Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014995.1 Kokia drynarioides strain JFW-HI SEQ_130039, 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: 341517
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 255 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:292947 original size:20 final size:20
Alignment explanation
Indices: 292906--292947 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
292896 CGAACCTCCA
* *
292906 AAATTTCCATTTTGACCTCG
1 AAATTACCATTTTGACCCCG
*
292926 AAATTACCATTTTGCCCCCG
1 AAATTACCATTTTGACCCCG
292946 AA
1 AA
292948 TATCCAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (20 bp):
AAATTACCATTTTGACCCCG
Found at i:298517 original size:3 final size:3
Alignment explanation
Indices: 298511--298550 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
298501 AAAAAACAAA
298511 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
298551 GAAAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:298588 original size:12 final size:12
Alignment explanation
Indices: 298511--298589 Score: 81
Period size: 12 Copynumber: 6.7 Consensus size: 12
298501 AAAAAACAAA
*
298511 AAGAAGAAGAAG
1 AAGAAAAAGAAG
*
298523 AAGAAGAAGAAG
1 AAGAAAAAGAAG
*
298535 AAGAAGAAGAAG
1 AAGAAAAAGAAG
*
298547 AAGAGAAAGAA-
1 AAGAAAAAGAAG
*
298558 AAAAAAAAGAA-
1 AAGAAAAAGAAG
*
298569 AAGCAAAAACAAG
1 AAG-AAAAAGAAG
298582 AAGAAAAA
1 AAGAAAAA
298590 TAAAAAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
11 11 0.19
12 45 0.76
13 3 0.05
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAG
Found at i:299981 original size:50 final size:49
Alignment explanation
Indices: 299855--300089 Score: 187
Period size: 49 Copynumber: 4.8 Consensus size: 49
299845 AGTACCACGA
* *
299855 AGACAT-AAGGGAAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCAG
1 AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGACCTAGTACCTAAG
* * *
299903 AGACATAAAGGGAAAGATCT-AGACCGCAACGGCGGATCC-AGTACCATAAAG
1 AGACATAAAGGGAAAGGTTTAAG-TCGCAACGGCGGA-CCTAGTACC-T-AAG
* * * * *
299954 ATACA-AAAGGGAAAGGTTTAAGTCGCAATGGTGGACCTAGTATCTCAG
1 AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGACCTAGTACCTAAG
* * * * *
300002 AGACATAAAGGGAAAGATCT-AGACTGCAACGGCAGATCC-AGTACCACAAAG
1 AGACATAAAGGGAAAGGTTTAAGTC-GCAACGGCGGA-CCTAGTA-C-CTAAG
* * *
300053 ATACA-AAAGGGAAAGGTTAAAGTCGCAACGACGGACC
1 AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGACC
300090 GTGAAGCTCA
Statistics
Matches: 144, Mismatches: 30, Indels: 25
0.72 0.15 0.13
Matches are distributed among these distances:
48 17 0.12
49 57 0.40
50 52 0.36
51 18 0.12
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (49 bp):
AGACATAAAGGGAAAGGTTTAAGTCGCAACGGCGGACCTAGTACCTAAG
Found at i:299994 original size:99 final size:99
Alignment explanation
Indices: 299805--300185 Score: 409
Period size: 99 Copynumber: 3.9 Consensus size: 99
299795 TCAGCACCAT
* * * * * *
299805 GAGACATGAAA-GGAAAGATCTA-AGTCACAACGACAAATCCAGTACCACGAAG--ACATAAGGG
1 GAGACAT-AAAGGGAAAGATCTAGA-CCGCAACGGCAGATCCAGTACCACAAAGATACAAAAGGG
299866 AAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCA
64 AAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCA
* *
299902 GAGACATAAAGGGAAAGATCTAGACCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGAA
1 GAGACATAAAGGGAAAGATCTAGACCGCAACGGCAGATCCAGTACCACAAAGATACAAAAGGGAA
* *
299967 AGGTTTAAGTCGCAATGGTGGACCTAGTATCTCA
66 AGGTTTAAGTCGCAATGGCGGACCTAGTACCTCA
*
300001 GAGACATAAAGGGAAAGATCTAGACTGCAACGGCAGATCCAGTACCACAAAGATACAAAAGGGAA
1 GAGACATAAAGGGAAAGATCTAGACCGCAACGGCAGATCCAGTACCACAAAGATACAAAAGGGAA
* * * * *
300066 AGGTTAAAGTCGCAACGACGGACCGT-GAAGCTCA
66 AGGTTTAAGTCGCAATGGCGGACC-TAGTACCTCA
* * * * * * *** *
300100 GAAGACA-AGAAGAGAAATATTTA-AGCCGCAACGG-TGAATCCAGTACCCCGAAGATTTGAAGG
1 G-AGACATA-AAGGGAAAGATCTAGA-CCGCAACGGCAG-ATCCAGTACCACAAAGATACAAAAG
300162 GGAAAGGTTTAAGTCGCAATGGCG
62 GGAAAGGTTTAAGTCGCAATGGCG
300186 AACCCGATAC
Statistics
Matches: 242, Mismatches: 33, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
96 3 0.01
97 39 0.16
98 1 0.00
99 134 0.55
100 65 0.27
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.15
Consensus pattern (99 bp):
GAGACATAAAGGGAAAGATCTAGACCGCAACGGCAGATCCAGTACCACAAAGATACAAAAGGGAA
AGGTTTAAGTCGCAATGGCGGACCTAGTACCTCA
Found at i:300597 original size:39 final size:39
Alignment explanation
Indices: 300541--300751 Score: 167
