Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014475.1 Corchorus olitorius cultivar O-4 contig14508, 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: 146310
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1864 original size:32 final size:33
Alignment explanation
Indices: 1819--1882 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
1809 CTCGTGAGAC
1819 AAACTCAGATATTGGCTTTATAATTAGTATAGA
1 AAACTCAGATATTGGCTTTATAATTAGTATAGA
*
1852 AAACT-AGGTATTGGCTTTATAATTAGTATAG
1 AAACTCAGATATTGGCTTTATAATTAGTATAG
1883 CTAAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 25 0.83
33 5 0.17
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (33 bp):
AAACTCAGATATTGGCTTTATAATTAGTATAGA
Found at i:5564 original size:4 final size:4
Alignment explanation
Indices: 5550--5602 Score: 90
Period size: 4 Copynumber: 13.2 Consensus size: 4
5540 AATAGTTTAG
5550 TCTT T-TT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT
5598 TCTT T
1 TCTT T
5603 TTTTTCGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.06
4 40 0.85
5 4 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:8530 original size:80 final size:80
Alignment explanation
Indices: 8397--8635 Score: 444
Period size: 80 Copynumber: 3.0 Consensus size: 80
8387 AAAATAGAGC
*
8397 GCTTACCTTCTCGGCCGATTATTTTCTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
1 GCTTACCTTCTCGGCCGATTATTTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
8462 CAAATCCGGATTAAT
66 CAAATCCGGATTAAT
* *
8477 GCTTACTTTCCCGGCCGATTATTTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
1 GCTTACCTTCTCGGCCGATTATTTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
8542 CAAATCCGGATTAAT
66 CAAATCCGGATTAAT
8557 GCTTACCTTCTCGGCCGATTA-TTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
1 GCTTACCTTCTCGGCCGATTATTTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
8621 CAAATCCGGATTAAT
66 CAAATCCGGATTAAT
8636 TAGAGCTAAA
Statistics
Matches: 154, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 58 0.38
80 96 0.62
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (80 bp):
GCTTACCTTCTCGGCCGATTATTTTTTGGTGTAGGGAACCTTTGATATCGAAACTTTGCACAGAT
CAAATCCGGATTAAT
Found at i:18336 original size:21 final size:22
Alignment explanation
Indices: 18288--18344 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
18278 TAGTGTGGCT
** *
18288 ATCAAAATTTCATAATGTGGTT
1 ATCAAAATTTCATAATAAGGTA
18310 ATCAAAATTTCATAA-AAGGTA
1 ATCAAAATTTCATAATAAGGTA
18331 ATCAAAATTTCATA
1 ATCAAAATTTCATA
18345 TTGTGCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAATAAGGTA
Found at i:18433 original size:22 final size:22
Alignment explanation
Indices: 18264--18434 Score: 132
Period size: 22 Copynumber: 7.8 Consensus size: 22
18254 ACTTTGCAGA
* *
18264 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
18286 CTATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGAGG
**
18308 TTATCAAAATTTCATA-AAAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
18329 TAATCAAAATTTCATATTGTGC
1 TTATCAAAATTTCATAGTGAGG
*
18351 TTATCAAAATTTCATAGTGAGA
1 TTATCAAAATTTCATAGTGAGG
*** * *
18373 TTAAGGAAA-TTCTATAGGGAAG
1 TTATCAAAATTTC-ATAGTGAGG
* *
18395 TTATCAACA-TTCTATAGGGAGG
1 TTATCAAAATTTC-ATAGTGAGG
18417 TTATCAAAATTTCATAGT
1 TTATCAAAATTTCATAGT
18435 ATACTAAATC
Statistics
Matches: 117, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
21 20 0.17
22 94 0.80
23 3 0.03
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:18577 original size:22 final size:22
Alignment explanation
Indices: 18513--18623 Score: 102
Period size: 22 Copynumber: 5.1 Consensus size: 22
18503 TCATTACCAC
* *
18513 AATTTTATAGTGTTGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
18535 AA-TTCATAG-GATGG-TATCAA
1 AATTTCATAGTG-TGGTTATCAA
18555 AATTTCATAGTGTGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
* * * * *
18577 AGTTTCATAGGGAGGTTTTCAT
1 AATTTCATAGTGTGGTTATCAA
* * *
18599 AATTTCTTAGAGAGGTTATCAA
1 AATTTCATAGTGTGGTTATCAA
18621 AAT
1 AAT
18624 AATATAGCAA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
20 9 0.12
21 18 0.25
22 46 0.63
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.40
