Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005618.1 Hibiscus syriacus cultivar Beakdansim tig00013066_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60046
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:993 original size:19 final size:19
Alignment explanation
Indices: 969--1010 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
959 AAATTCTTTT
969 TTAAAAT-TAAAAAATCACA
1 TTAAAATAT-AAAAATCACA
*
988 TTAAAATATATAAATCACA
1 TTAAAATATAAAAATCACA
1007 TTAA
1 TTAA
1011 TTCTTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAAATATAAAAATCACA
Found at i:2527 original size:25 final size:26
Alignment explanation
Indices: 2499--2554 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
2489 TACTTTATGA
2499 AAATT-AAATACAGACAAAATGTTGC
1 AAATTAAAATACAGACAAAATGTTGC
*
2524 AAATTAAAATACAGACACAATGTTGC
1 AAATTAAAATACAGACAAAATGTTGC
2550 AAATT
1 AAATT
2555 CATAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.25
Consensus pattern (26 bp):
AAATTAAAATACAGACAAAATGTTGC
Found at i:3260 original size:16 final size:16
Alignment explanation
Indices: 3241--3294 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3231 TTAACCAGAT
*
3241 CCGAAAGTAACTCAAA
1 CCGAAAGTAACTCGAA
* *
3257 CCGAAATTAACTTGAA
1 CCGAAAGTAACTCGAA
* *
3273 CCAAAAGTAATTCGAA
1 CCGAAAGTAACTCGAA
3289 CCGAAA
1 CCGAAA
3295 ATCCATATAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.22, G:0.13, T:0.17
Consensus pattern (16 bp):
CCGAAAGTAACTCGAA
Found at i:3280 original size:32 final size:32
Alignment explanation
Indices: 3194--3294 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
3184 TAACCCGAAT
* * *
3194 CGAAATTAA-TCTGAACCAAAAGCAACCCAAAT
1 CGAAATTAACT-TGAACCAAAAGTAACTCAAAC
* * ** * *
3226 TGAATTTAACCAGATCCGAAAGTAACTCAAAC
1 CGAAATTAACTTGAACCAAAAGTAACTCAAAC
* *
3258 CGAAATTAACTTGAACCAAAAGTAATTCGAAC
1 CGAAATTAACTTGAACCAAAAGTAACTCAAAC
3290 CGAAA
1 CGAAA
3295 ATCCATATAT
Statistics
Matches: 51, Mismatches: 17, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.19
Consensus pattern (32 bp):
CGAAATTAACTTGAACCAAAAGTAACTCAAAC
Found at i:4351 original size:26 final size:25
Alignment explanation
Indices: 4304--4356 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
4294 CTCAACAACT
* *
4304 AACTCTATTTTGCTCTTCTATTTGC
1 AACTCTATTTTACTCTTCTATTCGC
*
4329 AACTCTATTTTTACTCTTTTATTCGC
1 AACTCTA-TTTTACTCTTCTATTCGC
4355 AA
1 AA
4357 GTCAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.21, C:0.23, G:0.06, T:0.51
Consensus pattern (25 bp):
AACTCTATTTTACTCTTCTATTCGC
Found at i:15379 original size:20 final size:20
Alignment explanation
Indices: 15356--15407 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
15346 ATTTCGCAAC
* *
15356 GCGAATTTGGCTTTCGCGCT
1 GCGAATTTGACTTTCACGCT
* *
15376 GCGAATTTGACTTTTACGTT
1 GCGAATTTGACTTTCACGCT
15396 GCGAATTTGACT
1 GCGAATTTGACT
15408 ATCGCAACGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGCT
Found at i:17108 original size:42 final size:42
Alignment explanation
Indices: 17011--17110 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
17001 GGCGAGCAGG
* * * * *
17011 ACCTCTTGAATGATGATAGGAGCCTCTTGAACGGTGGGAGGG
1 ACCTCTTGAATGATGAGAGGAGCCTCTTAAACGATAGGAGGC
* * * *
17053 GCTTCATCG-ATGATGAGAGGGGCCTCTTAAACGATAGGAGGC
1 ACCTC-TTGAATGATGAGAGGAGCCTCTTAAACGATAGGAGGC
17095 ACCTCTTGAATGATGA
1 ACCTCTTGAATGATGA
17111 TAGGTGCATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
41 2 0.05
42 40 0.91
43 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (42 bp):
ACCTCTTGAATGATGAGAGGAGCCTCTTAAACGATAGGAGGC
Found at i:17284 original size:4 final size:4
Alignment explanation
Indices: 17254--17295 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
17244 GGGCCGCTGA
* * *
17254 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
17296 TGCCAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:19825 original size:20 final size:20
Alignment explanation
Indices: 19800--19848 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
19790 GCGTAAAAAC
19800 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
19820 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
19840 ATTTGACTT
1 ATTTGACTT
19849 ATATGTTGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:19876 original size:20 final size:20
Alignment explanation
Indices: 19853--19940 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
19843 TGACTTATAT
19853 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
19873 GTTGCGATTTACAGATTCGT
1 GTTGCGATTTACAAATTCGC
** *
19893 GTTGCGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** * *
19914 AATGCGTTTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
19934 GTTGCGA
1 GTTGCGA
19941 AATTGGAAAC
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
20 37 0.74
21 13 0.26
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:25368 original size:3 final size:3
Alignment explanation
Indices: 25362--25416 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
25352 ATTAGTAATA
* * *
25362 ATT ATT ATT A-T ATT ATT ATT ATT -TC ATT AAT ATT ATT A-T ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
25407 ATT AAT ATT A
1 ATT ATT ATT A
25417 CATTTTATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
2 5 0.12
3 36 0.88
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:25381 original size:14 final size:14
Alignment explanation
Indices: 25350--25410 Score: 70
Period size: 14 Copynumber: 4.2 Consensus size: 14
25340 GGATCTTTTT
*
25350 TTATTAGTAATAATTA
1 TTATTA-TATTAA-TA
*
25366 TTATTATATTATTA
1 TTATTATATTAATA
25380 TTATT-TCATTAATA
1 TTATTAT-ATTAATA
25394 TTATTATATTAATA
1 TTATTATATTAATA
25408 TTA
1 TTA
25411 ATATTACATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.03
14 28 0.70
15 5 0.12
