):
ATCAAATTAATCCCTATATTATTAAATG
Found at i:132797 original size:212 final size:201
Alignment explanation
Indices: 132361--132865 Score: 636
Period size: 212 Copynumber: 2.4 Consensus size: 201
132351 AAATAAGCAG
* * *
132361 AATTTTCAGTTTTTGAGAACTAAAAATCAACAATGATGGTAAATAATAATTACCCAGAAAGCGAA
1 AATTTTCAG-TTTTGA-CACTAAAAATCAATAATTATGGTAAATAATAATTACCCAGAAAGCGAA
** * *
132426 AACAGATGGTTATCAAGTGCTTCAAGCCTAAAACTACATATTTCGATGAAAAAAAAAAATTGTGA
64 AATTGATGATTATCAAGTGCTTCAAGCCTAAAACTACATAATTCGATGAAAAAAAAAAATTGTGA
* ** * * *
132491 CAGCACAATGTATCGTCTTACTAATTCAATTATTCAGTAAGTAACTGACTTCGAACAATAACTAG
129 CAGCACAATATATAATCTTACTAATTCAATTATTCAGTAAATAACTGACTTCAAACAATAACTAC
*
132556 ATTGACAG
194 ATTGACAA
*
132564 AATTCTCAGTTTTGAACACTAAAAATCAATAATTATGAGTAAATAATAATTACCCAGAAAGCGAA
1 AATTTTCAGTTTTG-ACACTAAAAATCAATAATTATG-GTAAATAATAATTACCCAGAAAGCGAA
*
132629 AATTGATGATTATCAAGTGCTTCAAGCCTAAACTATTACATAATTCGATGGAAACAAAAATTCAA
64 AATTGATGATTATCAAGTGCTTCAAGCCTAAA--ACTACATAATTCGAT-GAAA-AAAAA---AA
* * * * *
132694 CTT-TAGAGGTAGCACAATATATAATTTTACTCATTCAATTATTCAGTAAATAATTGACTTCAAA
122 ATTGT-GA--CAGCACAATATATAATCTTACTAATTCAATTATTCAGTAAATAACTGACTTCAAA
*
132758 CAATAAGTACA-TGAACAA
184 CAATAACTACATTG-ACAA
132776 AATTTTCAGTTTTGCACACTAAAAATCAATAATTATGGGTAAATAATAATTACCCAGAAAGCGAA
1 AATTTTCAGTTTTG-ACACTAAAAATCAATAATTAT-GGTAAATAATAATTACCCAGAAAGCGAA
*
132841 TATTGATGATTATCAAGTGCTTCAA
64 AATTGATGATTATCAAGTGCTTCAA
132866 ACGAATTTAT
Statistics
Matches: 263, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
202 23 0.09
203 65 0.25
205 13 0.05
206 4 0.02
207 5 0.02
209 1 0.00
210 6 0.02
211 2 0.01
212 143 0.54
213 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (201 bp):
AATTTTCAGTTTTGACACTAAAAATCAATAATTATGGTAAATAATAATTACCCAGAAAGCGAAAA
TTGATGATTATCAAGTGCTTCAAGCCTAAAACTACATAATTCGATGAAAAAAAAAAATTGTGACA
GCACAATATATAATCTTACTAATTCAATTATTCAGTAAATAACTGACTTCAAACAATAACTACAT
TGACAA
Found at i:143272 original size:34 final size:34
Alignment explanation
Indices: 143229--143300 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
143219 ACCACAGCCC
143229 GACCCAATCTGATCAGCCCAATTCCAACCGACAG
1 GACCCAATCTGATCAGCCCAATTCCAACCGACAG
*
143263 GACCCAATCTGATCAGTCCAATTCCAACCGACAG
1 GACCCAATCTGATCAGCCCAATTCCAACCGACAG
143297 GACC
1 GACC
143301 GGTTTAGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.38, G:0.15, T:0.15
Consensus pattern (34 bp):
GACCCAATCTGATCAGCCCAATTCCAACCGACAG
Found at i:147295 original size:18 final size:17
Alignment explanation
Indices: 147276--147350 Score: 62
Period size: 17 Copynumber: 4.3 Consensus size: 17
147266 AAAAACTATC
147276 ATAATTTTAAAAATTTT
1 ATAATTTTAAAAATTTT
** *
147293 CATATATTTTTTAATTTTT
1 -ATA-ATTTTAAAAATTTT
*
147312 TTAATTTTAATAAATTTT
1 ATAATTTTAA-AAATTTT
* *
147330 AT-ATTTTATATATTTT
1 ATAATTTTAAAAATTTT
147346 ATAAT
1 ATAAT
147351 GCCACATCAA
Statistics
Matches: 44, Mismatches: 10, Indels: 7
0.72 0.16 0.11
Matches are distributed among these distances:
16 8 0.18
17 13 0.30
18 12 0.27
19 11 0.25
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTTAAAAATTTT
Found at i:147329 original size:16 final size:16
Alignment explanation
Indices: 147295--147348 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
147285 AAAATTTTCA
* *
147295 TATATTTTTTAATTTT
1 TATATTTTATAAATTT
*
147311 TTTAATTTTAATAAATTT
1 TAT-ATTTT-ATAAATTT
*
147329 TATATTTTATATATTT
1 TATATTTTATAAATTT
147345 TATA
1 TATA
147349 ATGCCACATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 10 0.32
18 8 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTTATAAATTT
Found at i:152455 original size:11 final size:11
Alignment explanation
Indices: 152439--152476 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
152429 TGTCATATCA
152439 ATAAAAAATAT
1 ATAAAAAATAT
152450 ATAAAAAAT-T
1 ATAAAAAATAT
152460 CAT-AAAAATAT
1 -ATAAAAAATAT
152471 ATAAAA
1 ATAAAA
152477 CTTAAAGCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:154526 original size:5 final size:6
Alignment explanation
Indices: 154509--154540 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
154499 CGTGATCATC
154509 TATTTT TATTTT TATTTT TATTTT TATATTT T
1 TATTTT TATTTT TATTTT TATTTT TAT-TTT T
154541 TAAGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:156798 original size:18 final size:18
Alignment explanation
Indices: 156775--156817 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
156765 ATTTGTAAAA
156775 ATTATTTTGCTTTTCATT
1 ATTATTTTGCTTTTCATT
* * *
156793 ATTATTGTGTTTTTCTTT
1 ATTATTTTGCTTTTCATT
156811 ATT-TTTT
1 ATTATTTT
156818 TTAATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (18 bp):
ATTATTTTGCTTTTCATT
Found at i:159645 original size:42 final size:42
Alignment explanation
Indices: 159598--159893 Score: 448
Period size: 42 Copynumber: 7.0 Consensus size: 42
159588 ACCAAATGAG
* *
159598 GAATTGGTAGCTGATGAGACCAATGTTGCTGCTGTATCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* * * *
159640 GAATTGGTAGCTGATGATACCAATGTTGCTTCTGTATCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* * *
159682 GAATTGGTGGCTGATGAGACCAATGATGTTGTTGTTTCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* *
159724 GAATTGGTGGCTGATGAGACCAATGATGCTGTTGTTTCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* *
159766 GAATTGGTAGCTGATGAGACCAATGATGTTGTTGTTTCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
*
159808 GAATTGGTAGCTAATGAGACCAATGATGCTGCTGTTTCTGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
* *
159850 GAATTGGTAGCTGATGGGACCAATGATGCTGCTGTTTCCGAA
1 GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
159892 GA
1 GA
159894 TGCACTTGAG
Statistics
Matches: 236, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 236 1.00
