Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006956.1 Hibiscus syriacus cultivar Beakdansim tig00017890_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: 80852
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:140 original size:31 final size:31
Alignment explanation
Indices: 69--140 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
59 TTATTTTTGC
*
69 TGACGTGGCATGTTCATATCATAGATGATGA
1 TGACGTGGTATGTTCATATCATAGATGATGA
* *
100 TGACATGGTATGTTCATATCATATATGATGA
1 TGACGTGGTATGTTCATATCATAGATGATGA
*
131 TGATGTGGTA
1 TGACGTGGTA
141 GATCCACATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.36
Consensus pattern (31 bp):
TGACGTGGTATGTTCATATCATAGATGATGA
Found at i:2059 original size:3 final size:3
Alignment explanation
Indices: 2051--2079 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2041 GAATAGGGTT
2051 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2080 ATGTGACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:4927 original size:18 final size:18
Alignment explanation
Indices: 4904--4939 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4894 ATTTCTATGT
4904 TAGTTTTACTTGTATTCA
1 TAGTTTTACTTGTATTCA
4922 TAGTTTTACTTGTATTCA
1 TAGTTTTACTTGTATTCA
4940 GAAGCTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (18 bp):
TAGTTTTACTTGTATTCA
Found at i:10135 original size:18 final size:18
Alignment explanation
Indices: 10112--10156 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
10102 AATTTATTTA
*
10112 TTTATTTTATCCTTATCT
1 TTTATTTTATCCTTATAT
10130 TTTATTTTATCCTTATAT
1 TTTATTTTATCCTTATAT
10148 TTTATTTTA
1 TTTATTTTA
10157 AAATAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTATTTTATCCTTATAT
Found at i:12700 original size:24 final size:24
Alignment explanation
Indices: 12583--12709 Score: 132
Period size: 24 Copynumber: 5.3 Consensus size: 24
12573 AAACGGAGAT
* *
12583 ATCAAAAATCAAAACAGAATTTAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
12607 ATAAGATATCAGAACA-AAATCTAG
1 ATCAGAAATCAAAACAGAATTC-AG
* *
12631 ATCAGAAATCAGAACAGAATTCAT
1 ATCAGAAATCAAAACAGAATTCAG
*
12655 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
12679 ATCATAAATCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
12703 ATC-GAAA
1 ATCAGAAA
12710 ATCATATAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
23 6 0.07
24 76 0.88
25 4 0.05
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:16947 original size:24 final size:24
Alignment explanation
Indices: 16913--17031 Score: 132
Period size: 24 Copynumber: 5.0 Consensus size: 24
16903 AAACAGAGAT
*
16913 ATCAGAAATCAAAACAGAATTCAG
1 ATCATAAATCAAAACAGAATTCAG
* * * * *
16937 ATCATATATCAGAACAAAATCCAT
1 ATCATAAATCAAAACAGAATTCAG
16961 ATC-TGAAATCAAAACAGAATTCAG
1 ATCAT-AAATCAAAACAGAATTCAG
* * *
16985 ATCAGAAATCATAACTGAATTCAG
1 ATCATAAATCAAAACAGAATTCAG
*
17009 ATCAAAAATCAAAACAGAATTCA
1 ATCATAAATCAAAACAGAATTCA
17032 AATAGGAATT
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
23 1 0.01
24 75 0.99
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (24 bp):
ATCATAAATCAAAACAGAATTCAG
Found at i:16982 original size:48 final size:48
Alignment explanation
Indices: 16911--17031 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
16901 GTAAACAGAG
* *
16911 ATATCAGAAATCAAAACAGAATTCAGATCATATATCAGAACAAAATCC
1 ATATCAGAAATCAAAACAGAATTCAGATCAGAAATCAGAACAAAATCC
* * ** *
16959 ATATCTGAAATCAAAACAGAATTCAGATCAGAAATCATAACTGAATTC
1 ATATCAGAAATCAAAACAGAATTCAGATCAGAAATCAGAACAAAATCC
* *
17007 AGATCAAAAATCAAAACAGAATTCA
1 ATATCAGAAATCAAAACAGAATTCA
17032 AATAGGAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAAAACAGAATTCAGATCAGAAATCAGAACAAAATCC
Found at i:21386 original size:42 final size:42
Alignment explanation
Indices: 21327--21412 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
21317 TCTCTGAATA
21327 TATTCCAATTTCAATCGAATATACAACATTGGAGAAAGGTTT
1 TATTCCAATTTCAATCGAATATACAACATTGGAGAAAGGTTT
21369 TATTCCAATTTCAATCGAATATACAACATTGGAGAAAGGTTT