Period size: 39 Copynumber: 5.4 Consensus size: 39
300531 CATTGTTAAA
*
300541 CAATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAAC
* * ** **
300580 CAATCTCTTACCTCGAGCCTAGGGCAGAT-AGAAGTCATT
1 CAATCTCTTACCCCGAGCTTAGGGCAGATCATCA-TCAAC
** * * * *
300619 TGATCTTTTACCCCGAGCTTGGGGAAAATCATCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAAC
** * * * **
300658 CAATCTCTTACCCCGAGCCAAAGGCAGATTAT-AGTTATT
1 CAATCTCTTACCCCGAGCTTAGGGCAGATCATCA-TCAAC
* *
300697 CGATCTCTTACTCCGAGCTTAGGGCAGATCATCATCAAC
1 CAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAAC
*
300736 CAAAT-TCCTACCCCGA
1 C-AATCTCTTACCCCGA
300752 TCACGGGGCA
Statistics
Matches: 123, Mismatches: 44, Indels: 10
0.69 0.25 0.06
Matches are distributed among these distances:
38 3 0.02
39 115 0.93
40 5 0.04
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCTTAGGGCAGATCATCATCAAC
Found at i:300762 original size:78 final size:78
Alignment explanation
Indices: 300543--300751 Score: 278
Period size: 78 Copynumber: 2.7 Consensus size: 78
300533 TTGTTAAACA
* *
300543 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCTCGAGCCTAGGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAAGGGCAGA
*
300608 TAGAAGTCATTTG
66 TAGAAGTCATTCG
* * * *
300621 ATCTTTTACCCCGAGCTTGGGGAAAATCATCATCAACCAATCTCTTACCCCGAGCCAAAGGCAGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAAGGGCAGA
* *
300686 TTA-TAGTTATTCG
66 -TAGAAGTCATTCG
* * *
300699 ATCTCTTACTCCGAGCTTAGGGCAGATCATCATCAACCAAAT-TCCTACCCCGA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACC-AATCTCTTACCCCGA
300752 TCACGGGGCA
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
78 109 0.96
79 5 0.04
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCCAAGGGCAGA
TAGAAGTCATTCG
Found at i:301156 original size:206 final size:206
Alignment explanation
Indices: 300788--301861 Score: 1498
Period size: 206 Copynumber: 5.2 Consensus size: 206
300778 AAATAGTGTG
* * * * *
300788 GCGGTCATCTTCATGATGAGATACTAAGAAGAAGACCAAATGAAACTCACGCTCGGTGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
* * * * *
300853 ATCTTCTAATCATAGCTTCCTGATGAGATACTAAGAAGCGGGTCGAAGCAATAAAAGGGTTAGCT
66 ATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAATGGTTAGCT
** * * *
300918 TCCTGATGAGATACTGAGAAGCAGATCAAATTCATCTTCCTGATGAGATACAGAGAAGCGGATTG
131 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTG
*
300983 AAAAAAATGAC
196 AAAAAAACGAC
** * *
300994 GCTATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACTCACGCTCAATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
*
301059 ATCTTCGAATCCTAGCTTCCTGATGAGATATTGAGAAGCGAGTCGAAGCAATAAAATGGTTAGCT
66 ATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAATGGTTAGCT
** * * *
301124 TATTGATGATATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGGGATACAGAGAAGTGGATTG
131 TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTG
*
301189 AAACAAACGAC
196 AAAAAAACGAC
* *
301200 GCGGTCATCTTCTTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
* * *
301265 ATCTTCGAATCCCAGCTTCTTGATGAGATATTGAGAAGCG-GTTCGAAGCAATAAAATGGTTAGC
66 ATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGAG-TCGAAGCAATAAAATGGTTAGC
* *
301329 TTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATATAGAGAAGAGGATT
130 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGATT
301394 GAAACAAAA-GAC
195 GAAA-AAAACGAC
301406 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
* *
301471 ATCTTCGAAT-CTCAGCTTCCTGATGAGATACTGAGAAGAGGGTCGAAGCAATAAAATGGTTAGC
66 ATCTTCGAATCCT-AGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAATGGTTAGC
*
301535 TTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGAT-ATGATACAGAGAAGAGGAT
130 TTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGA-GATACAGAGAAGAGGAT
*
301599 TGAAACAAACGAC
194 TGAAAAAAACGAC
* *
301612 GCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCAAATCAAACCCACACTCGATGTGAGCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
* * * * **
301677 ATCTTCGAACCCTAGCTTCCGGATGAGATACTGAGAAGC-AGGTCGAAGTAATAAAGTTATTAGC
66 ATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGA-GTCGAAGCAATAAAATGGTTAGC
* * * * * *
301741 TCCCAT-ATGAGATACGGAGAAGTGAACCAAA-TCTGTCTTCCTGATGAAACACAGAGAAGTGGA
130 TTCC-TGATGAGATACTGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGATACAGAGAAGAGGA
* * *
301804 -TCAAAAAAAGTGAT
193 TTGAAAAAAA-CGAC
* * *