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.33
Consensus pattern (42 bp):
GAATTGGTAGCTGATGAGACCAATGATGCTGCTGTTTCTGAA
Found at i:160330 original size:201 final size:201
Alignment explanation
Indices: 159985--160393 Score: 809
Period size: 201 Copynumber: 2.0 Consensus size: 201
159975 AGTTGATGAG
159985 CCTGAAGTACTGGTTGCAAATGCTGAGGATATATCTGAAGAAGTCTTGGATCATTCTTCACCAGT
1 CCTGAAGTACTGGTTGCAAATGCTGAGGATATATCTGAAGAAGTCTTGGATCATTCTTCACCAGT
*
160050 GGAGGCTGTTAGTGTAGAAGAGCATGCTAATCAAGCTCCACAGGAAATTGAAGCAGTACATGATG
66 GGAGGCTGTTAGTGTAGAAGAGCATACTAATCAAGCTCCACAGGAAATTGAAGCAGTACATGATG
160115 ATCTAACCATACTTCCGAAAGCTGAAGAGTATGCAGATGGCGAAGTATCTCAAGATGTTCCTTCA
131 ATCTAACCATACTTCCGAAAGCTGAAGAGTATGCAGATGGCGAAGTATCTCAAGATGTTCCTTCA
160180 GTTCTC
196 GTTCTC
160186 CCTGAAGTACTGGTTGCAAATGCTGAGGATATATCTGAAGAAGTCTTGGATCATTCTTCACCAGT
1 CCTGAAGTACTGGTTGCAAATGCTGAGGATATATCTGAAGAAGTCTTGGATCATTCTTCACCAGT
160251 GGAGGCTGTTAGTGTAGAAGAGCATACTAATCAAGCTCCACAGGAAATTGAAGCAGTACATGATG
66 GGAGGCTGTTAGTGTAGAAGAGCATACTAATCAAGCTCCACAGGAAATTGAAGCAGTACATGATG
160316 ATCTAACCATACTTCCGAAAGCTGAAGAGTATGCAGATGGCGAAGTATCTCAAGATGTTCCTTCA
131 ATCTAACCATACTTCCGAAAGCTGAAGAGTATGCAGATGGCGAAGTATCTCAAGATGTTCCTTCA
160381 GTTCTC
196 GTTCTC
160387 CCTGAAG
1 CCTGAAG
160394 ATCATAGGGA
Statistics
Matches: 207, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 207 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (201 bp):
CCTGAAGTACTGGTTGCAAATGCTGAGGATATATCTGAAGAAGTCTTGGATCATTCTTCACCAGT
GGAGGCTGTTAGTGTAGAAGAGCATACTAATCAAGCTCCACAGGAAATTGAAGCAGTACATGATG
ATCTAACCATACTTCCGAAAGCTGAAGAGTATGCAGATGGCGAAGTATCTCAAGATGTTCCTTCA
GTTCTC
Found at i:163784 original size:13 final size:13
Alignment explanation
Indices: 163766--163806 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
163756 TACAGAGACC
*
163766 AATTTTTAATAGT
1 AATTTTTAATAGA
*
163779 AATTTTAAAT-GA
1 AATTTTTAATAGA
163791 AATTTTTAATAGA
1 AATTTTTAATAGA
163804 AAT
1 AAT
163807 ACCAGTCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
AATTTTTAATAGA
Found at i:174335 original size:17 final size:16
Alignment explanation
Indices: 174295--174336 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
174285 AACGAAAATT
174295 GAAAGAA-AAAAGAAA
1 GAAAGAAGAAAAGAAA
* *
174310 TAAAAAAGAGAAAGAAA
1 GAAAGAAGA-AAAGAAA
174327 GAAAGAAGAA
1 GAAAGAAGAA
174337 GGAAGAAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
15 5 0.24
16 2 0.10
17 14 0.67
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
GAAAGAAGAAAAGAAA
Found at i:174562 original size:12 final size:12
Alignment explanation
Indices: 174545--174570 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
174535 TTTAAGTATG
174545 ATTAATTTTAAA
1 ATTAATTTTAAA
174557 ATTAATTTTAAA
1 ATTAATTTTAAA
174569 AT
1 AT
174571 ATTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTTTAAA
Found at i:177129 original size:45 final size:45
Alignment explanation
Indices: 177011--177130 Score: 159
Period size: 45 Copynumber: 2.7 Consensus size: 45
177001 GCATAGCTCA
*
177011 TCAAGCCAAGGATATCAGCCTCAGTTTGACGACCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAACCACCGCAATAC
* * * *
177056 TTAAGCCAAAGATATCAACCTCAATTTGACGAACCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAACCACCGCAATAC
** * *
177101 TCAAGGGAAGGATATCAGGCTGAGTTTGAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGAC
177131 AAGCCATCGC
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAACCACCGCAATAC
Found at i:182447 original size:30 final size:31
Alignment explanation
Indices: 182411--182469 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
182401 CCCGATACTA
182411 AAATAAAAACTTTCGAA-AATTCAATGAATT
1 AAATAAAAACTTTCGAATAATTCAATGAATT
* *
182441 AAATAAAAACTTTTGAATAATTCATTGAA
1 AAATAAAAACTTTCGAATAATTCAATGAA
182470 CATTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (31 bp):
AAATAAAAACTTTCGAATAATTCAATGAATT
Found at i:184573 original size:24 final size:24
Alignment explanation
Indices: 184538--184603 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
184528 AGTATTTTAG
* *
184538 TTAAATTTTGTTTAATTGTATCAA
1 TTAAATTCTGTTTAATTATATCAA
* * *
184562 TTAAATTCTGTTTATTTATTTTAA
1 TTAAATTCTGTTTAATTATATCAA
184586 TTAAATTCTGTTT-ATTAT
1 TTAAATTCTGTTTAATTAT
184604 TATTTGATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (24 bp):
TTAAATTCTGTTTAATTATATCAA
Found at i:188800 original size:3 final size:3
Alignment explanation
Indices: 188792--188852 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
188782 GCAGATAGTG
* * * * *
188792 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAG GAG GAG GAA GGA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
188840 GAA GAA GAA GAA G
1 GAA GAA GAA GAA G
188853 CTGAAGATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:189174 original size:14 final size:14
Alignment explanation
Indices: 189151--189180 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
189141 AAAGAAGATT
*
189151 AAAGGTAAAGGAAA
1 AAAGGAAAAGGAAA
189165 AAAGGAAAAGGAAA
1 AAAGGAAAAGGAAA
189179 AA
1 AA
189181 GAAAAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (14 bp):
AAAGGAAAAGGAAA
Found at i:202981 original size:16 final size:15
Alignment explanation
Indices: 202930--202981 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
202920 TTTACAAATA
*
202930 AAAAAATAATTATAA
1 AAAAAATAATTATAT
**
202945 AAGAAAATAAAGATAT
1 AA-AAAATAATTATAT
*
202961 TAAAAATATATTATAT
1 AAAAAATA-ATTATAT
202977 AAAAA
1 AAAAA
202982 TATTCAATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 8 0.29
16 20 0.71
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (15 bp):
AAAAAATAATTATAT
Found at i:208526 original size:131 final size:133