16 6 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATTATATTAATA
Found at i:25428 original size:20 final size:20
Alignment explanation
Indices: 25387--25429 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
25377 TTATTATTTC
*
25387 ATTAATATTATTATATTAAT
1 ATTAATATTATCATATTAAT
*
25407 ATTAATATTA-CATTTTATAT
1 ATTAATATTATCATATTA-AT
25427 ATT
1 ATT
25430 TTTGTAGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTAATATTATCATATTAAT
Found at i:27106 original size:30 final size:31
Alignment explanation
Indices: 27050--27107 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
27040 AATTTATAGT
*
27050 CCTTTAAGTTTCTGATTTTTCTATTTTAGAC
1 CCTTTAAGTTTATGATTTTTCTATTTTAGAC
*
27081 CCTTT-AGTTTATG-TTTTTATCATTTTA
1 CCTTTAAGTTTATGATTTTTCT-ATTTTA
27108 ATCCCTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.25
30 13 0.54
31 5 0.21
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.59
Consensus pattern (31 bp):
CCTTTAAGTTTATGATTTTTCTATTTTAGAC
Found at i:30337 original size:22 final size:20
Alignment explanation
Indices: 30316--30354 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30306 ATTCCCTCTT
*
30316 TTTGAGACCTTGAAACATTC
1 TTTGAGACATTGAAACATTC
*
30336 TTTGTGACATTGAAACATT
1 TTTGAGACATTGAAACATT
30355 GAATTTATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTGAGACATTGAAACATTC
Found at i:31011 original size:26 final size:25
Alignment explanation
Indices: 30982--31062 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 25
30972 AACAAATAGC
*
30982 AAAAAGAAACAAAGAAAAATCAAAGG
1 AAAAAGAAACAAAGAAAAAGCAAA-G
* *
31008 AAAAA-TAGCAAACGAAAAAGCAAAG
1 AAAAAGAAACAAA-GAAAAAGCAAAG
31033 AAAAAGAAGACAAAAGAAAAAAGACAAAG
1 AAAAAGAA-AC-AAAG-AAAAAG-CAAAG
31062 A
1 A
31063 GTCCCTTGAC
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
25 11 0.25
26 16 0.36
27 2 0.05
28 9 0.20
29 6 0.14
ACGTcount: A:0.73, C:0.09, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAAGAAACAAAGAAAAAGCAAAG
Found at i:31058 original size:14 final size:14
Alignment explanation
Indices: 30947--31060 Score: 69
Period size: 14 Copynumber: 8.1 Consensus size: 14
30937 AAATCAAAAC
*
30947 AAAGAGAAAAAGAGA
1 AAAGA-AAAAAGACA
*
30962 AAAGAAAAAAAACA
1 AAAGAAAAAAGACA
* *
30976 AATAGCAAAAAGAAA
1 AA-AGAAAAAAGACA
*
30991 CAAAG-AAAAA-TCA
1 -AAAGAAAAAAGACA
*
31004 AAGGAAAAATAG-CA
1 AAAGAAAAA-AGACA
*
31018 AACG-AAAAAG-C-
1 AAAGAAAAAAGACA
31029 AAAGAAAAAGAAGACA
1 AAAG-AAAA-AAGACA
31045 AAAGAAAAAAGACA
1 AAAGAAAAAAGACA
31059 AA
1 AA
31061 GAGTCCCTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.04
12 6 0.08
13 12 0.15
14 31 0.39
15 21 0.27
16 6 0.08
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.03
Consensus pattern (14 bp):
AAAGAAAAAAGACA
Found at i:32532 original size:35 final size:35
Alignment explanation
Indices: 32472--32574 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 35
32462 GCTTCTTTTG
* * * *
32472 AAAAACAAATCTTATCTCGCTTGAGACAGTTTTC-T
1 AAAAATAAATTTTGTCTCTCTTGAGACA-TTTTCTT
*
32507 -AAAATCAAATTTTGTCTCATC-TGAGACAATTTCTT
1 AAAAAT-AAATTTTGTCTC-TCTTGAGACATTTTCTT
32542 GAAAAATAAATTTTGTCTCTCTTGAGACATTTT
1 -AAAAATAAATTTTGTCTCTCTTGAGACATTTT
32575 TCCTTTGAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
34 8 0.14
35 20 0.36
36 23 0.41
37 5 0.09
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (35 bp):
AAAAATAAATTTTGTCTCTCTTGAGACATTTTCTT
Found at i:32748 original size:133 final size:133
Alignment explanation
Indices: 32485--32764 Score: 302
Period size: 133 Copynumber: 2.1 Consensus size: 133
32475 AACAAATCTT
* *
32485 ATCTCGCTTGAGACAGTTTTCTAAAATCAAATTTTGTCTCATCTGAGACAATTTCTTGAAAAATA
1 ATCTCACTTGAGACAGTTTTCTAAAATCAAATTTTGTCTCATCTGAGACAATTTC-T--AAAACA
* * * * * *
32550 AATTTTGTCTCTCTTGAGACATTTTTCCTTTGAAATACAAATTTCGAATTTGTTTCACATTAAAC
63 AATTTCGTCTCACTTGAGACATTTTCCCTAT-AAATACAAATTTCAAAGTTGTTTCACATTAAAC
* *
32615 AAAGTTG
127 AAAATTA
* * *
32622 ATCTCACTTGAGATC-GTTTTCTCATAAA-CAAATTTTGTCTCGTTTGAGATAATTTC-AAAACA
1 ATCTCACTTGAGA-CAGTTTTCT-A-AAATCAAATTTTGTCTCATCTGAGACAATTTCTAAAACA
32684 AATTTCGTCTCACTTGAGACATTTTCCCTCAT-AATACAAATTTCAAAGTTGTTGT-AC-TTAAA
63 AATTTCGTCTCACTTGAGACATTTTCCCT-ATAAATACAAATTTCAAAGTTGTT-TCACATT-AA
32746 ACAAAATTA
125 ACAAAATTA
*
32755 ATATCACTTG
1 ATCTCACTTG
32765 GGATTTTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
132 2 0.02
133 39 0.32
134 32 0.26
135 1 0.01
137 19 0.15
138 27 0.22
139 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (133 bp):
ATCTCACTTGAGACAGTTTTCTAAAATCAAATTTTGTCTCATCTGAGACAATTTCTAAAACAAAT
TTCGTCTCACTTGAGACATTTTCCCTATAAATACAAATTTCAAAGTTGTTTCACATTAAACAAAA
TTA
Found at i:32974 original size:28 final size:26
Alignment explanation
Indices: 32943--33004 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 26
32933 ATAGTTTCTC
32943 TTGAAACAAATCTTTGAGTCTGTTCCTT
1 TTGAAA-AAATCTTTGAGT-TGTTCCTT
*
32971 TTGAGTAAAAATCTTTGAGTTGTTTCTT
1 TTGA--AAAAATCTTTGAGTTGTTCCTT
32999 TTGAAA
1 TTGAAA
33005 TAAAGTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 2 0.06
28 15 0.48
29 12 0.39
30 2 0.06
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.45
Consensus pattern (26 bp):
TTGAAAAAATCTTTGAGTTGTTCCTT
Found at i:33008 original size:29 final size:29
Alignment explanation
Indices: 32950--33008 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
32940 CTCTTGAAAC
*
32950 AAATCTTTGAGTCTGTTCCTTTTGAGTAA
1 AAATCTTTGAGTCTGTTCCTTTTGAATAA
*
32979 AAATCTTTGAGT-TGTTTCTTTTGAAATAA
1 AAATCTTTGAGTCTGTTCCTTTTG-AATAA
33008 A
1 A
33009 GTTTTGTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAATAA
Found at i:33071 original size:61 final size:60
Alignment explanation
Indices: 32977--33124 Score: 214
Period size: 59 Copynumber: 2.5 Consensus size: 60
32967 CCTTTTGAGT
*
32977 AAAAATCTTTGAGT-TGTTTCTTTTGAAATAAAGTTTTGTC-TCTCTTAAGACAATTTCGTG-