301818 GCGGTCACCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
1 GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
301862 TGAAACCAAA
Statistics
Matches: 781, Mismatches: 75, Indels: 24
0.89 0.09 0.03
Matches are distributed among these distances:
205 15 0.02
206 758 0.97
207 8 0.01
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (206 bp):
GCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAA
ATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCGAGTCGAAGCAATAAAATGGTTAGCT
TCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGAGGATTG
AAAAAAACGAC
Found at i:302931 original size:31 final size:31
Alignment explanation
Indices: 302887--302952 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
302877 TGAATATTTG
* *
302887 TATTCTTAATAATAATAATATTGACAATAAA
1 TATTCTTAATAATAATAACATTAACAATAAA
* * * *
302918 TATTGTTATTAATAATGACATTAATAATAAA
1 TATTCTTAATAATAATAACATTAACAATAAA
302949 TATT
1 TATT
302953 ATCAATAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (31 bp):
TATTCTTAATAATAATAACATTAACAATAAA
Found at i:303001 original size:21 final size:21
Alignment explanation
Indices: 302947--303018 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
302937 ATTAATAATA
* * *
302947 AATATTATCAATAAATAGCATT
1 AATAATATTAATAAA-AACATT
*
302969 AATAAGTATTAATAAAAATATT
1 AATAA-TATTAATAAAAACATT
*
302991 ATTAATATTAATAAAAACATT
1 AATAATATTAATAAAAACATT
303012 AATAATA
1 AATAATA
303019 ATAAAAGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.50
22 12 0.29
23 9 0.21
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (21 bp):
AATAATATTAATAAAAACATT
Found at i:304245 original size:30 final size:29
Alignment explanation
Indices: 304115--304370 Score: 335
Period size: 29 Copynumber: 8.8 Consensus size: 29
304105 GAAGGTCCCA
*
304115 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCG
304144 AAACTTCCAAAAATTCCATTTTTATCCCC-
1 AAACTTCCAAAAATTCCATTTTTA-CCCCG
304173 AAACTTCCAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTTACCCC-G
* *
304203 -AACTT-TAAAAATTCAATTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTTACCCCG
*
304231 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
*
304261 AAACTTCCAAAAATTCCATTTTTACTCTC-
1 AAACTTCCAAAAATTCCATTTTTAC-CCCG
*
304290 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCG
304320 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CG
*
304350 -AA-TGTCCAAAAACTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
304371 CGACCTCAAA
Statistics
Matches: 208, Mismatches: 7, Indels: 24
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.07
29 122 0.59
30 71 0.34
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCG
Found at i:304296 original size:59 final size:59
Alignment explanation
Indices: 304110--304390 Score: 337
Period size: 59 Copynumber: 4.8 Consensus size: 59
304100 ACCCTGAAGG
* *
304110 TCCCAAAACTTCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTA-
1 TCCC-AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
* * *
304168 TCCCCAAACTTCCAAAAATTCCATTTTT-ACCCCTG-AACTT-TAAAAATTCAATTTTTTAC
1 T-CCCAAACTTCCAAAAATTCCATTTTTGACCTC-GAAACTTCCAAAAATTCCA-TTTTTAC
304227 -CCCGAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 TCCC-AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
*
304286 TCTCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
1 TCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
* * * *
304345 -CCTCGAA-TGTCCAAAAACTCCATTTTCGACCTC-AAAATTCTCAAAA
1 TCC-CAAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTTC-CAAAA
304391 TTACCCTTTT
Statistics
Matches: 199, Mismatches: 12, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
57 12 0.06
58 72 0.36
59 104 0.52
60 11 0.06
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTAC
Found at i:304377 original size:29 final size:29
Alignment explanation
Indices: 304115--304434 Score: 282
Period size: 29 Copynumber: 11.0 Consensus size: 29
304105 GAAGGTCCCA
* * *
304115 AAACTTCCAAAAATTCCATTTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTGACCTCG
* *
304144 AAACTTCCAAAAATTCCATTTTTATCC-CC
1 AAACTTCCAAAAATTCCATTTTGA-CCTCG
* *
304173 AAACTTCCAAAAATTCCATTTTTACCCCTG
1 AAACTTCCAAAAATTCCATTTTGACCTC-G
* * * *
304203 -AACTT-TAAAAATTCAATTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCTCG
304231 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTGACCTCG
*