1 TATTCCAATTTCAATCGAATATACAACATTGGAGAAAGGTTT
21411 TA
1 TA
21413 CGTGTAAGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (42 bp):
TATTCCAATTTCAATCGAATATACAACATTGGAGAAAGGTTT
Found at i:21824 original size:87 final size:87
Alignment explanation
Indices: 21678--21840 Score: 290
Period size: 87 Copynumber: 1.9 Consensus size: 87
21668 TATGTTATAT
*
21678 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
21743 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
21765 TATTTAACGGGAAATATTATCAAGTACAATAAAATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACCGGAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
21830 AGCGCTTATAT
66 AGCGCTTATAT
21841 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAAAATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:23300 original size:6 final size:6
Alignment explanation
Indices: 23289--23339 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
23279 ACTTGTTTGG
* * * * *
23289 ATCATC ATCATC ATCATC GTCATC ATCGTC ATCTTC ATCGTC ATCTTC
1 ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC ATCATC
23337 ATC
1 ATC
23340 GTCAGCTTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (6 bp):
ATCATC
Found at i:23303 original size:9 final size:9
Alignment explanation
Indices: 23289--23339 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
23279 ACTTGTTTGG
23289 ATCATCATC
1 ATCATCATC
23298 ATCATCATC
1 ATCATCATC
*
23307 GTCATCATC
1 ATCATCATC
* *
23316 GTCATCTTC
1 ATCATCATC
*
23325 ATCGTCATC
1 ATCATCATC
*
23334 TTCATC
1 ATCATC
23340 GTCAGCTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (9 bp):
ATCATCATC
Found at i:23340 original size:12 final size:12
Alignment explanation
Indices: 23290--23356 Score: 77
Period size: 12 Copynumber: 5.8 Consensus size: 12
23280 CTTGTTTGGA
* *
23290 TCATCATCATCA
1 TCATCGTCATCT
23302 TCATCGTCA---
1 TCATCGTCATCT
23311 TCATCGTCATCT
1 TCATCGTCATCT
23323 TCATCGTCATCT
1 TCATCGTCATCT
*
23335 TCATCGTCAGCT
1 TCATCGTCATCT
*
23347 TCATCTTCAT
1 TCATCGTCAT
23357 TGACCGCTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.19
12 39 0.81
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:23354 original size:6 final size:6
Alignment explanation
Indices: 23311--23356 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
23301 ATCATCGTCA
* * * *
23311 TCATCG TCATCT TCATCG TCATCT TCATCG TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
23357 TGACCGCTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.41
Consensus pattern (6 bp):
TCATCT
Found at i:25170 original size:200 final size:200
Alignment explanation
Indices: 24868--26207 Score: 2365
Period size: 200 Copynumber: 6.7 Consensus size: 200
24858 TTATATACCA
* * * *
24868 ATTCTCCCATAAAACCGGTATACTTATACCGTTTAGATTGAAAAATTACCTAATACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * * *
24933 TTGGGTTTCGATGTTTATGGGATCGACACTGTTTATATATGGATCGACACTTTATGGTTGCACCT
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
*
24998 TGTTTGCCATTCATTATGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
25063 GACAT
196 GACAT
*
25068 ATTCTCTTATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
25133 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTTTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
25198 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
*
25263 GACCT
196 GACAT
* * *
25268 ATTCTCTCATAAAACCGATATACTTGTATCGGTTAGATTGAAAAATTACCTATTATATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
25333 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCAACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
*
25398 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
*
25463 GACCT
196 GACAT
*
25468 ATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
25533 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
*
25598 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAATGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
*
25663 GACCT
196 GACAT
*