1 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAG--TT-TCATCTCTTAAGACAATTTCGTGA
* *
33037 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTCATCTCTTGAGATAATTTCGTGA
1 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTCATCTCTTAAGACAATTTCGTGA
33097 AAAAATCTTTGAGTC-GTTTCTTTTGAAA
1 AAAAATCTTTGAGTCTGTTTCTTTTGAAA
33125 AAAATCTTTG
Statistics
Matches: 82, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
58 2 0.02
59 33 0.40
60 29 0.35
61 18 0.22
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.43
Consensus pattern (60 bp):
AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTCATCTCTTAAGACAATTTCGTGA
Found at i:33152 original size:27 final size:27
Alignment explanation
Indices: 33096--33161 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
33086 TAATTTCGTG
* *
33096 AAAAAATCTTTGAGTCGTTTCTTTTGA
1 AAAAAATCTTTGAGCCGTTTCTCTTGA
33123 AAAAAATCTTTGAGCCTGTTTCTCTT-A
1 AAAAAATCTTTGAGCC-GTTTCTCTTGA
* *
33150 AAACAATTTTTG
1 AAAAAATCTTTG
33162 TCTCTCTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 26 0.76
28 8 0.24
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (27 bp):
AAAAAATCTTTGAGCCGTTTCTCTTGA
Found at i:33199 original size:28 final size:27
Alignment explanation
Indices: 33168--33227 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
33158 TTTGTCTCTC
* *
33168 TTGAGACAGTTTCTTTTGAAACAAATCT
1 TTGAGACAG-TTCTTTTGAAAAAAACCT
* * *
33196 TTGAGTCTGTTCTTTTTAAAAAAACCT
1 TTGAGACAGTTCTTTTGAAAAAAACCT
33223 TTGAG
1 TTGAG
33228 TTTGTTTCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (27 bp):
TTGAGACAGTTCTTTTGAAAAAAACCT
Found at i:33219 original size:91 final size:87
Alignment explanation
Indices: 33037--33241 Score: 243
Period size: 91 Copynumber: 2.3 Consensus size: 87
33027 CAATTTCGTG
* * *
33037 AAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTCATCTCTTGAGATAATTTCGTGAAAAAA
1 AAAAATCTTTGAGTCTGTTTCTCTTAAAACAAAGTTTCATCTCTTGAGACAATTTCGTGAAAAAA
33102 TCTTTGAGTCGTTTCTTTTGAA
66 TCTTTGAGTCGTTTCTTTTGAA
* ** * *
33124 AAAAATCTTTGAGCCTGTTTCTCTTAAAACAATTTTTGTC-TCTCTTGAGACAGTTTCTTTTGAA
1 AAAAATCTTTGAGTCTGTTTCTCTTAAAACAA-AGTT-TCATCTCTTGAGACAATTTC--GTGAA
*
33188 ACAAATCTTTGAGTC-TGTTCTTTTTAA
62 A-AAATCTTTGAGTCGT-TTCTTTTGAA
* *
33215 AAAAACCTTTGAGTTTGTTTCTCTTAA
1 AAAAATCTTTGAGTCTGTTTCTCTTAA
33242 CAAAAATCAT
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
87 29 0.29
88 17 0.17
89 2 0.02
90 6 0.06
91 46 0.46
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (87 bp):
AAAAATCTTTGAGTCTGTTTCTCTTAAAACAAAGTTTCATCTCTTGAGACAATTTCGTGAAAAAA
TCTTTGAGTCGTTTCTTTTGAA
Found at i:33241 original size:27 final size:27
Alignment explanation
Indices: 33176--33268 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 27
33166 TCTTGAGACA
* *
33176 GTTTCTTTTGAAACAAATCTTTGAGTCT
1 GTTTCTTTT-AAAAAAACCTTTGAGTCT
*
33204 G-TTCTTTTTAAAAAAACCTTTGAGTTT
1 GTTTC-TTTTAAAAAAACCTTTGAGTCT
*
33231 GTTTCTCTTAACAAAAATCATCTTTGAGTCT
1 GTTTCTTTTAA-AAAAA-C--CTTTGAGTCT
*
33262 ATTTCTT
1 GTTTCTT
33269 CAAAAACAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
27 24 0.46
28 13 0.25
29 1 0.02
31 14 0.27
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (27 bp):
GTTTCTTTTAAAAAAACCTTTGAGTCT
Found at i:33408 original size:66 final size:66
Alignment explanation
Indices: 33271--33418 Score: 235
Period size: 66 Copynumber: 2.2 Consensus size: 66
33261 TATTTCTTCA
* *
33271 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTAATGAAAAATCAACCTTTGAGATTGTTTCTTT
1 AAAACAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAAACCAACCTTTGAGATTGTTTCTTT
33336 G
66 G
* *
33337 AAAACAAATTTTGTCTCTCTTGAGATAATTTTTAATGAAAAACCAACCTTTGAGATTGTTTCATT
1 AAAACAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAAACCAACCTTTGAGATTGTTTC-TT
33402 TG
65 TG
*
33404 -AAACAAATTTCGTCT
1 AAAACAAATTTTGTCT
33419 AACTTAAAAC
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
66 72 0.95
67 4 0.05
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (66 bp):
AAAACAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAAACCAACCTTTGAGATTGTTTCTTT
G
Found at i:33549 original size:36 final size:32
Alignment explanation
Indices: 33485--33634 Score: 101
Period size: 32 Copynumber: 4.4 Consensus size: 32
33475 TCTCGAGACA
* *
33485 GTTTCTTTGAGA-AAAAA--ATCTTTAAGTTT
1 GTTTCTTTGAAACAAAAACCATCTTTGAGTTT
33514 GTTTCTTTGAAAACAAAATTTACCATCTTTGAGTTT
1 GTTTCTTTG-AAACAAAA---ACCATCTTTGAGTTT
* * *
33550 GTTTCCCTTGAAACAAAACAAACAAAATCTTTGAGTGT
1 GTTT-CTTTGAAAC--AA-AAAC--CATCTTTGAGTTT
*
33588 GTTTTTCTTGAAACAAAAA-CATCTTTGAGTTT
1 GTTTCT-TTGAAACAAAAACCATCTTTGAGTTT
*
33620 GTTTCTCTCGAAACA
1 GTTTCT-TTGAAACA
33635 CCGATCTTTG
Statistics
Matches: 96, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
29 9 0.09
30 2 0.02
31 4 0.04
32 24 0.25
34 1 0.01
35 3 0.03
36 23 0.24
37 4 0.04
38 24 0.25
39 2 0.02
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (32 bp):
GTTTCTTTGAAACAAAAACCATCTTTGAGTTT
Found at i:33841 original size:28 final size:29
Alignment explanation
Indices: 33771--33850 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 29
33761 AACACATCAC
*
33771 CTTTGAGTATGTTT-TTCTTGAAACAAAT
1 CTTTGAGTCTGTTTCTTCTTGAAACAAAT
* *
33799 CTTTGAGTCTATTTCTT-TTGACACAAAT
1 CTTTGAGTCTGTTTCTTCTTGAAACAAAT
* *
33827 CTTTGAGTCGGTTTC-CCTTGAAAC
1 CTTTGAGTCTGTTTCTTCTTGAAAC
33851 CACAATCACT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 41 0.95
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (29 bp):
CTTTGAGTCTGTTTCTTCTTGAAACAAAT
Found at i:34099 original size:134 final size:134
Alignment explanation
Indices: 33879--34217 Score: 401
Period size: 134 Copynumber: 2.5 Consensus size: 134
33869 CCAACCGTCC
* * * * * *
33879 TCATCACGTAGGAGCGGTGTCATCCCCTGACCAGATCTCTTTATCGCGTAGGAGTCGTGTTACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