Alignment explanation
Indices: 208287--208553 Score: 371
Period size: 131 Copynumber: 2.0 Consensus size: 133
208277 CATACAAATG
* *
208287 TTTTCACCATAGAACTATTGGATCAAACATTTCAGAAGATAAAGTTGTTCCGTTTTACAATTAGT
1 TTTTCACCATAGAACTATTGGATCAAACATTTCAGAAGATAAAATTATTCCGTTTT---ATTAGT
* * *
208352 TTACATGTAATCCAGGATGTGTTTCATGCATGAACTCGAACAGCTTATTGACAGCAGTTTTCAGG
63 TTACATGTAATCCAGGATGTGTTTCATGCATGAACTCAAACAGCTTATTCACAACAGTTTTCAGG
208417 AACTTC
128 AACTTC
* * * *
208423 TTTTCGCCATAGAATTATTTGATCAAACATTTCAGAAGATAAAAATTATT-TG-TTT-TTAGTTT
1 TTTTCACCATAGAACTATTGGATCAAACATTTCAGAAGAT-AAAATTATTCCGTTTTATTAGTTT
*
208485 ACCTG-AACTCCAGGATGTGTTTCATGCATGAACTCAAACAGCTTATTCACAACAGTTTTCAGGA
65 ACATGTAA-TCCAGGATGTGTTTCATGCATGAACTCAAACAGCTTATTCACAACAGTTTTCAGGA
208549 ACTTC
129 ACTTC
208554 CAGTGAGCCC
Statistics
Matches: 119, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
130 2 0.02
131 69 0.58
135 3 0.03
136 38 0.32
137 7 0.06
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (133 bp):
TTTTCACCATAGAACTATTGGATCAAACATTTCAGAAGATAAAATTATTCCGTTTTATTAGTTTA
CATGTAATCCAGGATGTGTTTCATGCATGAACTCAAACAGCTTATTCACAACAGTTTTCAGGAAC
TTC
Found at i:221786 original size:23 final size:24
Alignment explanation
Indices: 221759--221805 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
221749 TTCAGGCTTA
*
221759 GTTCATTTA-ATGTTTGTGAACAT
1 GTTCATTTATATGTTTGCGAACAT
221782 GTTCATTTATATGTTTGCGAACAT
1 GTTCATTTATATGTTTGCGAACAT
221806 TAAACGAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (24 bp):
GTTCATTTATATGTTTGCGAACAT
Found at i:233422 original size:21 final size:22
Alignment explanation
Indices: 233398--233449 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
233388 ATAAATACTA
233398 AAACCTTAATTTTAAAAA-CCT
1 AAACCTTAATTTTAAAAATCCT
233419 AAA-CTCTAA-TTTAAAAATCCT
1 AAACCT-TAATTTTAAAAATCCT
233440 AAACC-TAATT
1 AAACCTTAATT
233450 AAAATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
20 13 0.48
21 13 0.48
22 1 0.04
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACCTTAATTTTAAAAATCCT
Found at i:233433 original size:20 final size:20
Alignment explanation
Indices: 233398--233453 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
233388 ATAAATACTA
233398 AAACCTTAATTTTAAAAA-CCT
1 AAACC-TAA-TTTAAAAATCCT
233419 AAACTCTAATTTAAAAATCCT
1 AAAC-CTAATTTAAAAATCCT
233440 AAACCTAA-TTAAAA
1 AAACCTAATTTAAAA
233454 TGAAAATACC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.18
20 12 0.36
21 14 0.42
22 1 0.03
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (20 bp):
AAACCTAATTTAAAAATCCT
Found at i:234833 original size:28 final size:29
Alignment explanation
Indices: 234785--234860 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
234775 ACAAATTATA
* * **
234785 TATTTTTAAGATAGTAAAAATATAATTTTAT
1 TATTTTTAAAATA-T-AAAATAAAATACTAT
234816 TATTTTTAAAA-ATAAAATAAAATACTAT
1 TATTTTTAAAATATAAAATAAAATACTAT
234844 TATTTTTAAAATATAAA
1 TATTTTTAAAATATAAA
234861 TTTATCATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 23 0.57
29 6 0.15
30 1 0.03
31 10 0.25
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (29 bp):
TATTTTTAAAATATAAAATAAAATACTAT
Found at i:234870 original size:22 final size:23
Alignment explanation
Indices: 234828--234875 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
234818 TTTTTAAAAA
*
234828 TAAAATAAAATACTATTATTT-T
1 TAAAATAAAATACTATCATTTAT
*
234850 TAAAATATAAAT-TTATCATTTAT
1 TAAAATA-AAATACTATCATTTAT
234873 TAA
1 TAA
234876 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAAATAAAATACTATCATTTAT
Found at i:237043 original size:9 final size:9
Alignment explanation
Indices: 237029--237053 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
237019 AACATTTATA
237029 TTAATGTTT
1 TTAATGTTT
237038 TTAATGTTT
1 TTAATGTTT
237047 TTAATGT
1 TTAATGT
237054 ATTTGATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (9 bp):
TTAATGTTT
Found at i:238191 original size:17 final size:16
Alignment explanation
Indices: 238164--238235 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 16
238154 AAATCCATTT
238164 TTAAGATTTATTTTAAGA
1 TTAA-ATTTATTTTAA-A
*
238182 TTAAATTTATTTTGAAT
1 TTAAATTTATTTT-AAA
*
238199 TTAAATTTGTTTTAAAA
1 TTAAATTTATTTT-AAA
*
238216 TTTTAAATTTAATTTAAA
1 --TTAAATTTATTTTAAA
238234 TT
1 TT
238236 TAGATTTAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 2 0.04
17 23 0.51
18 9 0.20
19 11 0.24
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAAATTTATTTTAAA
Found at i:238223 original size:36 final size:36
Alignment explanation
Indices: 238182--238277 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 36
238172 TATTTTAAGA
* *
238182 TTAAATTTATTTTGAATTTAAATTT-GTTTTAAAATT
1 TTAAATTTATTTTAAATTTAAATTTAGATTT-AAATT
* *
238218 TTAAATTTAATTTAAATTTAGATTTAGATTTAAATT
1 TTAAATTTATTTTAAATTTAAATTTAGATTTAAATT
* * *
238254 TAAAACTTATTATAAATATTAAAT
1 TTAAATTTATTTTAAAT-TTAAAT
238278 GTTCAATTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 40 0.82
37 9 0.18
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (36 bp):
TTAAATTTATTTTAAATTTAAATTTAGATTTAAATT
Found at i:238234 original size:18 final size:18
Alignment explanation
Indices: 238182--238277 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 18
238172 TATTTTAAGA
* *
238182 TTAAATTTATTTTGAA-T
1 TTAAATTTAATTTAAATT
**
238199 TTAAATTTGTTTTAAAATT
1 TTAAATTTAATTT-AAATT
238218 TTAAATTTAATTTAAA-T
1 TTAAATTTAATTTAAATT
*
238235 TTAGATTTAGATTTAAATT
1 TTAAATTTA-ATTTAAATT
* * *
238254 TAAAACTT-ATTATAAATA
1 TTAAATTTAATT-TAAATT
238272 TTAAAT
1 TTAAAT
238278 GTTCAATTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
17 24 0.38
18 21 0.33
19 18 0.29
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (18 bp):