25668 ATTCTCTCATAAAACCGGTATACTTGTACCAGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
25733 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCA
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
* * *
25798 TGTTTGTCATTCATTCTGGACCAAAAATATCGACACATACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
25863 GACAT
196 GACAT
* *
25868 ATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTATATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
*
25933 ATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
* *
25998 TGTTTACCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
26063 GACAT
196 GACAT
*
26068 ATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
* * *
26133 TTGGGTTTCGATGTTTATAGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
66 ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
26198 TGTTTGCCAT
131 TGTTTGCCAT
26208 ATTGTAAATT
Statistics
Matches: 1091, Mismatches: 49, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 1091 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
ATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACAT
Found at i:26452 original size:18 final size:18
Alignment explanation
Indices: 26429--26489 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
26419 TCTCATTCAT
*
26429 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
26447 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
26466 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
26485 AATTA
1 AATTA
26490 ACCATACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:26465 original size:19 final size:19
Alignment explanation
Indices: 26441--26489 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
26431 TTATATTCAC
26441 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
26460 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
26479 ATACAAAATTA
1 ATACAAAATTA
26490 ACCATACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:26768 original size:21 final size:21
Alignment explanation
Indices: 26743--26807 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
26733 CCCCTTATGC
* *
26743 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
26764 CTCTCTAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
26785 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
26806 CT
1 CT
26808 TGATTGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.15, C:0.31, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:29085 original size:20 final size:19
Alignment explanation
Indices: 29030--29076 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
29020 TCTGGTATCG
29030 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
29049 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
29070 TTTTACC
1 TTTTACC
29077 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:29310 original size:181 final size:182
Alignment explanation
Indices: 29004--29466 Score: 712
Period size: 181 Copynumber: 2.5 Consensus size: 182
28994 TACTTACGAA
* *
29004 CGACACTTTCAATATATCTGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATA
1 CGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATA
* * * *
29069 TTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTATAGGCGCT
66 TTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCT
*
29134 AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAGTAT
131 AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAC
*
29185 CGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACTGGTTTTATCATA
1 CGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATA
* * * **
29250 TTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTATAGGATTT
66 TTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCT
*
29315 AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGTTCCTTATATTAAAGTAC
131 AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAC
* * * * ** *
29367 CGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTTTGTCATA
1 CGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATA
* *
29432 GTTTTACCTGTTATATCGTTTTGGATCGACACATT
66 TTTTTACCTGTTATATCGTTTTGGATCGATACATT
29467 GTTAATTTGG
Statistics
Matches: 255, Mismatches: 26, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
181 160 0.63
182 95 0.37
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
CGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTTTATCATA
TTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATAGGAGCT
AAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTAC
Found at i:29639 original size:11 final size:11
Alignment explanation
Indices: 29623--29647 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29613 ATCCGGTAAC
29623 ACCGTATATTA
1 ACCGTATATTA
29634 ACCGTATATTA
1 ACCGTATATTA
29645 ACC
1 ACC
29648 CGCCTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ACCGTATATTA
Found at i:30563 original size:15 final size:15
Alignment explanation
Indices: 30543--30579 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
30533 GAATGCGAAA
30543 GTCACAGACAAGTTT
1 GTCACAGACAAGTTT
30558 GTCACAGACAAGTTT
1 GTCACAGACAAGTTT
30573 GTCACAG
1 GTCACAG
30580 TCAAAAGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (15 bp):
GTCACAGACAAGTTT
Found at i:32241 original size:48 final size:48
Alignment explanation
Indices: 32170--32265 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
32160 GAATATTTAC
32170 TTATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTT
1 TTATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTT
*
32218 TTATCTATTATCAAACGATTAAATTTTTTTCGAATATATACTTCCCTT
1 TTATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTT
32266 ATAATTATTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (48 bp):
TTATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTT
Found at i:32275 original size:48 final size:48
Alignment explanation
Indices: 32172--32276 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
32162 ATATTTACTT
*
32172 ATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTTTT
1 ATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTTTA
*
32220 ATCTATTATCAAACGATTAAATTTTTTTCGAATATATACTTCCCTTATA
1 ATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTT-TA
32269 AT-TATTAT
1 ATCTATTAT
32277 GAGATTGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
48 51 0.94
49 3 0.06
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.48
Consensus pattern (48 bp):
ATCTATTATCAAACGATTAAATTTTTTTCAAATATATACTTCCCTTTA
Found at i:33052 original size:16 final size:16
Alignment explanation
Indices: 33022--33059 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
33012 TATTTCAGAG
33022 TGATT-AAACGCTGAA
1 TGATTCAAACGCTGAA
*
33037 TGATTCAAATGCTGAA
1 TGATTCAAACGCTGAA
33053 TGATTCA
1 TGATTCA
33060 GAAACTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (16 bp):
TGATTCAAACGCTGAA
Found at i:40605 original size:2 final size:2
Alignment explanation
Indices: 40598--40631 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
40588 CAAATGTACC
40598 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
40632 TTGCATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41051 original size:2 final size:2
Alignment explanation
Indices: 41044--41090 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
41034 ATTATTTTTA
*
41044 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41085 AT AT AT
1 AT AT AT
41091 TCAAATCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42133 original size:38 final size:39
Alignment explanation
Indices: 42087--42175 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 39
42077 GGATTAAAAG
*
42087 AGAAATAAATAAAAATG-AAG-AA-AATATTAATTTTTAAA
1 AGAAATAAA-AAAAA-GAAAGAAAGAATATTAAATTTTAAA
* *
42125 AGAAATAAAAAAAAGAAAAGAAAGAATGTTAAATTTTAGA
1 AGAAATAAAAAAAAG-AAAGAAAGAATATTAAATTTTAAA
42165 AGAAATAAAAA
1 AGAAATAAAAA
42176 TAATAGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
36 1 0.02
37 5 0.11
38 12 0.27
39 2 0.05
40 24 0.55