* * * ** * * * *
33944 CTAGATAATGAGATGTCCTCATCACGTAGGAACCGTGTTATCGCCCTTTCTAAAAATGATCAAAA
66 ATAGATAATCAGACGTCCTCATCACGTAGGAACCAAGTTATCACCATTCCTAAAAATGACCAAAA
*
34009 TTCT
131 CTCT
34013 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
* * * * * *
34078 ATAGATAATCAGCCGTCCTCATCGCGTAGGAACTAAGTTATCACCATTCCTAAAGATGGCCAGAA
66 ATAGATAATCAGACGTCCTCATCACGTAGGAACCAAGTTATCACCATTCCTAAAAATGACCAAAA
34143 CTCT
131 CTCT
* * * * *
34147 TCATCATGTATTGAGCCATGTCATCCCCTGACCAGAT-TTTCTCATCACGTAAGAACCGTGTCAC
1 TCATCACGTA-TGAGCCGTGTCATCCCCTGACCAGATCTCT-TCATCACGTAGGAGCCGTGTCAC
*
34211 CCTTAGA
64 CCATAGA
34218 CGACCCAAAC
Statistics
Matches: 175, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
134 123 0.70
135 52 0.30
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (134 bp):
TCATCACGTATGAGCCGTGTCATCCCCTGACCAGATCTCTTCATCACGTAGGAGCCGTGTCACCC
ATAGATAATCAGACGTCCTCATCACGTAGGAACCAAGTTATCACCATTCCTAAAAATGACCAAAA
CTCT
Found at i:34423 original size:3 final size:3
Alignment explanation
Indices: 34417--34471 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
34407 ATTAGTAATA
* *
34417 ATT ATT ATT A-T ATT ATT ATT ATT -TC ATT AAT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
34462 ATT AAT ATT A
1 ATT ATT ATT A
34472 CATTTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.12
3 38 0.88
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:34433 original size:11 final size:11
Alignment explanation
Indices: 34417--34471 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
34407 ATTAGTAATA
34417 ATTATTATTAT
1 ATTATTATTAT
34428 ATTATTA-T-T
1 ATTATTATTAT
*
34437 ATT-TCATTA-
1 ATTATTATTAT
34446 A-TATTATTAT
1 ATTATTATTAT
34456 ATTATTATTAAT
1 ATTATTATT-AT
34468 ATTA
1 ATTA
34472 CATTTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
8 3 0.08
9 11 0.31
10 2 0.06
11 14 0.39
12 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:34436 original size:14 final size:14
Alignment explanation
Indices: 34417--34465 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
34407 ATTAGTAATA
34417 ATTATTATTATATT
1 ATTATTATTATATT
34431 ATTATTATT-TCATT
1 ATTATTATTAT-ATT
*
34445 AATATTATTATATT
1 ATTATTATTATATT
34459 ATTATTA
1 ATTATTA
34466 ATATTACATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:34451 original size:20 final size:20
Alignment explanation
Indices: 34417--34471 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
34407 ATTAGTAATA
*
34417 ATTATTATT-ATATTATTATT
1 ATTATCATTAATATTATTA-T
34437 ATT-TCATTAATATTATTAT
1 ATTATCATTAATATTATTAT
*
34456 ATTATTATTAATATTA
1 ATTATCATTAATATTA
34472 CATTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATCATTAATATTATTAT
Found at i:36462 original size:2 final size:2
Alignment explanation
Indices: 36444--36478 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
36434 TACGTATCAA
* *
36444 AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36479 AGTCAAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42045 original size:215 final size:213
Alignment explanation
Indices: 41785--42469 Score: 1025
Period size: 215 Copynumber: 3.2 Consensus size: 213
41775 ATTTAAGAAT
41785 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
41850 GGATCAAATCAAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAATAAATACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAA-AAATACTAAATTATAC
* * * *
41915 CCATTTAAAAAGTTAT-GTCCAATTAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTCATA
130 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAA-TAA-TAATAAGTATGGGTCAATTTCAGA
**
41979 TGCTGATAAAATTTGGAGGAC
193 TGCAAATAAAATTTGGAGGAC
* * * *
42000 TAAATAGAACAAATATGAAATTAAAAATATAAATATAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
42065 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAA-TACTAAATTATAC
*
42130 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAACTAATAAGTATGGGTCAATTTCGGA
130 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAG-AATAA-TAATAAGTATGGGTCAATTTCAGA
*
42195 TGCAAATAAAATTTGAAGGAC
193 TGCAAATAAAATTTGGAGGAC
*
42216 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* * * *
42275 GGATCAAATCGAAATAATTTTAAATTTTGAGATTAAAATTAATACAAAAAGTACTAAATTATACC
66 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACC
* *
42340 CATTTAAAAAGTTATGGGCCAATTTAAAAATAG----A-AATAAGTATGGGTCAATTTTAGGTGC
131 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAATAATAATAAGTATGGGTCAATTTCAGATGC
42400 AAATAAAATTTGGAGGAC
196 AAATAAAATTTGGAGGAC
* *
42418 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATATATTAAACAAC
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAC
42470 TAATATATAT
Statistics
Matches: 437, Mismatches: 30, Indels: 19
0.90 0.06 0.04
Matches are distributed among these distances:
202 91 0.21
204 1 0.00
209 47 0.11
210 48 0.11
212 1 0.00
214 3 0.01
215 137 0.31
216 107 0.24
217 2 0.00
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (213 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAATACTAAATTATACC
CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAATAATAATAAGTATGGGTCAATTTCAGATGC
AAATAAAATTTGGAGGAC
Found at i:42477 original size:2 final size:2
Alignment explanation
Indices: 42472--42588 Score: 132
Period size: 2 Copynumber: 58.0 Consensus size: 2
42462 TAAACAACTA
42472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
42514 AT AT AT AT AT AT AT AA ACT AT AT AGT -T AT AT AT A- AT GT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
42556 GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
42589 TATGTATAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
1 3 0.03
2 91 0.93
3 4 0.04
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42681 original size:39 final size:41