TTAAATTTAATTTAAATT
Found at i:238235 original size:6 final size:6
Alignment explanation
Indices: 238182--238257 Score: 59
Period size: 6 Copynumber: 12.8 Consensus size: 6
238172 TATTTTAAGA
* * **
238182 TTAAAT TT-ATT TTGAAT TTAAAT TT-GTT TTAAAATT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAA-T TTAAAT TTAAAT
* *
238229 TTAAAT TTAGAT TTAGAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
238258 ACTTATTATA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
5 12 0.21
6 38 0.68
7 3 0.05
8 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:243131 original size:62 final size:61
Alignment explanation
Indices: 243011--243124 Score: 178
Period size: 62 Copynumber: 1.9 Consensus size: 61
243001 AGAAATTATC
*
243011 TTAATATTAAATTTAATTTAATATTTATCTTGAAGTTAAAAATTATATTATTTTATTAAGAT
1 TTAATATTAAATTTAATCTAATATTTATCTTGAAG-TAAAAATTATATTATTTTATTAAGAT
* *
243073 TTAATATTAAATTTAATCTAATATTTATCTTG-A-TAAATATTATATTAATTTA
1 TTAATATTAAATTTAATCTAATATTTATCTTGAAGTAAAAATTATATTATTTTA
243125 ATATTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
59 17 0.35
61 1 0.02
62 31 0.63
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (61 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGAAGTAAAAATTATATTATTTTATTAAGAT
Found at i:243961 original size:22 final size:23
Alignment explanation
Indices: 243936--243979 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
243926 TTTCGTTTTA
243936 CTTCTTTCTTCCCTTT-TTTGTC
1 CTTCTTTCTTCCCTTTCTTTGTC
*
243958 CTTCTTTCTTCTCTTTCTTTGT
1 CTTCTTTCTTCCCTTTCTTTGT
243980 TTTTCTTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.00, C:0.30, G:0.05, T:0.66
Consensus pattern (23 bp):
CTTCTTTCTTCCCTTTCTTTGTC
Found at i:250516 original size:22 final size:23
Alignment explanation
Indices: 250465--250516 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 23
250455 TGTGTTCATG
250465 TTATATATT-ATAAAAATAATATA
1 TTATA-ATTCATAAAAATAATATA
*
250488 GT-T-ATTCATAAAAA-AATATA
1 TTATAATTCATAAAAATAATATA
250508 TTATAATTC
1 TTATAATTC
250517 TTTTGTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
20 10 0.42
21 8 0.33
22 5 0.21
23 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (23 bp):
TTATAATTCATAAAAATAATATA
Found at i:250647 original size:16 final size:16
Alignment explanation
Indices: 250626--250656 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
250616 AAAACATTAT
250626 TTATAAATTTCATATA
1 TTATAAATTTCATATA
250642 TTATAAATTTCATAT
1 TTATAAATTTCATAT
250657 TACTTACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATAAATTTCATATA
Found at i:262015 original size:30 final size:30
Alignment explanation
Indices: 261935--262015 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
261925 CAGGAGGCTC
* * * *
261935 ATCAGGTGGTGGGGGAGGAACTTGTTCATT
1 ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
* *
261965 ATCAGGAGGAGGTGGTGGAATTTGTTCAGT
1 ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
261995 ATCAGGAGGTGGTGGAGGAAT
1 ATCAGGAGGTGGTGGAGGAAT
262016 CCACTCCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.23, C:0.07, G:0.42, T:0.27
Consensus pattern (30 bp):
ATCAGGAGGTGGTGGAGGAATTTGTTCAGT
Found at i:270331 original size:27 final size:25
Alignment explanation
Indices: 270272--270323 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
270262 TTCATATATT
* *
270272 AAAATATTAATAATGATTCACTAAA
1 AAAATATTAATAATAATTCAATAAA
270297 AAAATATTAATAATAAGTTGCAATAAA
1 AAAATATTAATAATAA-TT-CAATAAA
270324 TTAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAAATATTAATAATAATTCAATAAA
Found at i:271104 original size:17 final size:17
Alignment explanation
Indices: 271052--271106 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
271042 GTTAGTATTT
*
271052 TAAAATTTA-ATTAATA
1 TAAAATTTATATAAATA
271068 T-AAA-TTAT-TAAATTA
1 TAAAATTTATATAAA-TA
271083 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
271101 TAAAAT
1 TAAAAT
271107 ATTTCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
14 6 0.19
15 5 0.16
16 2 0.06
17 9 0.28
18 6 0.19
19 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:271262 original size:28 final size:26
Alignment explanation
Indices: 271214--271274 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
271204 AATTTCGAAA
*
271214 TTGAATTAATTAATTTATTTTTAAAATT
1 TTGAAATAATTAATTTA-TTTT-AAATT
* *
271242 TTGAAATAATTTAA-TTCTTTTCAATT
1 TTGAAATAA-TTAATTTATTTTAAATT
271268 TTGAAAT
1 TTGAAAT
271275 GAACAACTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 11 0.38
27 4 0.14
28 10 0.34
29 4 0.14
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (26 bp):
TTGAAATAATTAATTTATTTTAAATT
Found at i:277767 original size:13 final size:13
Alignment explanation
Indices: 277751--277787 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
277741 TCTTAAAACC
277751 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
277764 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
277777 AAAAAAGAAAA
1 AAAAAAGAAAA
277788 GGCCAGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:284214 original size:16 final size:15
Alignment explanation
Indices: 284193--284223 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
284183 AAATTTATAC
284193 ATAAAATAATCAAAAT
1 ATAAAATAAT-AAAAT
284209 ATAAAATAATAAAAT
1 ATAAAATAATAAAAT
284224 GAAGTGCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAATAATAAAAT
Found at i:285298 original size:22 final size:20
Alignment explanation
Indices: 285272--285324 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
285262 TTGGTTTTAA
285272 AATTTTATAAATATATTAAATT
1 AATTTTATAAATAT-TTAAA-T
* *
285294 AATTTTTTAAATATTTTAAT
1 AATTTTATAAATATTTAAAT
285314 AATTATTATAA
1 AATT-TTATAA