304261 AAACTTCCAAAAATTCCATTTTTACTCTC-
1 AAACTTCCAAAAATTCCATTTTGAC-CTCG
304290 AAACTTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCA-TTTTGACCTCG
*
304320 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGA-CCTCG
*
304350 -AA-TGTCCAAAAACTCCATTTTCGACCTC-
1 AAACT-TCCAAAAATTCCATTTT-GACCTCG
* *
304378 AAAATTCTC-AAAATTACCCTTTT-ACCCTCG
1 AAACTTC-CAAAAATT-CCATTTTGA-CCTCG
* * * *
304408 -ATCCTCTAAAATTTCCATTTTGACCTC
1 AAACTTCCAAAAATTCCATTTTGACCTC
304435 AAAATTACCA
Statistics
Matches: 251, Mismatches: 20, Indels: 41
0.80 0.06 0.13
Matches are distributed among these distances:
28 24 0.10
29 147 0.59
30 80 0.32
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCTCG
Found at i:304425 original size:58 final size:58
Alignment explanation
Indices: 304236--304513 Score: 237
Period size: 59 Copynumber: 4.9 Consensus size: 58
304226 CCCCGAAACT
* * * *
304236 TCCAAAAATTCCATTTTTGACCTCGAAACTTC-CAAAAATT-CCATTTTTACTCTCAAACT-
1 TCCAAAAATTCCATTTTCGACCTC-AAAATTCTC-AAAATTACCA-TTTTACCCTCGAA-TG
* *
304295 TCCAAAAATTCCATTTTTGACCTCGAAACTTC-CAAAAATT-CCATTTTTACCCTCGAATG
1 TCCAAAAATTCCATTTTCGACCTC-AAAATTCTC-AAAATTACCA-TTTTACCCTCGAATG
* * *
304354 TCCAAAAACTCCATTTTCGACCTCAAAATTCTCAAAATTACCCTTTTACCCTCG-ATCC
1 TCCAAAAATTCCATTTTCGACCTCAAAATTCTCAAAATTACCATTTTACCCTCGAAT-G
* *
304412 TCTAAAATTTCCATTTT-GA---C------CTCAAAATTACCATTTTACCCTCGAATG
1 TCCAAAAATTCCATTTTCGACCTCAAAATTCTCAAAATTACCATTTTACCCTCGAATG
* * * *
304460 TCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATTACCGTTTTACCCTCG
1 TCCAAAAATTCCATTTTCGACCTCAAAATTCTCAAAATTACCATTTTACCCTCG
304514 CATATCTAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 31
0.80 0.07 0.13
Matches are distributed among these distances:
48 37 0.20
49 4 0.02
52 1 0.01
54 1 0.01
57 4 0.02
58 61 0.32
59 80 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.33
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTCGACCTCAAAATTCTCAAAATTACCATTTTACCCTCGAATG
Found at i:304454 original size:20 final size:21
Alignment explanation
Indices: 304410--304448 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
304400 TACCCTCGAT
*
304410 CCTCTAAAATTTCCATTTTGA
1 CCTCTAAAATTACCATTTTGA
304431 CCTC-AAAATTACCATTTT
1 CCTCTAAAATTACCATTTT
304449 ACCCTCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.26, G:0.03, T:0.41
Consensus pattern (21 bp):
CCTCTAAAATTACCATTTTGA
Found at i:304457 original size:106 final size:105
Alignment explanation
Indices: 304329--304533 Score: 333
Period size: 106 Copynumber: 1.9 Consensus size: 105
304319 GAAACTTCCA
*
304329 AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCAAAATTCTCAAAATTA
1 AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCAAAACTCTCAAAATTA
*
304394 CCCTTTTACCCTCG-ATCCTCTAAAATTTCCATTTTGACCTC
66 CCCTTTTACCCTCGCAT-ATCTAAAATTT-CATTTTGACCTC
*
304435 AAAATTACCA-TTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATT
1 AAAATT-CCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCAAAACTCTCAAAATT
*
304499 ACCGTTTTACCCTCGCATATCTAAAATTTCATTTT
65 ACCCTTTTACCCTCGCATATCTAAAATTTCATTTT
304534 AAACCCCAAA
Statistics
Matches: 93, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
105 6 0.06
106 82 0.88
107 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (105 bp):
AAAATTCCATTTTTACCCTCGAATGTCCAAAAACTCCATTTTCGACCTCAAAACTCTCAAAATTA
CCCTTTTACCCTCGCATATCTAAAATTTCATTTTGACCTC
Found at i:304466 original size:28 final size:28
Alignment explanation
Indices: 304434--304596 Score: 86
Period size: 29 Copynumber: 5.7 Consensus size: 28
304424 ATTTTGACCT
*
304434 CAAAATTACCATTTTACCCTCGAATGTC
1 CAAAATTACCATTTTACCCTCGAATATC
*
304462 CAAAAACT-CCATTTT-CGACCTCGAA-ACTC
1 C-AAAATTACCATTTTAC--CCTCGAATA-TC
* *
304491 TCAAAATTACCGTTTTACCCTCGCATATC
1 -CAAAATTACCATTTTACCCTCGAATATC
* * * *
304520 TAAAATT-TCATTTTAAACCC-CAAATTTTCC
1 CAAAATTACCATTTT--ACCCTCGAA-TAT-C
* * *
304550 CAGAATTACCATTTTGCCCCCGAGA-ATC
1 CAAAATTACCATTTTACCCTCGA-ATATC
*
304578 TAAAATTACCATTTTACCC
1 CAAAATTACCATTTTACCC
304597 CTAGGTATCC
Statistics
Matches: 100, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
27 6 0.06
28 33 0.33
29 37 0.37
30 16 0.16
31 8 0.08
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCTCGAATATC
Found at i:304473 original size:48 final size:49
Alignment explanation
Indices: 304384--304483 Score: 132
Period size: 48 Copynumber: 2.1 Consensus size: 49