Alignment explanation
Indices: 42627--42717 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 41
42617 ATGTATAAAC
* *
42627 TATAATACTATATAGTTTATATATAAA-CTAT-TGAACTATA
1 TATAA-ACTACATAGTTTATATATAAATATATATGAACTATA
*
42667 TATAAACTACATAGTTTATATATAAATTATATATGAATTATA
1 TATAAACTACATAGTTTATATATAAA-TATATATGAACTATA
42709 TATAAACTA
1 TATAAACTA
42718 TACAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 20 0.44
40 5 0.11
41 3 0.07
42 17 0.38
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (41 bp):
TATAAACTACATAGTTTATATATAAATATATATGAACTATA
Found at i:42698 original size:11 final size:11
Alignment explanation
Indices: 42682--42719 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
42672 ACTACATAGT
42682 TTATATATAAA
1 TTATATATAAA
*
42693 TTATATATGAA
1 TTATATATAAA
42704 TTATATATAAA
1 TTATATATAAA
*
42715 CTATA
1 TTATA
42720 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:42727 original size:20 final size:20
Alignment explanation
Indices: 42467--42729 Score: 110
Period size: 20 Copynumber: 12.8 Consensus size: 20
42457 TATATTAAAC
*
42467 AACTAATATATATATATATATA
1 AACT-ATATA-ATTTATATATA
* *
42489 TA-TATATATATATATATATA
1 AACTATATA-ATTTATATATA
* *
42509 TA-TATATATATATATATATA
1 AACTATATA-ATTTATATATA
*
42529 AACTATAT-AGTTATATATA
1 AACTATATAATTTATATATA
** *
42548 ATGTATATGTATTATATATATA
1 AACTATAT-AATT-TATATATA
*
42570 AACTATATAGTTTATATAT-
1 AACTATATAATTTATATATA
* * ** *
42589 TA-TGTATAAAGTATAAACTA
1 AACTATATAATTTATATA-TA
* ** *
42609 TA-TATACCATGTATAAACTATA
1 AACTATATAAT-T-TATA-TATA
*
42631 ATACTATATAGTTTATATATA
1 A-ACTATATAATTTATATATA
*
42652 AACTAT-TGAA-CTATATATA
1 AACTATAT-AATTTATATATA
* *
42671 AACTACATAGTTTATATATA
1 AACTATATAATTTATATATA
* *
42691 AATTATATATGAATTATATATA
1 AACTATATA--ATTTATATATA
*
42713 AACTATACAATTTATAT
1 AACTATATAATTTATAT
42730 TTATATACTA
Statistics
Matches: 184, Mismatches: 41, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
18 10 0.05
19 32 0.17
20 80 0.43
21 15 0.08
22 39 0.21
23 3 0.02
24 5 0.03
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (20 bp):
AACTATATAATTTATATATA
Found at i:42912 original size:12 final size:12
Alignment explanation
Indices: 42872--42916 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
42862 TATAAACTAC
*
42872 ATACTATAATTT
1 ATACTATATTTT
*
42884 ATATTTATATTTAT
1 ATA-CTATATTT-T
42898 ATACTATATTTT
1 ATACTATATTTT
42910 ATACTAT
1 ATACTAT
42917 TTATATAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (12 bp):
ATACTATATTTT
Found at i:42923 original size:25 final size:26
Alignment explanation
Indices: 42872--42944 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
42862 TATAAACTAC
*
42872 ATACTATAATTTATATTTATATTTAT
1 ATACTATAATTTATATCTATATTTAT
*
42898 ATACTATATTTTATA-CTAT-TTATAT
1 ATACTATAATTTATATCTATATT-TAT
* * *
42923 AAACTATAGTTTATATTTATAT
1 ATACTATAATTTATATCTATAT
42945 ACTATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.05
25 19 0.49
26 17 0.44
27 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (26 bp):
ATACTATAATTTATATCTATATTTAT
Found at i:42951 original size:58 final size:58
Alignment explanation
Indices: 42856--42968 Score: 133
Period size: 58 Copynumber: 1.9 Consensus size: 58
42846 TTAAGGTTTA
* * *
42856 TATTTATATAAACTACATACTATAATTTATATTTATATTTAT-ATACTATATTTTATAC
1 TATTTATATAAACTACATACTATAATTTATATCTATATATATGA-ACTATAGTTTATAC
* *
42914 TATTTATATAAACT--ATAGTTTATATTTATATACTATATATATGAACTATAGTTTA
1 TATTTATATAAACTACATACTATA-ATTTATAT-CTATATATATGAACTATAGTTTA
42969 CATATGAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
56 6 0.13
57 8 0.17
58 32 0.68
59 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (58 bp):
TATTTATATAAACTACATACTATAATTTATATCTATATATATGAACTATAGTTTATAC
Found at i:42955 original size:33 final size:33
Alignment explanation
Indices: 42902--42993 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
42892 ATTTATATAC
*
42902 TATATTT-TATACTATTTATATAAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
42934 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTTATATACTATATATATAAACTATAGTT
*
42967 TACA--TATGA-ACTATATATATAAA-TATA
1 TATATTTAT-ATACTATATATATAAACTATA
42994 TATATATACT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.07
31 16 0.30
32 8 0.15
33 26 0.48
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (33 bp):
TATATTTATATACTATATATATAAACTATAGTT
Found at i:43035 original size:18 final size:18
Alignment explanation
Indices: 43014--43146 Score: 75
Period size: 18 Copynumber: 7.4 Consensus size: 18
43004 AAGGTTGATA
43014 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* *
43032 TTTACATATAAACTATAG
1 TTTATATATGAACTATAG
43050 TTAATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
*
43074 TTTACATATGAACTATA-
1 TTTATATATGAACTATAG
43091 --TATATA--AACTATATAG
1 TTTATATATGAAC--TATAG
* *
43107 TTTACATATGACCTATA-
1 TTTATATATGAACTATAG
*
43124 TATATATAT--ACTATAG
1 TTTATATATGAACTATAG
*
43140 TTGATAT
1 TTTATAT
43147 TTATATACTA
Statistics
Matches: 88, Mismatches: 13, Indels: 30
0.67 0.10 0.23
Matches are distributed among these distances:
13 3 0.03
15 14 0.16
16 5 0.06
17 7 0.08
18 39 0.44
20 4 0.05
22 2 0.02
24 14 0.16
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:43057 original size:42 final size:42
Alignment explanation
Indices: 43011--43090 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
43001 ACTAAGGTTG
*
43011 ATATTTATATATGAACTATAGTTTACATATAAACTATAGTTA
1 ATATTTACATATGAACTATAGTTTACATATAAACTATAGTTA
*
43053 ATATTTACATATGAACTATAGTTTACATATGAACTATA
1 ATATTTACATATGAACTATAGTTTACATATAAACTATA
43091 TATATAAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (42 bp):
ATATTTACATATGAACTATAGTTTACATATAAACTATAGTTA
Found at i:43127 original size:2 final size:2
Alignment explanation
Indices: 43120--43247 Score: 53