285325 TAAAAGGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 13 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTTATAAATATTTAAAT
Found at i:285985 original size:24 final size:26
Alignment explanation
Indices: 285953--286002 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
285943 TCCATCAACC
* *
285953 ATATCAAA-TTTTAA-CAATAAAAAT
1 ATATAAAATTTTTAACCAAAAAAAAT
285977 ATATAAAATTTTTAACCAAAAAAAAT
1 ATATAAAATTTTTAACCAAAAAAAAT
286003 TAATTTACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 6 0.27
26 9 0.41
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (26 bp):
ATATAAAATTTTTAACCAAAAAAAAT
Found at i:288300 original size:3 final size:3
Alignment explanation
Indices: 288266--288333 Score: 52
Period size: 3 Copynumber: 22.7 Consensus size: 3
288256 TTCATTTTTC
* *
288266 TCT TCT TCAT TC- TGT TCC TCT TCCT T-T TCT TCT TCCT T-T TCT TCT
1 TCT TCT TC-T TCT TCT TCT TCT T-CT TCT TCT TCT T-CT TCT TCT TCT
* *
288311 TCT TCC TCC TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC
288334 AGACTCATCC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
2 5 0.09
3 39 0.74
4 9 0.17
ACGTcount: A:0.01, C:0.37, G:0.01, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:288301 original size:12 final size:12
Alignment explanation
Indices: 288284--288312 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
288274 ATTCTGTTCC
288284 TCTTCCTTTTCT
1 TCTTCCTTTTCT
288296 TCTTCCTTTTCT
1 TCTTCCTTTTCT
288308 TCTTC
1 TCTTC
288313 TTCCTCCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TCTTCCTTTTCT
Found at i:288301 original size:18 final size:18
Alignment explanation
Indices: 288265--288333 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
288255 TTTCATTTTT
*
288265 CTCTTCTTCATTC-TGTTC
1 CTCTTCTTC-TTCTTCTTC
288283 CTCTTCCTT-TTCTTCTTC
1 CTCTT-CTTCTTCTTCTTC
* *
288301 CTTTTCTTCTTCTTCCTC
1 CTCTTCTTCTTCTTCTTC
288319 CTCTTCTTCTTCTTC
1 CTCTTCTTCTTCTTC
288334 AGACTCATCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.14
18 35 0.80
19 3 0.07
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.59
Consensus pattern (18 bp):
CTCTTCTTCTTCTTCTTC
Found at i:288312 original size:15 final size:15
Alignment explanation
Indices: 288287--288330 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
288277 CTGTTCCTCT
*
288287 TCCTTTTCTTCTTCC
1 TCCTCTTCTTCTTCC
**
288302 TTTTCTTCTTCTTCC
1 TCCTCTTCTTCTTCC
288317 TCCTCTTCTTCTTC
1 TCCTCTTCTTCTTC
288331 TTCAGACTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (15 bp):
TCCTCTTCTTCTTCC
Found at i:290873 original size:21 final size:21
Alignment explanation
Indices: 290847--290917 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
290837 CTTCTTGCTC
*
290847 CTCTTCATCATCCCCATCCTT
1 CTCTTCATCATCTCCATCCTT
290868 CTCTTCATCATCTCCATCCTT
1 CTCTTCATCATCTCCATCCTT
290889 CTCTTCATCATCTCCATCCTT
1 CTCTTCATCATCTCCATCCTT
290910 CTCTTCAT
1 CTCTTCAT
290918 GCTCCTCTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.14, C:0.44, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCTTCATCATCTCCATCCTT
Found at i:290938 original size:24 final size:24
Alignment explanation
Indices: 290907--290989 Score: 71
Period size: 24 Copynumber: 3.4 Consensus size: 24
290897 CATCTCCATC
*
290907 CTTC-TCTTCATGCTCCTCTTCAT
1 CTTCTTCTTCATGCTCTTCTTCAT
* * *
290930 CTTCTTCTTCTTTCAACTCTTCTTCAG
1 CTTCTTCTTC-AT--GCTCTTCTTCAT
*
290957 CTT-TCTCTTCCTGCTCTTCTTCAT
1 CTTCT-TCTTCATGCTCTTCTTCAT
290981 CTTCTTCTT
1 CTTCTTCTT
290990 TCAACTCATC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
23 4 0.09
24 22 0.47
25 2 0.04
26 2 0.04
27 17 0.36
ACGTcount: A:0.07, C:0.36, G:0.04, T:0.53
Consensus pattern (24 bp):
CTTCTTCTTCATGCTCTTCTTCAT
Found at i:293073 original size:18 final size:19
Alignment explanation
Indices: 293050--293086 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
293040 TGAGAATTTG
293050 TAATTTTTTGA-ATTTTTA
1 TAATTTTTTGATATTTTTA
*
293068 TAATTTTTTTATATTTTTA
1 TAATTTTTTGATATTTTTA
293087 AACTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
TAATTTTTTGATATTTTTA
Found at i:308105 original size:15 final size:16
Alignment explanation
Indices: 308085--308118 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
308075 TTAAATTTTC
*
308085 AAATTTA-TGAAAATT
1 AAATTTATTAAAAATT
308100 AAATTTATTAAAAATT
1 AAATTTATTAAAAATT
308116 AAA
1 AAA
308119 AAATAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATTTATTAAAAATT
Found at i:308324 original size:26 final size:25
Alignment explanation
Indices: 308295--308369 Score: 64
Period size: 26 Copynumber: 3.0 Consensus size: 25
308285 TTTAATTCAA
308295 TTTAAATAAATTATATAAAAATAATT
1 TTTAAATAAATTATATAAAAAT-ATT
* * *
308321 TTT-AGTTAATTTTAGTAAAAATATT
1 TTTAAATAAATTATA-TAAAAATATT
* **
308346 TTTAATTAAAAAATAT-AAAATATT
1 TTTAAATAAATTATATAAAAATATT
308370 AATGTAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
24 8 0.21
25 15 0.38
26 16 0.41
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (25 bp):
TTTAAATAAATTATATAAAAATATT
Found at i:311807 original size:24 final size:24
Alignment explanation
Indices: 311774--311824 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
311764 AAAAATAATT
*
311774 TTTCAGTTAAACTT-TGTTTATTTG
1 TTTCAATTAAA-TTCTGTTTATTTG
311798 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAATTCTGTTTATTTG
311822 TTT
1 TTT
311825 GAGTCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.22, C:0.08, G:0.10, T:0.61
Consensus pattern (24 bp):
TTTCAATTAAATTCTGTTTATTTG
Found at i:321436 original size:31 final size:31
Alignment explanation
Indices: 321398--321458 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
321388 GTATATAGAT
321398 GAAATAGTTAGACTTCATGGTGTGCCTGTAC
1 GAAATAGTTAGACTTCATGGTGTGCCTGTAC