304374 CCTCAAAATT
* * **
304384 CTCAAAATTACCCTTTTACCCTCGATCCTCTAAAATTTCCATTTT-GAC
1 CTCAAAATTACCATTTTACCCTCGATCCTCCAAAAACTCCATTTTCGAC
*
304432 CTCAAAATTACCATTTTACCCTCGAAT-GTCCAAAAACTCCATTTTCGAC
1 CTCAAAATTACCATTTTACCCTCG-ATCCTCCAAAAACTCCATTTTCGAC
304481 CTC
1 CTC
304484 GAAACTCTCA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
48 37 0.82
49 8 0.18
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (49 bp):
CTCAAAATTACCATTTTACCCTCGATCCTCCAAAAACTCCATTTTCGAC
Found at i:304610 original size:28 final size:28
Alignment explanation
Indices: 304553--304610 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
304543 ATTTTCCCAG
* * *
304553 AATTACCATTTTGCCCCCGAGAATCTAA
1 AATTACCATTTTACCCCAGAGAATCCAA
*
304581 AATTACCATTTTACCCCTAG-GTATCCAA
1 AATTACCATTTTACCCC-AGAGAATCCAA
304609 AA
1 AA
304611 AGTCTCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.29
Consensus pattern (28 bp):
AATTACCATTTTACCCCAGAGAATCCAA
Found at i:317393 original size:72 final size:72
Alignment explanation
Indices: 317311--317457 Score: 267
Period size: 72 Copynumber: 2.0 Consensus size: 72
317301 ATAAGAAAAA
* *
317311 TATATCAAAATAAATAGTTAGTTTAATAAATAAAATATATTCAACATAATGATATATTAAAAATA
1 TATATCAAAATAAATAGTTAATTTAATAAATAAAATATATTCAACATAATGATATATTAAAAAAA
317376 TATATTT
66 TATATTT
*
317383 TATATCAAAATAAATAGTTAATTTAATAAATAAAATATATTCAACGTAATGATATATTAAAAAAA
1 TATATCAAAATAAATAGTTAATTTAATAAATAAAATATATTCAACATAATGATATATTAAAAAAA
317448 TATATTT
66 TATATTT
317455 TAT
1 TAT
317458 TATATATTTA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (72 bp):
TATATCAAAATAAATAGTTAATTTAATAAATAAAATATATTCAACATAATGATATATTAAAAAAA
TATATTT
Found at i:317422 original size:35 final size:35
Alignment explanation
Indices: 317307--317422 Score: 114
Period size: 35 Copynumber: 3.3 Consensus size: 35
317297 ATATATAAGA
*
317307 AAAATATATCAAAATAAATAGTTAGTTTAATAAAT
1 AAAATATATCAAAATAAATAGTTAATTTAATAAAT
* *
317342 AAAATATATTCAACAT-AAT-GAT-ATATTAA-AAAT
1 AAAATATA-TCAAAATAAATAGTTAAT-TTAATAAAT
*
317375 ATATATTTTATATCAAAATAAATAGTTAATTTAATAAAT
1 A-A-A--ATATATCAAAATAAATAGTTAATTTAATAAAT
317414 AAAATATAT
1 AAAATATAT
317423 TCAACGTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
33 6 0.09
34 7 0.11
35 17 0.27
36 12 0.19
37 8 0.12
38 7 0.11
39 7 0.11
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (35 bp):
AAAATATATCAAAATAAATAGTTAATTTAATAAAT
Found at i:321216 original size:26 final size:26
Alignment explanation
Indices: 321185--321239 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
321175 CCGAATTAGT
321185 TCGGTTAACCAACCGAATTTGATTAA
1 TCGGTTAACCAACCGAATTTGATTAA
**** *
321211 TCGGTTGGTTAATCGAATTTGATTAA
1 TCGGTTAACCAACCGAATTTGATTAA
321237 TCG
1 TCG
321240 ATCAGTTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (26 bp):
TCGGTTAACCAACCGAATTTGATTAA
Found at i:321238 original size:14 final size:14
Alignment explanation
Indices: 321198--321240 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
321188 GTTAACCAAC
321198 CGAATTTGATTAAT
1 CGAATTTGATTAAT
* *
321212 CG--GTTGGTTAAT
1 CGAATTTGATTAAT
321224 CGAATTTGATTAAT
1 CGAATTTGATTAAT
321238 CGA
1 CGA
321241 TCAGTTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (14 bp):
CGAATTTGATTAAT
Found at i:321255 original size:26 final size:26
Alignment explanation
Indices: 321198--321247 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
321188 GTTAACCAAC
* **
321198 CGAATTTGATTAATCGGTTGGTTAAT
1 CGAATTTGATTAATCGATCAGTTAAT
321224 CGAATTTGATTAATCGATCAGTTA
1 CGAATTTGATTAATCGATCAGTTA
321248 CCTGAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (26 bp):
CGAATTTGATTAATCGATCAGTTAAT
Found at i:323017 original size:91 final size:91
Alignment explanation
Indices: 322901--323069 Score: 234
Period size: 91 Copynumber: 1.9 Consensus size: 91
322891 ATGTGGTACC
* * * * * *
322901 TGAACTATTAATTTATGAATTATTTGGTACT-TGTACTTTCATAAAATGTTTGATGTGGTATCTA
1 TGAACTATCAATTTATGAATTATTTGGTA-TATATACTTTCATAAAATATCTAATGTGATATCTA
322965 TACTTTAAAAATGTCCAACGTGATACT
65 TACTTTAAAAATGTCCAACGTGATACT
*
322992 TGAACTATCAATTTAT-ATATTATTTGGTATATATACTTTCATAAAATATCTAATGTGATATTTA
1 TGAACTATCAATTTATGA-ATTATTTGGTATATATACTTTCATAAAATATCTAATGTGATATCTA
*
323056 TACTTTGAAAATGT
65 TACTTTAAAAATGT
323070 TCAATGAGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
90 2 0.03
91 66 0.97
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.44