ACGTcount: A:0.66, C:0.00, G:0.11, T:0.22
Consensus pattern (39 bp):
AGAAATAAAAAAAAGAAAGAAAGAATATTAAATTTTAAA
Found at i:44620 original size:5 final size:5
Alignment explanation
Indices: 44610--45161 Score: 887
Period size: 5 Copynumber: 113.4 Consensus size: 5
44600 CTGGACCTAA
44610 ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT A-ATAT AATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT ATAAT
44660 AT-AT A-AAT A-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44705 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44753 ATAAT ATAAT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT AT-A- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT
44803 ATAAT ATAAT AT-AT ATAAT AT-AT ATAAT AT-AT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44850 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44899 ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44947 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
44995 ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
45043 ATAAT AT-AT ATAAT ATAAT ATAAT ATAATAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT
45094 ATAAT ATAAT ATAAT ATAAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT AT-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
45145 ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT AT
45162 TATAATGCCC
Statistics
Matches: 519, Mismatches: 0, Indels: 56
0.90 0.00 0.10
Matches are distributed among these distances:
3 8 0.02
4 57 0.11
5 433 0.83
6 12 0.02
7 9 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:46040 original size:22 final size:22
Alignment explanation
Indices: 46008--46050 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
45998 TATCGATACC
46008 GTATAAGAGTATCAATACCATA
1 GTATAAGAGTATCAATACCATA
* *
46030 GTATAATAGTATCGATACCAT
1 GTATAAGAGTATCAATACCAT
46051 GGTGAGGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
GTATAAGAGTATCAATACCATA
Found at i:46495 original size:55 final size:55
Alignment explanation
Indices: 46391--46834 Score: 611
Period size: 55 Copynumber: 8.0 Consensus size: 55
46381 TGATTACCAA
* * * * ** **
46391 ATGGGCACTTTGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGT
1 ATGGGCACTTTATGTG--TAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* *
46448 ATGGGCACTTTATGTGTAAACTTAATAAATTCATACTAAGTGGATGAATTTCCGC
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* * *
46503 ATGGGTACTTTATGTGTAAACTTAAGAAATTCATACTACGTGGATGAGTTTCCGT
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* * *
46558 ATGAGCACTTTATGTCTAAACTTAAGAAATTCATACTAAGTGAATGAATTTCCGT
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* * *
46613 ATGGCCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTTCGT
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* *
46668 ATGGGTACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCAGT
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* *
46723 ATGGACACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCTGT
1 ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
* * * *
46778 ATGGGCACTTTATGTGCAAAAC-TAGGAAATTCATACTAAGTGTATAAATTTCCGT
1 ATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
46833 AT
1 AT
46835 TGGTAGTGGG
Statistics
Matches: 345, Mismatches: 41, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
55 326 0.94
56 4 0.01
57 15 0.04
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (55 bp):
ATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGT
Found at i:53477 original size:55 final size:55
Alignment explanation
Indices: 53431--53884 Score: 621
Period size: 55 Copynumber: 8.3 Consensus size: 55
53421 TAATTTGTTT
*
53431 ATGAATTTTCGTATGAGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
53486 ATAAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
*
53541 ATTAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGT-G
1 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
53595 ATTGAA-TTTCAATATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTGAGTGA
1 A-TGAATTTTC-GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
53651 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
53706 ATAAATTTCCATTTGGGCACTTTATGTGTAAACTTAAGAAATCCATACTAAGTGG
1 ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * * *
53761 ATGAA-TTTCAATATGGGCACTTTATCTGTAAACTTAAGAAATTCAGACAAAGTGA
1 ATGAATTTTC-GTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * * *
53816 ATGAA-TTTCTGTATGGTCACTTTATGTGAAAAAC-TAGGAAATTCATACTAAGTGT
1 ATGAATTTTC-GTATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTAAGTGG
* *
53871 ATAAATTTCCGTAT
1 ATGAATTTTCGTAT
53885 TGGTAGTGGG
Statistics
Matches: 356, Mismatches: 36, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
54 9 0.03
55 335 0.94
56 12 0.03
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (55 bp):
ATGAATTTTCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:53687 original size:165 final size:165
Alignment explanation
Indices: 53442--53884 Score: 685
Period size: 165 Copynumber: 2.7 Consensus size: 165
53432 TGAATTTTCG
* * * *
53442 TATGAGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTATGGGCACT
1 TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGAATGAATTTTCGTATGGGCACT
* *
53507 TTATGTGTAAACTTAAGAAATTCATACTAAGTGGATTAATTTTCGTATGGGCACTTTATGTGTAA
66 TTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTATGGGCACTTTATGTGTAA
*
53572 ACTTAAGAAATTCATACTAAGT-GATTGAATTTCAA
131 ACTTAAGAAATCCATACTAAGTGGA-TGAATTTCAA
*
53607 TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTGAGTGAATGAATTTTCGTATGGGCACT
1 TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGAATGAATTTTCGTATGGGCACT
* *
53672 TTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCATTTGGGCACTTTATGTGTAA
66 TTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTATGGGCACTTTATGTGTAA
53737 ACTTAAGAAATCCATACTAAGTGGATGAATTTCAA
131 ACTTAAGAAATCCATACTAAGTGGATGAATTTCAA
* * * *
53772 TATGGGCACTTTATCTGTAAACTTAAGAAATTCAGACAAAGTGAATGAA-TTTCTGTATGGTCAC
1 TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGAATGAATTTTC-GTATGGGCAC
* * *
53836 TTTATGTGAAAAAC-TAGGAAATTCATACTAAGTGTATAAATTTCCGTAT
65 TTTATGTG-TAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTAT
53885 TGGTAGTGGG
Statistics
Matches: 255, Mismatches: 20, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
164 4 0.02
165 245 0.96
166 6 0.02
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (165 bp):
TATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGAATGAATTTTCGTATGGGCACT
TTATGTGTAAACTTAAGAAATTCATACTAAGTGGATAAATTTCCGTATGGGCACTTTATGTGTAA
ACTTAAGAAATCCATACTAAGTGGATGAATTTCAA
Found at i:54621 original size:36 final size:36
Alignment explanation
Indices: 54543--54824 Score: 289
Period size: 37 Copynumber: 7.6 Consensus size: 36
54533 TATATATATA
**
54543 TATATATTATACATTTTCAAAACCATTTTTAAAAAAAC
1 TATATATTATATGTTTTCAAAACCATTTTT--AAAAAC
* *
54581 -ATATATTATATGTTTTCAAAACCGTTTTTAAAAAT
1 TATATATTATATGTTTTCAAAACCATTTTTAAAAAC
** * *
54616 TATATATTATACATTTTCAAAACTATTTTAAAAAAC
1 TATATATTATATGTTTTCAAAACCATTTTTAAAAAC
** *
54652 TATATATTATACATTTTCAAAACCATTTTTTAAAAAAAA
1 TATATATTATATGTTTTCAAAACCA-TTTTT--AAAAAC
*
54691 TATATATTATATGTTTTCAAAACCGTTTTTTAAAAAC
1 TATATATTATATGTTTTCAAAACC-ATTTTTAAAAAC
** * *
54728 TATATACCATATGTTTTCAAAACTATTTTTCCAAAAC
1 TATATATTATATGTTTTCAAAACCATTTTT-AAAAAC
* * *
54765 TATAT-TATATATGTTTTCAAAAATACGTTTTCAAAAAC
1 TATATAT-TATATGTTTTC-AAAA-CCATTTTTAAAAAC
54803 TATATATTATATGTTTTCAAAA
1 TATATATTATATGTTTTCAAAA
54825 ACTATCTATG
Statistics
Matches: 205, Mismatches: 29, Indels: 21
0.80 0.11 0.08
Matches are distributed among these distances:
35 5 0.02
36 58 0.28
37 80 0.39
38 25 0.12
39 37 0.18
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATATTATATGTTTTCAAAACCATTTTTAAAAAC
Found at i:54757 original size:75 final size:73
Alignment explanation
Indices: 54542--54824 Score: 297
Period size: 75 Copynumber: 3.8 Consensus size: 73
54532 ATATATATAT