Period size: 2 Copynumber: 59.0 Consensus size: 2
43110 ACATATGACC
* *
43120 TA TA TA TA TA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA GTT
1 TA TA TA TA TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA -TA
* ** * * *
43164 TA CA TA TGA CC TA TA AA TA TA TA CTA TA GTT TA TA TT TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA TA
*
43207 CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA TA GTA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA -TA TA
43248 ATTTACATAT
Statistics
Matches: 94, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
1 2 0.02
2 74 0.79
3 18 0.19
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:43139 original size:33 final size:34
Alignment explanation
Indices: 43067--43141 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
43057 TTACATATGA
* *
43067 ACTATAGTTTACATATGAACTATATATATAAACT
1 ACTATAGTTTACATATGACCTATATATATATACT
43101 A-TATAGTTTACATATGACCTATATATATATA-T
1 ACTATAGTTTACATATGACCTATATATATATACT
43133 ACTATAGTT
1 ACTATAGTT
43142 GATATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.92
34 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (34 bp):
ACTATAGTTTACATATGACCTATATATATATACT
Found at i:43204 original size:20 final size:20
Alignment explanation
Indices: 43175--43247 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
43165 ACATATGACC
*
43175 TATAAATATATACTATAGT-T
1 TATATATATATACTATA-TAT
*
43195 TATATTTATATACTATATAT
1 TATATATATATACTATATAT
*
43215 TATATATATAAACTATATA-
1 TATATATATATACTATATAT
43234 TACTATATAGTATA
1 TA-TATATA-TATA
43248 ATTTACATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATATATACTATATAT
Found at i:43207 original size:53 final size:55
Alignment explanation
Indices: 43087--43252 Score: 221
Period size: 53 Copynumber: 3.0 Consensus size: 55
43077 ACATATGAAC
* *
43087 TATATATATAAACTATATAGTTTACATATGACCTATATATATATATACTATAGTT
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATATACTATAGTT
*
43142 GATATTTATATACTATATAGTTTACATATGACCTATA-A-ATATATACTATAGTT
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATATACTATAGTT
* * * * *
43195 TATATTTATATACTATATA-TTATATATATAAACTATATATACTATATAGTATAATT
1 TATATTTATATACTATATAGTT-TACATATGACCTATATATA-TATATACTATAGTT
43251 TA
1 TA
43253 CATATGAACT
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
52 2 0.02
53 45 0.46
54 2 0.02
55 35 0.36
56 14 0.14
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (55 bp):
TATATTTATATACTATATAGTTTACATATGACCTATATATATATATACTATAGTT
Found at i:43264 original size:34 final size:36
Alignment explanation
Indices: 43201--43269 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
43191 AGTTTATATT
*
43201 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
43237 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
43270 AAAATCCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:43340 original size:33 final size:33
Alignment explanation
Indices: 43291--43554 Score: 147
Period size: 33 Copynumber: 7.5 Consensus size: 33
43281 CCCTAAACCC
* * * *
43291 TAAAGTATATATTATATAGTTTATTTGTATATA
1 TAAACTATATAATATATAGTTCATTAGTATATA
* * *
43324 TAAACTATATAATATATA-TAGACTATATGGTATATT
1 TAAACTATATAATATATAGT--TC-AT-TAGTATATA
* *
43360 TAAATTATACATTATATATAGTTCATTAGTATATA
1 TAAACTAT--ATAATATATAGTTCATTAGTATATA
*
43395 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATAATATATAGTTCATTAGTATATA
* * *
43428 TAAACTATATAGTACATATAAACTATATATTA-TATAGTTCA
1 TAAAC--TATA-TA-ATATATAGT-T-CATTAGTATA--T-A
*** ** *
43469 TTAGTATATATAACCTATATAGTATATGA-TATATA
1 -TAAACTATATAA--TATATAGTTCATTAGTATATA
* *
43504 CAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATAATATATAGTTCATTAGTATATA
*
43537 TAAACTATATAGTATATA
1 TAAACTATATAATATATA
43555 TAAACTATAT
Statistics
Matches: 176, Mismatches: 35, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
32 12 0.07
33 66 0.38
34 7 0.04
35 21 0.12
36 19 0.11
37 7 0.04
38 23 0.13
39 7 0.04
40 11 0.06
41 1 0.01
42 2 0.01
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (33 bp):
TAAACTATATAATATATAGTTCATTAGTATATA
Found at i:43341 original size:18 final size:18
Alignment explanation
Indices: 43317--43565 Score: 155
Period size: 18 Copynumber: 14.0 Consensus size: 18
43307 TAGTTTATTT
43317 GTATATATAAACTATATA
1 GTATATATAAACTATATA
* * *
43335 ATATATATAGACTATATG
1 GTATATATAAACTATATA
* * *
43353 GTATATTTAAATTATACA
1 GTATATATAAACTATATA
* **
43371 TTATATAT-AGTTCAT-TA
1 GTATATATAAACT-ATATA
43388 GTATATATAAACTATATA
1 GTATATATAAACTATATA
**
43406 -T-TATAT-AGTTCAT-TA
1 GTATATATAAACT-ATATA
43421 GTATATATAAACTATATA
1 GTATATATAAACTATATA
*
43439 GTACATATAAACTATATA
1 GTATATATAAACTATATA
**
43457 -T-TATAT-AGTTCAT-TA
1 GTATATATAAACT-ATATA
*
43472 GTATATATAACCTATATA
1 GTATATATAAACTATATA
*
43490 GTATATGATATATAC-AAACTA
1 GTATAT-ATA-A-ACTATA-TA
* *
43511 -TATATTATATAGT-TCATTA
1 GTATA-TATAAACTAT-A-TA
43530 GTATATATAAACTATATA
1 GTATATATAAACTATATA
43548 GTATATATAAACTATATA
1 GTATATATAAACTATATA
43566 TTAATTTATT
Statistics
Matches: 175, Mismatches: 34, Indels: 44
0.69 0.13 0.17
Matches are distributed among these distances:
15 8 0.05
16 15 0.09
17 29 0.17
18 91 0.52
19 13 0.07
20 15 0.09
21 4 0.02
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (18 bp):
GTATATATAAACTATATA
Found at i:43358 original size:51 final size:51
Alignment explanation
Indices: 43291--43568 Score: 303
Period size: 51 Copynumber: 5.3 Consensus size: 51
43281 CCCTAAACCC
* * * *
43291 TAAAGTATATATTATATAGTTTATTTGTATATATAAACTATATAATATATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
* ** * * *
43342 TAGACTATATGGTATAT--TTAAATTA-TACATTATATA-TAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTT-CATTAGTATA-TATAAACTA--T-A-TAGTATATA
*