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTATCAA
Found at i:18652 original size:22 final size:22
Alignment explanation
Indices: 18527--18652 Score: 100
Period size: 22 Copynumber: 5.8 Consensus size: 22
18517 TTATAGTGTT
*
18527 GTTATCAAAA-TTCATAGGATG
1 GTTATCAAAATTTCATAGGAAG
*
18548 G-TATCAAAATTTCATAGTG-TG
1 GTTATCAAAATTTCATAG-GAAG
* *
18569 GTTATCAAAGTTTCATAGGGAG
1 GTTATCAAAATTTCATAGGAAG
* * *
18591 GTTTTCATAATTTCTTA-GAGAG
1 GTTATCAAAATTTCATAGGA-AG
* *
18613 GTTATCAAAATAAT-ATAGCAAG
1 GTTATCAAAAT-TTCATAGGAAG
*
18635 ATTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
18653 TAAGTAGGAG
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
20 8 0.10
21 14 0.17
22 59 0.71
23 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGGAAG
Found at i:18879 original size:22 final size:22
Alignment explanation
Indices: 18854--18958 Score: 61
Period size: 22 Copynumber: 4.8 Consensus size: 22
18844 ATAGAGAAGT
*
18854 TTATTAAAATTTAATAGTTAGG
1 TTATCAAAATTTAATAGTTAGG
* * * ** *
18876 TTATCAAAGTTTCATTGGGAGT
1 TTATCAAAATTTAATAGTTAGG
* * *
18898 TTATCAAAATTTTATAGGATA-A
1 TTATCAAAATTTAATA-GTTAGG
*
18920 TTATCAAAATTTCATAGTGT-GG
1 TTATCAAAATTTAATAGT-TAGG
* *
18942 TTCTTAAAATTTAATAG
1 TTATCAAAATTTAATAG
18959 AAATATTATA
Statistics
Matches: 61, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
21 1 0.02
22 58 0.95
23 2 0.03
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTAATAGTTAGG
Found at i:18972 original size:2 final size:2
Alignment explanation
Indices: 18961--18990 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18951 TTTAATAGAA
18961 AT AT -T AT 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 A
18991 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20176 original size:9 final size:10
Alignment explanation
Indices: 20151--20177 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
20141 AAAAAAGGTG
20151 TTAAAAATGC
1 TTAAAAATGC
20161 TTAAAAATGC
1 TTAAAAATGC
20171 TTAAAAA
1 TTAAAAA
20178 CTTCCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (10 bp):
TTAAAAATGC
Found at i:20567 original size:20 final size:20
Alignment explanation
Indices: 20534--20573 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
20524 TACTTTATAC
*
20534 TAAAAATACTTATATAGTTTA
1 TAAAAAAACTTATATA-TTTA
20555 TAAAAAAAC-TATATATTTA
1 TAAAAAAACTTATATATTTA
20574 CAGACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 6 0.33
21 8 0.44
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (20 bp):
TAAAAAAACTTATATATTTA
Found at i:20643 original size:12 final size:12
Alignment explanation
Indices: 20621--20649 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20611 TTATTATCAA
20621 TTTAT-TTTTAT
1 TTTATCTTTTAT
20632 TTTATCTTTTAT
1 TTTATCTTTTAT
20644 TTTATC
1 TTTATC
20650 ATTCATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTATCTTTTAT
Found at i:24722 original size:18 final size:17
Alignment explanation
Indices: 24699--24732 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24689 TGTTAGGCTA
24699 AAAAGAATAAAAGAAATG
1 AAAAGAA-AAAAGAAATG
*
24717 AAAAGAAAAAGGAAAT
1 AAAAGAAAAAAGAAAT
24733 AATTAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAAAGAAATG
Found at i:27602 original size:2 final size:2
Alignment explanation
Indices: 27548--27582 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
27538 TGAGTTCATG
*
27548 AT AT TT AT AT AT 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
27583 GAGTAAGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:36633 original size:34 final size:34
Alignment explanation
Indices: 36590--36654 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
36580 TATATCATAT
36590 TAAAATCCATAAATAACATACATTTCAAATGTAA
1 TAAAATCCATAAATAACATACATTTCAAATGTAA
**
36624 TAAAATCCATAAATAACATTTATTTCAAATG
1 TAAAATCCATAAATAACATACATTTCAAATG
36655 CACCATATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (34 bp):
TAAAATCCATAAATAACATACATTTCAAATGTAA
Found at i:38487 original size:63 final size:62
Alignment explanation
Indices: 38286--38480 Score: 284
Period size: 63 Copynumber: 3.1 Consensus size: 62
38276 ATTCCACTAA