* *
54542 ATATATATTATACATTTTCAAAACCATTTTTAAAAAAAC-ATATATTATATGTTTTCAAAACCGT
1 ATATATATTATACATTTTCAAAACCGTTTTT-AAAAAACTATATATTATATGTTTTCAAAACCAT
54606 TTTTAAAAA
65 TTTTAAAAA
* **
54615 TTATATATTATACATTTTCAAAA-C-TATTTTAAAAAACTATATATTATACATTTTCAAAACCAT
1 ATATATATTATACATTTTCAAAACCGT-TTTTAAAAAACTATATATTATATGTTTTCAAAACCA-
54678 TTTTTAAAAAAA
64 TTTTT--AAAAA
** * ** *
54690 ATATATATTATATGTTTTCAAAACCGTTTTTTAAAAACTATATACCATATGTTTTCAAAACTATT
1 ATATATATTATACATTTTCAAAACCGTTTTTAAAAAACTATATATTATATGTTTTCAAAACCATT
*
54755 TTTCCAAAA
66 TTT-AAAAA
* ** * *
54764 CTATAT-TATATATGTTTTCAAAAATACG-TTTTCAAAAACTATATATTATATGTTTTCAAAA
1 ATATATAT-TATACATTTTC-AAAA-CCGTTTTTAAAAAACTATATATTATATGTTTTCAAAA
54825 ACTATCTATG
Statistics
Matches: 180, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
71 8 0.04
72 26 0.14
73 28 0.16
74 20 0.11
75 64 0.36
76 33 0.18
77 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (73 bp):
ATATATATTATACATTTTCAAAACCGTTTTTAAAAAACTATATATTATATGTTTTCAAAACCATT
TTTAAAAA
Found at i:55221 original size:81 final size:81
Alignment explanation
Indices: 55124--55302 Score: 277
Period size: 81 Copynumber: 2.2 Consensus size: 81
55114 GGTGATTCCA
* *
55124 TCGTCGTGAGGTTGAGTTGATATTGAGATGTCTTTGAACATGATATCATTCGTCATGAAGTTGAA
1 TCGTCGTGAAGTTGAGTTGATATTGAGATGTCTTTGAACATGACATCATTCGTCATGAAGTTGAA
55189 ATCATGGTTGACCCAT
66 ATCATGGTTGACCCAT
* * *
55205 TCGTCGTGAAGTTGAGTTGATCTTGAGATGTCTTTGAATATGACATCCTTCGTCATGAAGTTGAA
1 TCGTCGTGAAGTTGAGTTGATATTGAGATGTCTTTGAACATGACATCATTCGTCATGAAGTTGAA
* *
55270 ATCTTGGTTGACCCCT
66 ATCATGGTTGACCCAT
* *
55286 TTGTCCTGAAGTTGAGT
1 TCGTCGTGAAGTTGAGT
55303 CAGTCGAGCA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 89 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (81 bp):
TCGTCGTGAAGTTGAGTTGATATTGAGATGTCTTTGAACATGACATCATTCGTCATGAAGTTGAA
ATCATGGTTGACCCAT
Found at i:62390 original size:30 final size:30
Alignment explanation
Indices: 62356--62435 Score: 144
Period size: 30 Copynumber: 2.7 Consensus size: 30
62346 CAAAATGGTT
62356 TTTGGACTTGAATTGAATTTACAAAACGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
*
62386 TTTGGACTTGAATTGAATTTACAAAATGTA
1 TTTGGACTTGAATTGAATTTACAAAACGTA
62416 TTTGGACTT-AATTGAATTTA
1 TTTGGACTTGAATTGAATTTA
62436 TTCAAAATTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 11 0.22
30 38 0.78
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.41
Consensus pattern (30 bp):
TTTGGACTTGAATTGAATTTACAAAACGTA
Found at i:62572 original size:21 final size:21
Alignment explanation
Indices: 62546--62587 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
62536 ATTTGAATAT
*
62546 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
62567 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
62588 CCTATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:67727 original size:16 final size:16
Alignment explanation
Indices: 67707--67736 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
67697 ATCAAAAAGA
67707 AAAAAAT-TTAAATTT
1 AAAAAATGTTAAATTT
67722 AAAAAATGTTAAATT
1 AAAAAATGTTAAATT
67737 AAGAAATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AAAAAATGTTAAATTT
Found at i:67748 original size:41 final size:43
Alignment explanation
Indices: 67679--67759 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 43
67669 TAAAATAAAA
*
67679 TAAATAAATGTTAAATAAATCAAAAAGAAAA-AAATTTAAATT
1 TAAATAAATGTTAAATAAATCAAAAAGAAAATAAAGTTAAATT
* *
67721 TAAA-AAATGTTAAATTAA-GAAATAAGAAAATAAAGTTAA
1 TAAATAAATGTTAAATAAATCAAA-AAGAAAATAAAGTTAA
67760 GATAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 3 0.09
41 20 0.59
42 11 0.32
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.27
Consensus pattern (43 bp):
TAAATAAATGTTAAATAAATCAAAAAGAAAATAAAGTTAAATT
Found at i:67766 original size:41 final size:39
Alignment explanation
Indices: 67676--67768 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 39
67666 TCGTAAAATA
*
67676 AAATAAATAAATGTTAAATAAATCAAAAAGAAAAAAATTT