43395 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTACATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
*
43446 TAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATGATATA
1 TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAG----T-ATATA
43502 TACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
1 T--AAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
43555 TAAACTATATATTA
1 TAAACTATATATTA
43569 ATTTATTAAT
Statistics
Matches: 191, Mismatches: 19, Indels: 34
0.78 0.08 0.14
Matches are distributed among these distances:
49 7 0.04
50 8 0.04
51 79 0.41
52 2 0.01
53 29 0.15
54 10 0.05
55 8 0.04
56 5 0.03
58 43 0.23
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (51 bp):
TAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATA
Found at i:43394 original size:17 final size:17
Alignment explanation
Indices: 43372--43429 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
43362 AATTATACAT
43372 TATATATAGTTCATTAG
1 TATATATAGTTCATTAG
**
43389 TATATATA-AAC-TATA-
1 TATATATAGTTCAT-TAG
43404 TATTATATAGTTCATTAG
1 TA-TATATAGTTCATTAG
43422 TATATATA
1 TATATATA
43430 AACTATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATATAGTTCATTAG
Found at i:43475 original size:84 final size:86
Alignment explanation
Indices: 43336--43495 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 86
43326 AACTATATAA
* * * * *
43336 TATATATAGACTATATGGTATATTTAAATTATACATTATATATAGTTCATTAGTATATATAAACT
1 TATATATAAACTATATAGTACATATAAACTATACATTATATATAGTTCATTAGTATATATAAACT
*
43401 ATATATTATATAGTTCATTAG
66 ATATAGTATATAGTTCATTAG
* *
43422 TATATATAAACTATATAGTACATATAAACTATATA-T-TATATAGTTCATTAGTATATATAACCT
1 TATATATAAACTATATAGTACATATAAACTATACATTATATATAGTTCATTAGTATATATAAACT
43485 ATATAGTATAT
66 ATATAGTATAT
43496 GATATATACA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
84 36 0.55
85 1 0.02
86 29 0.44
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (86 bp):
TATATATAAACTATATAGTACATATAAACTATACATTATATATAGTTCATTAGTATATATAAACT
ATATAGTATATAGTTCATTAG
Found at i:43690 original size:62 final size:62
Alignment explanation
Indices: 43618--43765 Score: 187
Period size: 62 Copynumber: 2.4 Consensus size: 62
43608 AAATATATAA
* * *
43618 GGATCAAATTGAAAAT-TTTTTAAATATGAAGCTTAAATTAATAAATTATAACATCAAAATTT
1 GGATTAAATTGAAAATAATTTAAAATATGAAGCTTAAATTAATAAATTATAACAT-AAAATTT
* * *
43680 GGATTAAATTG-AAATAATTTAAAATATGAAGCTTAAATTAATATATTATATCATTAAATTT
1 GGATTAAATTGAAAATAATTTAAAATATGAAGCTTAAATTAATAAATTATAACATAAAATTT
*
43741 GGACTAAATTG--AATACATTTAAAAT
1 GGATTAAATTGAAAATA-ATTTAAAAT
43766 TAATAGACAA
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
60 4 0.05
61 29 0.38
62 44 0.57
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (62 bp):
GGATTAAATTGAAAATAATTTAAAATATGAAGCTTAAATTAATAAATTATAACATAAAATTT
Found at i:43749 original size:61 final size:62
Alignment explanation
Indices: 43639--43765 Score: 195
Period size: 62 Copynumber: 2.1 Consensus size: 62
43629 AAAATTTTTT
*
43639 AAATATGAAGCTTAAATTAATAAATTATAACATCAAAATTTGGATTAAATTGAAATA-ATTTA
1 AAATATGAAGCTTAAATTAATAAATTATAACATCAAAATTTGGACTAAATTG-AATACATTTA
* * *
43701 AAATATGAAGCTTAAATTAATATATTATATCAT-TAAATTTGGACTAAATTGAATACATTTA
1 AAATATGAAGCTTAAATTAATAAATTATAACATCAAAATTTGGACTAAATTGAATACATTTA
43762 AAAT
1 AAAT
43766 TAATAGACAA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 4 0.07
61 25 0.42
62 31 0.52
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (62 bp):
AAATATGAAGCTTAAATTAATAAATTATAACATCAAAATTTGGACTAAATTGAATACATTTA
Found at i:46532 original size:27 final size:27
Alignment explanation
Indices: 46502--46593 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 27
46492 TAATTTAGTG
46502 ATTATAAATAAAATTTATAATATAAGA
1 ATTATAAATAAAATTTATAATATAAGA
* * *
46529 ATTATAAATAATATATATAGA-ATTAGA
1 ATTATAAATAAAATTTATA-ATATAAGA
*
46556 ATTAATATAAAATCAAATTTATAATATACA-A
1 A-T--TAT-AAATAAAATTTATAATATA-AGA
46587 ATTATAA
1 ATTATAA
46594 TTAATATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
27 25 0.49
28 5 0.10
30 5 0.10
31 15 0.29
32 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (27 bp):
ATTATAAATAAAATTTATAATATAAGA
Found at i:46552 original size:21 final size:20
Alignment explanation
Indices: 46521--46564 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
46511 AAAATTTATA
*
46521 ATATAAGAATTATAAATAAT
1 ATATAAGAATTAGAAATAAT
*
46541 ATATATAGAATTAGAATTAAT
1 ATATA-AGAATTAGAAATAAT
46562 ATA
1 ATA
46565 AAATCAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (20 bp):
ATATAAGAATTAGAAATAAT
Found at i:46779 original size:16 final size:16
Alignment explanation
Indices: 46760--46798 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46750 TGAGTTAACT
* *
46760 ACAGGTCATGTTCATA
1 ACAGGTCAGGTTCAAA
*
46776 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
46792 ACAGGTC
1 ACAGGTC
46799 GAGTAATATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:47829 original size:34 final size:31
Alignment explanation
Indices: 47789--47851 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
47779 ATATTCCAAA
*
47789 CAACAACAAGAAGATTTTAAACTCGGATCAT
1 CAACAACAACAAGATTTTAAACTCGGATCAT
47820 CAACAACAACAAGATTTTAAACTCGGATCAT
1 CAACAACAACAAGATTTTAAACTCGGATCAT
47851 C
1 C
47852 TAGTGAATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (31 bp):
CAACAACAACAAGATTTTAAACTCGGATCAT
Found at i:48480 original size:19 final size:21
Alignment explanation
Indices: 48456--48494 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
48446 AAATCTTTCA
48456 CATTTTTTTT-TA-AATTTGT
1 CATTTTTTTTATAGAATTTGT
48475 CATTTTTTTTATAGAATTTG
1 CATTTTTTTTATAGAATTTG
48495 CAAATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (21 bp):
CATTTTTTTTATAGAATTTGT
Found at i:50302 original size:64 final size:65
Alignment explanation
Indices: 50195--50324 Score: 217