Consensus pattern (91 bp):
TGAACTATCAATTTATGAATTATTTGGTATATATACTTTCATAAAATATCTAATGTGATATCTAT
ACTTTAAAAATGTCCAACGTGATACT
Found at i:323766 original size:62 final size:62
Alignment explanation
Indices: 323628--323773 Score: 213
Period size: 62 Copynumber: 2.4 Consensus size: 62
323618 TTTCAAAATA
*
323628 TAAGTACCACATTGAAAATTTTATGAAAGTTCAAGTACCAAATAATACACAAATTGATAGTT
1 TAAGTACCACATTGGAAATTTTATGAAAGTTCAAGTACCAAATAATACACAAATTGATAGTT
* * * *
323690 TAGGTACCACATTGGATATTTTATGAAAGTAT-AAGTTCCAAATAATACATAAATTGATAGTT
1 TAAGTACCACATTGGAAATTTTATGAAAGT-TCAAGTACCAAATAATACACAAATTGATAGTT
* *
323752 TAAGTACTACATTGGACATTTT
1 TAAGTACCACATTGGAAATTTT
323774 CAAATACAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
62 74 0.99
63 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (62 bp):
TAAGTACCACATTGGAAATTTTATGAAAGTTCAAGTACCAAATAATACACAAATTGATAGTT
Found at i:323800 original size:28 final size:28
Alignment explanation
Indices: 323760--323847 Score: 140
Period size: 28 Copynumber: 3.0 Consensus size: 28
323750 TTTAAGTACT
323760 ACATTGGACATTTTCAAATACAAATACC
1 ACATTGGACATTTTCAAATACAAATACC
323788 ACATTGGACATTTTCAAATACAAATACC
1 ACATTGGACATTTTCAAATACAAATACC
*
323816 ACATTGGACATTTTATATAAATACAAATACC
1 ACATTGGACA-TTT-T-CAAATACAAATACC
323847 A
1 A
323848 AATGTGACAT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
28 38 0.68
29 3 0.05
30 1 0.02
31 14 0.25
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (28 bp):
ACATTGGACATTTTCAAATACAAATACC
Found at i:325965 original size:30 final size:30
Alignment explanation
Indices: 325931--326039 Score: 184
Period size: 30 Copynumber: 3.6 Consensus size: 30
325921 TTAAAAATCC
325931 CATTTTGACCCTCAAACTTCTCCAAAATTA
1 CATTTTGACCCTCAAACTTCTCCAAAATTA
325961 CATTTTGACCCTCAAACTTCTCCAAAATTA
1 CATTTTGACCCTCAAACTTCTCCAAAATTA
* *
325991 CATTTTAACCTTCAAACTTCTCCAAAATTA
1 CATTTTGACCCTCAAACTTCTCCAAAATTA
326021 CATTTTGATCCCT-AAACTT
1 CATTTTGA-CCCTCAAACTT
326040 TCTAAGAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
30 71 0.96
31 3 0.04
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
CATTTTGACCCTCAAACTTCTCCAAAATTA
Found at i:329140 original size:84 final size:82
Alignment explanation
Indices: 328976--329149 Score: 312
Period size: 84 Copynumber: 2.1 Consensus size: 82
328966 AATATAAGAC
*
328976 GAGGTAGTTTATCCCTACGACTCATGGCCTAGCCCAGTACGAGTTCACATACAAAGAGAATGATT
1 GAGGTAGCTTATCCCTACGACTCATGGCCTAGCCCAGTACGAGTTCACATACAAAGAGAATGATT
329041 ACAAGAAAAGGATTCGA
66 ACAAGAAAAGGATTCGA
*
329058 GAGGTAGCNTATCCCTACGACTCATGGCCTAGCCCAGTACGAGAGTTCACATACAAAGAGAATGA
1 GAGGTAGCTTATCCCTACGACTCATGGCCTAGCCCAGTAC--GAGTTCACATACAAAGAGAATGA
329123 TTACAAGAAAAGGATTCGA
64 TTACAAGAAAAGGATTCGA
329142 GAGGTAGC
1 GAGGTAGC
329150 GAATGCATGA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
82 38 0.43
84 50 0.57
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (82 bp):
GAGGTAGCTTATCCCTACGACTCATGGCCTAGCCCAGTACGAGTTCACATACAAAGAGAATGATT
ACAAGAAAAGGATTCGA
Found at i:330789 original size:12 final size:12
Alignment explanation
Indices: 330772--330826 Score: 101
Period size: 12 Copynumber: 4.6 Consensus size: 12
330762 TATAAGCGAT
*
330772 TAGAGGAGAAGA
1 TAGAGGCGAAGA
330784 TAGAGGCGAAGA
1 TAGAGGCGAAGA
330796 TAGAGGCGAAGA
1 TAGAGGCGAAGA
330808 TAGAGGCGAAGA
1 TAGAGGCGAAGA
330820 TAGAGGC
1 TAGAGGC
330827 AATGCAAGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.42, C:0.07, G:0.42, T:0.09
Consensus pattern (12 bp):
TAGAGGCGAAGA
Found at i:338663 original size:38 final size:38
Alignment explanation
Indices: 338612--338750 Score: 142
Period size: 38 Copynumber: 3.7 Consensus size: 38
338602 ATCCAATATT
*
338612 TTTA-CCCAGAGCTTGGGGTAGATCACAGTCATTCGACC
1 TTTACCCCA-AGCTTGGGGCAGATCACAGTCATTCGACC
* *
338650 TTTACCCCAAGCTTGGGGTAGATCACAGTCATTCGATCT
1 TTTACCCCAAGCTTGGGGCAGATCACAGTCATTCGA-CC
* * * * *
338689 TTTACCCCGAGCTTGAGGCATATCAC---CATCCGATC
1 TTTACCCCAAGCTTGGGGCAGATCACAGTCATTCGACC
*
338724 TCTTACCCCGAGCTTGGGGCAGATCAC
1 T-TTACCCCAAGCTTGGGGCAGATCAC
338751 CATTAGCCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
35 1 0.01
36 29 0.33
38 31 0.35
39 27 0.31
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (38 bp):
TTTACCCCAAGCTTGGGGCAGATCACAGTCATTCGACC
Found at i:338775 original size:39 final size:39
Alignment explanation
Indices: 338685--339315 Score: 234
Period size: 39 Copynumber: 16.3 Consensus size: 39