1 AAATAAA-AAATGTTAAATAAATCAAAAAGAAAAAAAGTT
* *
67716 AAATTTAAAAAATGTTAAATTAA-GAAATAAGAAAATAAAGTT
1 AAA--TAAAAAATGTTAAATAAATCAAA-AAGAAAA-AAAGTT
67758 AAGATAAAAAA
1 AA-ATAAAAAA
67769 AAAGAAAGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
40 6 0.13
41 27 0.60
42 11 0.24
43 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.08, T:0.25
Consensus pattern (39 bp):
AAATAAAAAATGTTAAATAAATCAAAAAGAAAAAAAGTT
Found at i:67771 original size:21 final size:21
Alignment explanation
Indices: 67731--67776 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
67721 TAAAAAATGT
*
67731 TAAA-TTAAGAAATAAGAAAA
1 TAAAGTTAAGAAATAAAAAAA
67751 TAAAGTTAAGATAA-AAAAAAA
1 TAAAGTTAAGA-AATAAAAAAA
*
67772 GAAAG
1 TAAAG
67777 AATAATAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 4 0.18
21 16 0.73
22 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (21 bp):
TAAAGTTAAGAAATAAAAAAA
Found at i:67861 original size:24 final size:22
Alignment explanation
Indices: 67816--67875 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
67806 AAATAAATAA
*
67816 AAAATGAAGAAAATATTAATTTTT
1 AAAA-GAAAAAAATATTAA-TTTT
*
67840 AAAAGAAAAAAATGTTACATTTT
1 AAAAGAAAAAAATATTA-ATTTT
*
67863 AGAAGAAATAAAA
1 AAAAGAAA-AAAA
67876 ATAATAGGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 22 0.71
24 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.28
Consensus pattern (22 bp):
AAAAGAAAAAAATATTAATTTT
Found at i:68538 original size:15 final size:16
Alignment explanation
Indices: 68506--68538 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
68496 ATATATATAA
*
68506 TGGATTATTTATATTT
1 TGGATTATTTAGATTT
68522 TGGATTA-TTAGATTT
1 TGGATTATTTAGATTT
68537 TG
1 TG
68539 TATTTATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TGGATTATTTAGATTT
Found at i:69239 original size:21 final size:21
Alignment explanation
Indices: 69213--69254 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
69203 AGCATCTTAC
69213 TCCGCTCTGATGATTCACACG
1 TCCGCTCTGATGATTCACACG
69234 TCCGCTCTGATGATTCACACG
1 TCCGCTCTGATGATTCACACG
69255 AAGAAGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (21 bp):
TCCGCTCTGATGATTCACACG
Found at i:71708 original size:25 final size:24
Alignment explanation
Indices: 71657--71708 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
71647 GTAAATTCCT
* * * *
71657 ATATTTAAAATTTTGATATTTATA
1 ATATTTAAAATTTTGAAAATGACA
71681 ATATTTAAATATTTTGAAAATGACA
1 ATATTTAAA-ATTTTGAAAATGACA
71706 ATA
1 ATA
71709 AATAATATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (24 bp):
ATATTTAAAATTTTGAAAATGACA
Found at i:71900 original size:31 final size:31
Alignment explanation
Indices: 71865--71934 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
71855 AATATTAATT
71865 GTTTAATTATACTAACATAATACTTTTGACA
1 GTTTAATTATACTAACATAATACTTTTGACA
71896 GTTTAATTATACTAACATAATACTTTTGACA
1 GTTTAATTATACTAACATAATACTTTTGACA
71927 GTTTAATT
1 GTTTAATT
71935 GGATGTCTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.44
Consensus pattern (31 bp):
GTTTAATTATACTAACATAATACTTTTGACA
Found at i:73036 original size:16 final size:16
Alignment explanation
Indices: 72979--73041 Score: 69
Period size: 16 Copynumber: 3.9 Consensus size: 16
72969 AACATAAATG
72979 AAAAAT-ATTTAATT-
1 AAAAATAATTTAATTA
72993 AAAAATAACTTTTAATTA
1 AAAAATAA--TTTAATTA
73011 AAATAA-AATTTAATTA
1 AAA-AATAATTTAATTA
*
73027 AAAAATAATTCAATT
1 AAAAATAATTTAATT
73042 TAGTGTAGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 6 0.14
15 3 0.07
16 19 0.45
17 7 0.17
18 5 0.12
19 2 0.05
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATAATTTAATTA
Found at i:80036 original size:15 final size:15
Alignment explanation
Indices: 80016--80046 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
80006 TCAATGATAG
80016 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
80031 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
80046 A
1 A
80047 CTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Done.