Period size: 64 Copynumber: 2.0 Consensus size: 65
50185 AACATTATCA
** *
50195 TTCTTGTTGAATTTGAATGAATTGAATTGTGGGTATGGTATAAAAAATAAATAATTGAAGAATAT
1 TTCTTGTTGAATTTGAATGAATTGAATTGTAAGTATGGTATAAAAAAGAAATAATTGAAGAATAT
*
50260 TTCTT-TTGAATTTGAATGAATTGAATTGTAAGTATGGTATAAAAAAGGAATAATTGAAGAATAT
1 TTCTTGTTGAATTTGAATGAATTGAATTGTAAGTATGGTATAAAAAAGAAATAATTGAAGAATAT
50324 T
1 T
50325 AAATTAGGGA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
64 56 0.92
65 5 0.08
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.38
Consensus pattern (65 bp):
TTCTTGTTGAATTTGAATGAATTGAATTGTAAGTATGGTATAAAAAAGAAATAATTGAAGAATAT
Found at i:54761 original size:20 final size:20
Alignment explanation
Indices: 54733--54782 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
54723 CAATTTTGAA
*
54733 TTCGCAACATGAAAGCCAAT
1 TTCGCAACACGAAAGCCAAT
* *
54753 TTCGTAACACGAAAGCTAAT
1 TTCGCAACACGAAAGCCAAT
54773 TTCGCAACAC
1 TTCGCAACAC
54783 AGTTTCCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (20 bp):
TTCGCAACACGAAAGCCAAT
Found at i:54796 original size:20 final size:19
Alignment explanation
Indices: 54773--54824 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
54763 GAAAGCTAAT
*
54773 TTCGCAACACAGTTTCCGAA
1 TTCGCAACACAATTT-CGAA
* *
54793 TTCGCAACTCGAATTTGGAA
1 TTCGCAACAC-AATTTCGAA
54813 TTCGCAACACAA
1 TTCGCAACACAA
54825 AAGTCAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.07
20 21 0.78
21 4 0.15
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (19 bp):
TTCGCAACACAATTTCGAA
Found at i:54817 original size:40 final size:39
Alignment explanation
Indices: 54773--55017 Score: 129
Period size: 40 Copynumber: 6.1 Consensus size: 39
54763 GAAAGCTAAT
54773 TTCGCAACAC-AGTTTCCGAATTCGCAACTCGAATTTGGAA
1 TTCGCAACACAAGTTT-CGAATTCGCAACTCGAATTT-GAA
***
54813 TTCGCAACACAAAAGTC-AATTTCGCAACTCGAATTTGATA
1 TTCGCAACACAAGTTTCGAA-TTCGCAACTCGAATTTGA-A
* *** * *
54853 TTTTCGCAACACAAATTTCTTTTTCGCAACTCGATTTTTAAA
1 --TTCGCAACACAAGTTTCGAATTCGCAACTCGA-ATTTGAA
* ** * *
54895 TTCGCAACACGAGTTTCGTTTTCGCAACTCGATTTTCTAA
1 TTCGCAACACAAGTTTCGAATTCGCAACTCGAATTT-GAA
* * * * **
54935 TTCGCAACGCGAGTTTC-AATTTTGCAA-TAAGAATTTTGTT
1 TTCGCAACACAAGTTTCGAA-TTCGCAACT-CGAA-TTTGAA
* * * * *
54975 TTCGCAACTCGATTTTCGAATTCGCAACGCAAATTTCGAA
1 TTCGCAACACAAGTTTCGAATTCGCAACTCGAATTT-GAA
55015 TTC
1 TTC
55018 ACAATGCGAA
Statistics
Matches: 161, Mismatches: 30, Indels: 28
0.74 0.14 0.13
Matches are distributed among these distances:
39 12 0.07
40 110 0.68
41 7 0.04
42 28 0.17
43 4 0.02
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (39 bp):
TTCGCAACACAAGTTTCGAATTCGCAACTCGAATTTGAA
Found at i:54860 original size:22 final size:20
Alignment explanation
Indices: 54832--54926 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
54822 CAAAAGTCAA
54832 TTTCGCAACTCGAATTTGATAT
1 TTTCGCAACTCGAATTT-AT-T
* * *
54854 TTTCGCAACACAAATTTCTT
1 TTTCGCAACTCGAATTTATT
54874 TTTCGCAACTCG-ATTT-TT
1 TTTCGCAACTCGAATTTATT
* * * **
54892 AAATTCGCAACACGAGTTTCGT
1 --TTTCGCAACTCGAATTTATT
54914 TTTCGCAACTCGA
1 TTTCGCAACTCGA
54927 TTTTCTAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
18 2 0.03
19 4 0.07
20 32 0.55
21 4 0.07
22 16 0.28
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTCGCAACTCGAATTTATT
Found at i:54939 original size:60 final size:60
Alignment explanation
Indices: 54875--55004 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 60
54865 AAATTTCTTT
* * * * * *
54875 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCGTTTTCGCAACTCGATTTTCTAA
1 TTCGCAACGCGAGTTTCAAATTCGCAACAAGAATTTCGTTTTCGCAACTCGATTTTCGAA
* * * *
54935 TTCGCAACGCGAGTTTCAATTTTGCAATAAGAATTTTGTTTTCGCAACTCGATTTTCGAA
1 TTCGCAACGCGAGTTTCAAATTCGCAACAAGAATTTCGTTTTCGCAACTCGATTTTCGAA
54995 TTCGCAACGC
1 TTCGCAACGC
55005 AAATTTCGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.37
Consensus pattern (60 bp):
TTCGCAACGCGAGTTTCAAATTCGCAACAAGAATTTCGTTTTCGCAACTCGATTTTCGAA
Found at i:54998 original size:20 final size:20
Alignment explanation
Indices: 54875--55017 Score: 94
Period size: 20 Copynumber: 7.2 Consensus size: 20
54865 AAATTTCTTT
**
54875 TTCGCAACTCGATTTTTAAA
1 TTCGCAACTCGATTTTCGAA
* * **
54895 TTCGCAACACGAGTTTCGTT
1 TTCGCAACTCGATTTTCGAA
*
54915 TTCGCAACTCGATTTTCTAA
1 TTCGCAACTCGATTTTCGAA
* *
54935 TTCGCAACGCGAGTTTC-AA
1 TTCGCAACTCGATTTTCGAA
* * **
54954 TTTTGCAA-TAAGAATTTT-GTT
1 -TTCGCAACT-CG-ATTTTCGAA
54975 TTCGCAACTCGATTTTCGAA
1 TTCGCAACTCGATTTTCGAA
* * *
54995 TTCGCAACGCAAATTTCGAA
1 TTCGCAACTCGATTTTCGAA
55015 TTC
1 TTC
55018 ACAATGCGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
19 7 0.08
20 79 0.87
21 5 0.05
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (20 bp):
TTCGCAACTCGATTTTCGAA
Found at i:58424 original size:25 final size:24
Alignment explanation
Indices: 58391--58446 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
58381 TTTTCTATAT
58391 ATATGTTTTAAAACATT-AATATTAAA
1 ATAT-TTTTAAAA-ATTAAAT-TTAAA
*
58417 TTATTTTTAAAAATTAAATTTAAA
1 ATATTTTTAAAAATTAAATTTAAA
58441 ATATTT
1 ATATTT
58447 ATTATGATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 13 0.48
25 11 0.41
26 3 0.11
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
ATATTTTTAAAAATTAAATTTAAA
Found at i:58508 original size:28 final size:26
Alignment explanation
Indices: 58475--58542 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 26
58465 AAATTTAAAA
58475 TTAAATAATATTAAAAAT-TATTTAT
1 TTAAATAATATTAAAAATATATTTAT
*
58500 ATCATAAATAAT-TTAAATATATATTTAT
1 -T--TAAATAATATTAAAAATATATTTAT
*
58528 TTAATTAATATTAAA
1 TTAAATAATATTAAA
58543 TTAATTGAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 7 0.19
26 6 0.17
27 8 0.22
28 15 0.42
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAATAATATTAAAAATATATTTAT
Done.