338675 CAGTCATTCG
* * * *
338685 ATCTTTTACCCCGAGCTTGAGGCATATCACCA-T--CCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
338721 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* * * *
338760 ATCTGTTACCCCGAGCTTGGGGTAGATTGTAGCCA-T--CCG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATTAGCCA
*
338799 ATCTCTTTCCCCGAGCTTGGGGCAGATCACCATT-GACCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAG-CCA
* * **
338838 ATCTCTTACCCCAAGCCTATGGCAGATTACAGCCATCT-G---
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCAT-TAGCCA
* * * * * *
338877 ATCTTTTACCACGAGCCTGGGGTAGATCACTATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* *
338916 ATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCA-T-G---
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCATTAGCCA
* ** * * * *
338953 ATCTCTTACCCCGAGCCTAAGGCAAATCACCATCAACAA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* * *
338992 ATCTCTTACCCCGAGCTTGGAGTAGATTGCAGCCATT---CG
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATTAGCCA
* * * * * * *
339031 ACCTGTTACTCCGAACCTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* * *
339070 ATCTCTTACCCCGAACTTGGGGTAGATTGCAACCATTTGACC-
1 ATCTCTTACCCCGAGCTTGGGGCAGA-T-C-ACCATTAG-CCA
* * * *
339112 -T-T-TTACCCCGATCATGGGGTAGATCA-CATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* * * ** * * **
339147 ATCTCTTACCCCGAGCCTGAGGCGGATTGCAATCATTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* *** * *
339186 A-CTTGTTACCTAAAGCTTGGGGCAAATCACCATCAGCCA
1 ATC-TCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
* * * * * ** *
339225 ATCTCTTACCTCAAGCTTGGGACAGAT-AGCAACTATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCA-CCATTAGCCA
* * * **
339264 ATCTTTTACCCCGATCATGGGGCAGATCACTGTTAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
*
339303 ATCTCTTTCCCCG
1 ATCTCTTACCCCG
339316 TGACAGGGGT
Statistics
Matches: 436, Mismatches: 115, Indels: 85
0.69 0.18 0.13
Matches are distributed among these distances:
34 6 0.01
35 5 0.01
36 43 0.10
37 33 0.08
38 23 0.05
39 285 0.65
40 9 0.02
41 9 0.02
42 20 0.05
43 3 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCA
Found at i:338817 original size:78 final size:78
Alignment explanation
Indices: 338585--339351 Score: 530
Period size: 78 Copynumber: 9.9 Consensus size: 78
338575 ACGTCGATCA
* * * * * * ** * * *
338585 TGGGGTAGATCACAATCATCCAATATTTTTACCCAGAGCTTGGGGTAGATCACAGTCATTCGACC
1 TGGGGCAGATCACCATCAGCCAAT-CTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATC
* *
338650 T-TTACCCCAAGCT
65 TCTTACCCCGAGCC
* ** * * * * *
338663 TGGGGTAGATCA-CAGTCATTCGATCTTTTACCCCGAGCTTGAGGCATA-T-CA-CCATCCGATC
1 TGGGGCAGATCACCA-TCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATC
*
338724 TCTTACCCCGAGCT
65 TCTTACCCCGAGCC
* * *
338738 TGGGGCAGATCACCATTAGCCAATCTGTTACCCCGAGCTTGGGGTAGATTGTAGCCATCCGATCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
* *
338803 CTTTCCCCGAGCT
66 CTTACCCCGAGCC
* * * ** * * *
338816 TGGGGCAGATCACCAT-TGACCAATCTCTTACCCCAAGCCTATGGCAGATTACAGCCATCTGATC
1 TGGGGCAGATCACCATCAG-CCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATC
* *
338880 TTTTACCACGAGCC
65 TCTTACCCCGAGCC
* * * * * *
338894 TGGGGTAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCAT--GATCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
338957 CTTACCCCGAGCC
66 CTTACCCCGAGCC
** * * * * * *
338970 TAAGGCAAATCACCATCAACAAATCTCTTACCCCGAGCTTGGAGTAGATTGCAGCCATTCGACCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
* * *
339035 GTTACTCCGAACC
66 CTTACCCCGAGCC
* * * ** *
339048 TGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAACTTGGGGTAGATTGCAACCATTTGACCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
* * *
339113 TTTACCCCGATCA
66 CTTACCCCGAGCC
* * * ** ** * *
339126 TGGGGTAGATCA-CATCAGCCAATCTCTTACCCCGAGCCTGAGGCGGATTGCAATCATTC-AACT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATC-
* *** *
339189 TGTTACCTAAAGCT
65 TCTTACCCCGAGCC
* * * ** * * * *
339203 TGGGGCAAATCACCATCAGCCAATCTCTTACCTCAAGCTTGGGACAGATAGCAACTATTCGATCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
* * *
339268 TTTACCCCGATCA
66 CTTACCCCGAGCC
** * * * * * * *
339281 TGGGGCAGATCACTGTTAGCCAATCTCTTTCCCCGTGAC-AGGGGTAGATTGCAACCATCCAATA
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAG-CTTGGGGTAGATTGCAGCCATCCGATC
339345 TCTTACC
65 TCTTACC