321429 GAAATAGTTAGACTTCATGGTGTGCCTGTA
1 GAAATAGTTAGACTTCATGGTGTGCCTGTA
321459 TCTATTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (31 bp):
GAAATAGTTAGACTTCATGGTGTGCCTGTAC
Found at i:324059 original size:22 final size:22
Alignment explanation
Indices: 324015--324094 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 22
324005 TTCGCACTTC
*
324015 GTGTGCCTACTGATTTGCGCTAT
1 GTGTGCCTACTGA-TTGCACTAT
*
324038 GTGCGCCTACTGATTGCACTAT
1 GTGTGCCTACTGATTGCACTAT
* *
324060 GTGTGCTTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTAT
*
324083 GTGTGCTTACTG
1 GTGTGCCTACTG
324095 TTTCCCCAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
22 18 0.35
23 33 0.65
ACGTcount: A:0.14, C:0.21, G:0.28, T:0.38
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTAT
Found at i:324094 original size:45 final size:46
Alignment explanation
Indices: 323994--324094 Score: 109
Period size: 45 Copynumber: 2.2 Consensus size: 46
323984 GGAACGCTAC
* *
323994 GCGCTTACTGTTTCGCACTTCGTGTGCCTACTGATTTGCGCTATGT
1 GCGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTATGT
* * *
324040 GCGCCTACTGATT-GCACTAT-GTGTGCTTACTGGA-TTGCACTGTGT
1 GCGCTTACTGATTCGCACT-TCGTGTGCCTACT-GATTTGCACTATGT
*
324085 GTGCTTACTG
1 GCGCTTACTG
324095 TTTCCCCAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
45 32 0.70
46 14 0.30
ACGTcount: A:0.13, C:0.24, G:0.26, T:0.38
Consensus pattern (46 bp):
GCGCTTACTGATTCGCACTTCGTGTGCCTACTGATTTGCACTATGT
Found at i:326286 original size:81 final size:81
Alignment explanation
Indices: 326151--326308 Score: 316
Period size: 81 Copynumber: 2.0 Consensus size: 81
326141 TACAACTTGC
326151 ACCTAATTGGTAGTTTAGTGAGTGCATTTGAACCAATGATATCTTAGTTCCTAACATTAGTTATG
1 ACCTAATTGGTAGTTTAGTGAGTGCATTTGAACCAATGATATCTTAGTTCCTAACATTAGTTATG
326216 GTCATACTTTAAAACT
66 GTCATACTTTAAAACT
326232 ACCTAATTGGTAGTTTAGTGAGTGCATTTGAACCAATGATATCTTAGTTCCTAACATTAGTTATG
1 ACCTAATTGGTAGTTTAGTGAGTGCATTTGAACCAATGATATCTTAGTTCCTAACATTAGTTATG
326297 GTCATACTTTAA
66 GTCATACTTTAA
326309 TAGTTTTATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (81 bp):
ACCTAATTGGTAGTTTAGTGAGTGCATTTGAACCAATGATATCTTAGTTCCTAACATTAGTTATG
GTCATACTTTAAAACT
Found at i:327781 original size:19 final size:19
Alignment explanation
Indices: 327759--327839 Score: 90
Period size: 19 Copynumber: 4.1 Consensus size: 19
327749 CTAAAAATAT
*
327759 TAAAATAAATGTTATACAA
1 TAAAACAAATGTTATACAA
*
327778 TAAAACAAGTGTTATACAATA
1 TAAAACAAATGTTATAC-A-A
* *
327799 TTAAAATAAATGGTATACAA
1 -TAAAACAAATGTTATACAA
*
327819 TAAAACAAGTGTTATACAA
1 TAAAACAAATGTTATACAA
327838 TA
1 TA
327840 TTCAAACATT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
19 33 0.65
20 2 0.04
21 2 0.04
22 14 0.27
ACGTcount: A:0.54, C:0.07, G:0.09, T:0.30
Consensus pattern (19 bp):
TAAAACAAATGTTATACAA
Found at i:327799 original size:41 final size:41
Alignment explanation
Indices: 327754--327841 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
327744 ATACACTAAA
*
327754 AATATTAAAATAAATGTTATACAATAAAACAAGTGTTATAC
1 AATATTAAAATAAATGGTATACAATAAAACAAGTGTTATAC
327795 AATATTAAAATAAATGGTATACAATAAAACAAGTGTTATAC
1 AATATTAAAATAAATGGTATACAATAAAACAAGTGTTATAC
327836 AATATT
1 AATATT
327842 CAAACATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (41 bp):
AATATTAAAATAAATGGTATACAATAAAACAAGTGTTATAC
Found at i:340761 original size:21 final size:21
Alignment explanation
Indices: 340735--340776 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
340725 TAAAGTATCA
340735 AATTGAAAAAAGCCGCAATGT
1 AATTGAAAAAAGCCGCAATGT
* *
340756 AATTGAAAAAATCTGCAATGT
1 AATTGAAAAAAGCCGCAATGT
340777 TTCAAGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.17, T:0.24
Consensus pattern (21 bp):
AATTGAAAAAAGCCGCAATGT
Found at i:342645 original size:24 final size:24
Alignment explanation
Indices: 342618--342668 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
342608 CTATTTTAGC
* *
342618 TTAATTTTTAATTAATTAATATTT
1 TTAATTATAAATTAATTAATATTT
*
342642 TTAATTATAAATTTATTAATATTT
1 TTAATTATAAATTAATTAATATTT
342666 TTA
1 TTA
342669 CCGTATGCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAATTATAAATTAATTAATATTT
Found at i:343050 original size:28 final size:27
Alignment explanation
Indices: 343019--343082 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 27
343009 TTTTTTAAAA
343019 TATTTTAATATTT-AATATT-ATAGTTTT
1 TATTTTAATATTTAAAT-TTAAT-GTTTT
343046 CTATTTTTAA-ATTTAAATTTAATGTTTT
1 -TA-TTTTAATATTTAAATTTAATGTTTT
343074 TATTTTAAT
1 TATTTTAAT
343083 TACCAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
26 6 0.19
27 2 0.06
28 13 0.41
29 11 0.34
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (27 bp):
TATTTTAATATTTAAATTTAATGTTTT
Found at i:343169 original size:13 final size:13
Alignment explanation
Indices: 343151--343175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343141 ATTACCTAAC
343151 GGATTTTGTTAAT
1 GGATTTTGTTAAT
343164 GGATTTTGTTAA
1 GGATTTTGTTAA
343176 GATTTTTGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (13 bp):
GGATTTTGTTAAT
Found at i:343408 original size:2 final size:2
Alignment explanation
Indices: 343401--343428 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
343391 ACTTAACATA
343401 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
343429 TAAGAGACTT
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:345115 original size:32 final size:32
Alignment explanation
Indices: 345034--345118 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 32
345024 TTTAGATCTT
* * *
345034 TTAAAAGTTGATAAAAATAATAAATTTGGACTC
1 TTAAAAATTGATAAAAA-AATAAATTTGAACCC
* *
345067 TTAAAAACT-A-AAAAAAAAAAATTTTGAAGCCC
1 TTAAAAATTGATAAAAAAATAAA-TTTGAA-CCC
345099 TTAAAAATTGATAAAAAAAT