339352 AAAAAAAAAT
Statistics
Matches: 544, Mismatches: 131, Indels: 28
0.77 0.19 0.04
Matches are distributed among these distances:
74 8 0.01
75 49 0.09
76 67 0.12
77 79 0.15
78 337 0.62
79 4 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (78 bp):
TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCT
CTTACCCCGAGCC
Found at i:339019 original size:232 final size:232
Alignment explanation
Indices: 338646--339178 Score: 603
Period size: 232 Copynumber: 2.3 Consensus size: 232
338636 ACAGTCATTC
* * * ** * * *
338646 GACC-TTTACCCCAAGCTTGGGGTAGATCACAGTCATTCGATCTTTTACCCCGAGCTTGAGGCAT
1 GACCTTTTACCACGAGCATGGGGTAGATCACA-TCAGCCAATCTCTTACCCCGAGCTTGAGGCAA
* ** * * * * *
338710 A-T-C-ACCATCCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAGCCAATCTGTTACCCC
65 ATTGCAACCAT-CGATCTCTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCC
* * * * * * *
338772 GAGCTTGGGGTAGATTGTAGCCATCCGATCTCTTTCCCCGAGCTTGGGGCAGATCACCAT-TGAC
129 GAGCTTGGAGTAGATTGCAGCCATCCGACCTCTTACCCCGAACCTGGGGCAGATCACCATCAG-C
* *
338836 CAATCTCTTACCCC-AAGCCTATGGCAGATTACAGCCATCT
193 CAATCTCTTACCCCGAA-CCTAGGGCAGATTACAACCATCT
* *
338876 GATCTTTTACCACGAGCCTGGGGTAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGAGGCAA
1 GACCTTTTACCACGAGCATGGGGTAGATCAC-ATCAGCCAATCTCTTACCCCGAGCTTGAGGCAA
338941 ATTGCAACCAT-GATCTCTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCG
65 ATTGCAACCATCGATCTCTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCG
* * * *
339005 AGCTTGGAGTAGATTGCAGCCATTCGACCTGTTACTCCGAACCTGGGGCAGATCACCATCAGTCA
130 AGCTTGGAGTAGATTGCAGCCATCCGACCTCTTACCCCGAACCTGGGGCAGATCACCATCAGCCA
* * * * *
339070 ATCTCTTACCCCGAACTTGGGGTAGATTGCAACCATTT
195 ATCTCTTACCCCGAACCTAGGGCAGATTACAACCATCT
* * * **
339108 GACCTTTTACCCCGATCATGGGGTAGATCACATCAGCCAATCTCTTACCCCGAGCCTGAGGCGGA
1 GACCTTTTACCACGAGCATGGGGTAGATCACATCAGCCAATCTCTTACCCCGAGCTTGAGGCAAA
339173 TTGCAA
66 TTGCAA
339179 TCATTCAACT
Statistics
Matches: 254, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
230 3 0.01
231 88 0.35
232 154 0.61
233 4 0.02
234 5 0.02
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (232 bp):
GACCTTTTACCACGAGCATGGGGTAGATCACATCAGCCAATCTCTTACCCCGAGCTTGAGGCAAA
TTGCAACCATCGATCTCTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCGA
GCTTGGAGTAGATTGCAGCCATCCGACCTCTTACCCCGAACCTGGGGCAGATCACCATCAGCCAA
TCTCTTACCCCGAACCTAGGGCAGATTACAACCATCT
Found at i:339050 original size:154 final size:155
Alignment explanation
Indices: 338738--339277 Score: 443
Period size: 154 Copynumber: 3.5 Consensus size: 155
338728 ACCCCGAGCT
* * * *
338738 TGGGGCAGATCACCATTAGCCAATCTGTTACCCCGAGCTTGGGGTAGATTGTAGCCATCCGATCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCAT-CGATCT
* * ** * ** *
338803 CTTTCCCCGAGCTTGGGGCAGATCACCATTGACCAATCTCTTACCCCAAGCCTATGGCAGATTAC
65 CTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCAAGCCTATGGCAGATTAC
* * *
338868 AGCCATCTGATCTTTTACCACGAGCC
130 AGCCATCTGACCTGTTACCACGAACC
* * * * *
338894 TGGGGTAGATCACTATCAGCCAATCTCTTACCCCGAGCTTGAGGCAAATTGCAACCAT-GATCTC
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATCGATCTC
* * *
338958 TTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCGAG-CT-TGGAGTAGATTG
66 TTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCAAGCCTAT-G-GCAGATTA
339021 CAGCCAT-TCGACCTGTTACTC-CGAACC
129 CAGCCATCT-GACCTGTTAC-CACGAACC
* * * *
339048 TGGGGCAGATCACCATCAGTCAATCTCTTACCCCGAACTTGGGGTAGATTGCAACCATTTGACCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCA-TCGATCT
* * * ** * * * * * * *
339113 TTTACCCCGATCATGGGGTAGATCA-CATCAGCCAATCTCTTACCCCGAGCCTGA-GGCGGATTG
65 CTTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCAAGCCT-ATGGCAGATTA
** * * *
339176 CAATCAT-TCAACTTGTTACCTA--AAGCT
129 CAGCCATCT-GACCTGTTACC-ACGAA-CC
* * * ** * *
339203 TGGGGCAAATCACCATCAGCCAATCTCTTACCTCAAGCTTGGGACAGATAGCAACTATTCGATCT
1 TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCA-TCGATCT
*
339268 TTTACCCCGA
65 CTTACCCCGA
339278 TCATGGGGCA
Statistics
Matches: 314, Mismatches: 58, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
152 1 0.00
153 4 0.01
154 125 0.40
155 110 0.35
156 74 0.24
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (155 bp):
TGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTGCAACCATCGATCTC
TTACCCCGAGCCTAAGGCAAATCACCATCAACAAATCTCTTACCCCAAGCCTATGGCAGATTACA
GCCATCTGACCTGTTACCACGAACC
Done.