1 TTAAAAATTGATAAAAAAAT
345119 TTTTAACTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
30 5 0.12
31 10 0.24
32 11 0.27
33 8 0.20
34 7 0.17
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.28
Consensus pattern (32 bp):
TTAAAAATTGATAAAAAAATAAATTTGAACCC
Found at i:354947 original size:23 final size:23
Alignment explanation
Indices: 354921--354990 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
354911 TTCATTTAAT
354921 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * *
354944 TTAATCGAACATATTCATGAATA
1 TTAATCGAACATGTTCACGAACA
* * *
354967 TATAATTGAATACGTTCACGAACA
1 T-TAATCGAACATGTTCACGAACA
354991 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:362651 original size:69 final size:69
Alignment explanation
Indices: 362540--362724 Score: 343
Period size: 69 Copynumber: 2.7 Consensus size: 69
362530 AAGAAACCAC
*
362540 ATAATTAATTCAAAGAAATGGGATTTCAAACATGAGGCATCTGCAAAGTTGTTTCACTTGAATGA
1 ATAATTAATTCAAAGAATTGGGATTTCAAACATGAGGCATCTGCAAAGTTGTTTCACTTGAATGA
362605 TCTA
66 TCTA
* *
362609 ATAATTAATTCAAAGAATTGAGATTTCAAACACGAGGCATCTGCAAAGTTGTTTCACTTGAATGA
1 ATAATTAATTCAAAGAATTGGGATTTCAAACATGAGGCATCTGCAAAGTTGTTTCACTTGAATGA
362674 TCTA
66 TCTA
362678 ATAATTAATTCAAAGAATTGGGATTTCAAACATGAGGCATCTGCAAA
1 ATAATTAATTCAAAGAATTGGGATTTCAAACATGAGGCATCTGCAAA
362725 TTATGTCAAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 111 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (69 bp):
ATAATTAATTCAAAGAATTGGGATTTCAAACATGAGGCATCTGCAAAGTTGTTTCACTTGAATGA
TCTA
Found at i:372559 original size:10 final size:9
Alignment explanation
Indices: 372539--372588 Score: 61
Period size: 8 Copynumber: 5.8 Consensus size: 9
372529 AATTATGTTT
372539 AAAAT-TTA
1 AAAATATTA
372547 AAAATCATTA
1 AAAAT-ATTA
*
372557 AAATTATTA
1 AAAATATTA
372566 AAAATA-TA
1 AAAATATTA
372574 AAAATA-TA
1 AAAATATTA
372582 AAAATAT
1 AAAATAT
372589 ATTTTTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
8 21 0.57
9 9 0.24
10 7 0.19
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:372577 original size:27 final size:27
Alignment explanation
Indices: 372523--372591 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
372513 TTTAAGAATT
* * *
372523 TATAAAAATTATGTTTAAAATTTAAAAA
1 TATAAAAA-TATATTAAAAATATAAAAA
*
372551 TCATTAAAAT-TATTAAAAATATAAAAA
1 T-ATAAAAATATATTAAAAATATAAAAA
372578 TATAAAAATATATT
1 TATAAAAATATATT
372592 TTTTTAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
26 7 0.21
27 19 0.56
28 2 0.06
29 6 0.18
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
TATAAAAATATATTAAAAATATAAAAA
Found at i:374753 original size:19 final size:18
Alignment explanation
Indices: 374714--374750 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
374704 GTGTGCCATG
374714 ATTTTTTTAAATATATAA
1 ATTTTTTTAAATATATAA
374732 ATTTTTTATAAAT-TATAA
1 ATTTTTT-TAAATATATAA
374750 A
1 A
374751 ATTATAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTTTTAAATATATAA
Found at i:374755 original size:15 final size:16
Alignment explanation
Indices: 374737--374767 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
374727 TATAAATTTT
374737 TTATAAATT-ATAAAA
1 TTATAAATTAATAAAA
374752 TTATAAATTAATAAAA
1 TTATAAATTAATAAAA
374768 ATAAATTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATAAATTAATAAAA
Found at i:398579 original size:31 final size:31
Alignment explanation
Indices: 398538--398616 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
398528 ATATTTTATA
* *
398538 TATCAATATATTAAATTATTTAAATATCATT
1 TATCATTATATTAAATTATTAAAATATCATT
* *
398569 TATCATTATATTAAATTATTAAAATTTTATT
1 TATCATTATATTAAATTATTAAAATATCATT
* *
398600 TATTATTATATTTAATT
1 TATCATTATATTAAATT
398617 TTTTTTGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (31 bp):
TATCATTATATTAAATTATTAAAATATCATT
Found at i:405233 original size:252 final size:249
Alignment explanation
Indices: 404763--405261 Score: 838
Period size: 252 Copynumber: 2.0 Consensus size: 249
404753 AATGTCAAAT
*
404763 CAACAGTGTGCGATATCCCTCCGAATTGAAAATGGCATCAACATTCATTGGAAACTTGACTTCCA
1 CAACAGTGTGCGATATCCCTCCGAATTGAAAATGGCATCAACATTCATTGGAAACTCGACTTCCA
*
404828 TACAGGAGATGTTCAGGTGTGCGAGTGAACAGTTCACAGCCACGTTTAGGAGAAAGGCTTTCTTG
66 TACAGGAGATGTTCAGGTGTGCGAGTGAACAATTCACAGCCACGTTTAGGAGAAAGGCTTTCTTG
*
404893 CATTGGTACACGGGCAAAGGTATGGACGAGATGGAGTTCACAGAAGCCGAAAGCAACATGAACGA
131 CATTGGTACACGGGCAAAGGTATGGACGAGATGGAGTTCACAGAAGCAGAAAGCAACATGAACGA
*
404958 TCTGGTGTCGGAGTATCAGCAGTACCAGGATGCAACTGCAGACGATGAGGAAAG
196 TATGGTGTCGGAGTATCAGCAGTACCAGGATGCAACTGCAGACGATGAGGAAAG
* * *
405012 CAACAGTGTGCGCTATCCCTCC-AATGGGTTGAAAATGGCATCAACATTCATTGGAACCTCGGCT
1 CAACAGTGTGCGATATCCCTCCGAA----TTGAAAATGGCATCAACATTCATTGGAAACTCGACT
* *
405076 TCCATACAGGAGATGTTCAGGTGTGTGAGTGAACAATTCACAGCCATGTTTAGGAGAAAGGCTTT
62 TCCATACAGGAGATGTTCAGGTGTGCGAGTGAACAATTCACAGCCACGTTTAGGAGAAAGGCTTT
* **
405141 CTTGCATTGGTACATGGGCAAAGGTATGGACGAGATGGAGTTCACAGAAGCAGAAATTAACATGA
127 CTTGCATTGGTACACGGGCAAAGGTATGGACGAGATGGAGTTCACAGAAGCAGAAAGCAACATGA
*
405206 ATGATATGGTGTCGGAGTATCAGCAGTACCAGGATGCAACTGCAGACGATGAGGAA
192 ACGATATGGTGTCGGAGTATCAGCAGTACCAGGATGCAACTGCAGACGATGAGGAA
405262 GAGTACGAGG
Statistics
Matches: 233, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
248 2 0.01
249 21 0.09
252 210 0.90
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (249 bp):
CAACAGTGTGCGATATCCCTCCGAATTGAAAATGGCATCAACATTCATTGGAAACTCGACTTCCA
TACAGGAGATGTTCAGGTGTGCGAGTGAACAATTCACAGCCACGTTTAGGAGAAAGGCTTTCTTG
CATTGGTACACGGGCAAAGGTATGGACGAGATGGAGTTCACAGAAGCAGAAAGCAACATGAACGA
TATGGTGTCGGAGTATCAGCAGTACCAGGATGCAACTGCAGACGATGAGGAAAG
Found at i:408507 original size:21 final size:20
Alignment explanation
Indices: 408483--408536 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
408473 TTAAAAAATA
**
408483 TAAAAATACATAAATATTTTT
1 TAAAAATA-ATAAATAAATTT
*
408504 TAAATATAAT-AATAAATTT
1 TAAAAATAATAAATAAATTT
408523 TAAAAATAAATAAA
1 TAAAAAT-AATAAA
408537 AATAAAAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 13 0.48
20 5 0.19
21 9 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATAATAAATAAATTT
Found at i:408539 original size:19 final size:19
Alignment explanation
Indices: 408483--408539 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
408473 TTAAAAAATA
* *
408483 TAAAAATACATAAATATTT
1 TAAAAATAAATAAAAATTT
**
408502 TTTAAATATAATAATAAATTT
1 TAAAAATA-AATAA-AAATTT
408523 TAAAAATAAATAAAAAT
1 TAAAAATAAATAAAAAT
408540 AAAAGATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 10 0.33
20 9 0.30
21 11 0.37
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATAAATAAAAATTT
Found at i:408564 original size:49 final size:49
Alignment explanation
Indices: 408469--408591 Score: 112
Period size: 49 Copynumber: 2.4 Consensus size: 49
408459 TCAATTTCCT
* *
408469 AATTTTAAAAA-ATATAAAAATACATAAATATTTTTTAAATATAATAATA
1 AATTTTAAAAATAAATAAAAATACATAAATATTTTGTAAATATAATAA-A
408518 AATTTTAAAAATAAATAAAAATA-A-AAGATATTGTTGTATAA-A-AATAAA
1 AATTTTAAAAATAAATAAAAATACATAA-ATATT-TTGTA-AATATAATAAA
*
408566 TATTTTCAAAAAATATAATAATAAAT
1 AATTTT--AAAAATA-AATAA-AAAT
408592 TTAAATTTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
48 8 0.13
49 22 0.35
50 22 0.35
51 7 0.11
52 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (49 bp):
AATTTTAAAAATAAATAAAAATACATAAATATTTTGTAAATATAATAAA
Found at i:408610 original size:6 final size:6
Alignment explanation
Indices: 408601--408625 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
408591 TTTAAATTTT
408601 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
408626 ATAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:413005 original size:6 final size:6
Alignment explanation
Indices: 412987--413027 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
412977 ATGTTGAACC
*
412987 ACAGAG ACGGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGA
1 ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGAG ACAGA
413028 CAATGAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.49, C:0.17, G:0.34, T:0.00
Consensus pattern (6 bp):
ACAGAG
Found at i:413781 original size:16 final size:16
Alignment explanation
Indices: 413760--413793 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
413750 TGACTTTTCA
413760 ATGAGGATTGGCAAGG
1 ATGAGGATTGGCAAGG
413776 ATGAGGATTGGCAAGG
1 ATGAGGATTGGCAAGG
413792 AT
1 AT
413794 TTCATGTTTC
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:0.32, C:0.06, G:0.41, T:0.21
Consensus pattern (16 bp):
ATGAGGATTGGCAAGG
Found at i:420804 original size:6 final size:6
Alignment explanation
Indices: 420793--420818 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
420783 ATTTCTGTGG
420793 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
420819 ATTCCTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:422212 original size:65 final size:65
Alignment explanation
Indices: 422108--422235 Score: 220
Period size: 65 Copynumber: 2.0 Consensus size: 65
422098 ACTCGTCGCA
*
422108 TGGAAGATGAAATGTGTGCATCTCGGGTCTCCATCTTTCCACCAACGCGCTTACAAGTATGGGAG
1 TGGAAGATGAAATGTGTGCATCTCGGGTCTCCATCTTTCCACCAACACGCTTACAAGTATGGGAG
* * *
422173 TGGAAGATGAAATGTGTGTATCTCGGGTCTCCATTTTTCCACCAACACGCTTACAAGTGTGGG
1 TGGAAGATGAAATGTGTGCATCTCGGGTCTCCATCTTTCCACCAACACGCTTACAAGTATGGG
422236 GGTCCAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (65 bp):
TGGAAGATGAAATGTGTGCATCTCGGGTCTCCATCTTTCCACCAACACGCTTACAAGTATGGGAG
Found at i:439702 original size:22 final size:20
Alignment explanation
Indices: 439677--439716 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
439667 AAGAATTTGT
439677 TTATAACTCCATTAAATATGAG
1 TTATAACTCCA--AAATATGAG
*
439699 TTATAATTCCAAAATATG
1 TTATAACTCCAAAATATG
439717 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (20 bp):
TTATAACTCCAAAATATGAG
Found at i:441209 original size:21 final size:20
Alignment explanation
Indices: 441171--441343 Score: 76
Period size: 23 Copynumber: 7.5 Consensus size: 20
441161 ATACGGAACA
* *
441171 AACAGAGAGTACCAAAGTACT
1 AACAGAGAGCA-CAAAGTGCT
441192 AACAGAGAGCACATAAGTGCTGGGT
1 AACAGAGAGCACA-AAGTGC----T
* *
441217 AATAGAGAACACACACAGTGCT
1 AACAGAGAGCACA-A-AGTGCT
*
441239 AAACAGAGAGTACACAAAGTACT
1 -AACAGAGAG--CACAAAGTGCT
441262 AATCAGAGAGCACACAAAGTGCT
1 AA-CAGAGAG--CACAAAGTGCT
*
441285 AGTCAGAGAGCACACACAGTGCTAAT
1 A-ACAGAGAGCACA-A-AGTGC---T
*
441311 AACAGAGAGCACGAGACGTGCT
1 AACAGAGAGCAC-A-AAGTGCT
441333 AAACAGAGAGC
1 -AACAGAGAGC
441344 GCGCTAATGT
Statistics
Matches: 120, Mismatches: 14, Indels: 34
0.71 0.08 0.20
Matches are distributed among these distances:
20 2 0.02
21 19 0.16
22 5 0.04
23 53 0.44
24 1 0.01
25 31 0.26
26 9 0.08
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (20 bp):
AACAGAGAGCACAAAGTGCT
Found at i:441253 original size:23 final size:23
Alignment explanation
Indices: 441220--441343 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
441210 GCTGGGTAAT
*
441220 AGAGAACACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * * *
441243 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACACAGTGCTAAAC
* **
441266 AGAGAGCACACAAAGTGCTAGTC
1 AGAGAGCACACACAGTGCTAAAC
441289 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACAGTGCT-A-AAC
*
441314 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAC
441337 AGAGAGC
1 AGAGAGC
441344 GCGCTAATGT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
23 66 0.77
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Done.