* *
38286 AAAAAACAGCATCTTTTACCTC-AACTTATAAAAACAGAATTTTTGTATATATGGAAACCTC
1 AAAAAACAACATCTTTTACCTCAAACTTATAAAAACAGAAATTTTGTATATATGGAAACCTC
* * * *
38347 AAAAAACAACATCTTTTACCTGAAGCTTATAAAAGACAGAAAATTTGTATCTATGGAAACCTC
1 AAAAAACAACATCTTTTACCTCAAACTTATAAAA-ACAGAAATTTTGTATATATGGAAACCTC
* * *
38410 AAATAACAACATTTTTTACCTCAAACATATAACAAACAGAAATTTTGTATATATGGAAACCTC
1 AAAAAACAACATCTTTTACCTCAAACTTATAA-AAACAGAAATTTTGTATATATGGAAACCTC
38473 AAAAAACA
1 AAAAAACA
38481 GCATTTTGGT
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
61 20 0.17
62 10 0.09
63 85 0.73
64 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.28
Consensus pattern (62 bp):
AAAAAACAACATCTTTTACCTCAAACTTATAAAAACAGAAATTTTGTATATATGGAAACCTC
Found at i:38966 original size:18 final size:18
Alignment explanation
Indices: 38939--38989 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
38929 GGAAGGATTG
38939 ACAATAGGGACCTCATTC
1 ACAATAGGGACCTCATTC
* *
38957 ACACTAGGGACCTCATTG
1 ACAATAGGGACCTCATTC
38975 ACAATAGGGACCTCA
1 ACAATAGGGACCTCA
38990 GAAGGAGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (18 bp):
ACAATAGGGACCTCATTC
Found at i:46497 original size:23 final size:24
Alignment explanation
Indices: 46462--46508 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
46452 TTATGTTTTT
46462 TGTTGTTTTGATCTTCTT-TTCTC
1 TGTTGTTTTGATCTTCTTCTTCTC
46485 TGTT-TTTTCGATCTTCTTCTTCTC
1 TGTTGTTTT-GATCTTCTTCTTCTC
46509 ATTCAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.04, C:0.21, G:0.11, T:0.64
Consensus pattern (24 bp):
TGTTGTTTTGATCTTCTTCTTCTC
Found at i:53382 original size:28 final size:30
Alignment explanation
Indices: 53321--53385 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
53311 GATTCAATAT
** *
53321 TTAATTTTTTGTGTATTATTAGTATGTTACA
1 TTAATTTTTTGTGTATTATTAG-ATAATAAA
53352 TTAATTTTTTGTGTATTA-TA-ATAATAAA
1 TTAATTTTTTGTGTATTATTAGATAATAAA
53380 TTAATT
1 TTAATT
53386 ATAGTTTGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 11 0.35
30 2 0.06
31 18 0.58
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (30 bp):
TTAATTTTTTGTGTATTATTAGATAATAAA
Found at i:56658 original size:27 final size:27
Alignment explanation
Indices: 56616--56676 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
56606 TCTTCATTAT
* *
56616 AGGGGTAAAATCGTAATTTTATCAATC
1 AGGGGTAAAATAGTAAATTTATCAATC
* * *
56643 AGGGGTAACATAGTAAATTTGTCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
56670 ACGGGTA
1 AGGGGTA
56677 TTTTTGGTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Found at i:60315 original size:21 final size:21
Alignment explanation
Indices: 60275--60315 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
60265 ACAAAAATGG
* * *
60275 AACCCAAAATATGAACAACCA
1 AACCCAAAACATAAAAAACCA
60296 AACCCAAAACATAAAAAACC
1 AACCCAAAACATAAAAAACC
60316 TTGTCTAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.29, G:0.02, T:0.07
Consensus pattern (21 bp):
AACCCAAAACATAAAAAACCA
Found at i:63064 original size:16 final size:16
Alignment explanation
Indices: 63043--63073 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63033 TAATTGGTGG
63043 GGAACTTTTATTTAAT
1 GGAACTTTTATTTAAT
63059 GGAACTTTTATTTAA
1 GGAACTTTTATTTAA
63074 CTTTGATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.48
Consensus pattern (16 bp):
GGAACTTTTATTTAAT
Found at i:63758 original size:24 final size:25
Alignment explanation
Indices: 63714--63762 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
63704 TTAGTTTTTC
63714 TACTTTCTTTACTTCAGTTTAATCA
1 TACTTTCTTTACTTCAGTTTAATCA
*
63739 TACTTT-TTTGCTTCTA-TTTAATCA
1 TACTTTCTTTACTTC-AGTTTAATCA
63763 ATTAAGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.55
Consensus pattern (25 bp):
TACTTTCTTTACTTCAGTTTAATCA
Found at i:64833 original size:22 final size:22
Alignment explanation
Indices: 64799--64845 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
64789 ATTTTCTTAA
64799 GTAACCATTAATAAGAAAATTG
1 GTAACCATTAATAAGAAAATTG
*
64821 GTAACC-TTGAATAAGAAGATTG
1 GTAACCATT-AATAAGAAAATTG
64843 GTA
1 GTA
64846 TAACCTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (22 bp):
GTAACCATTAATAAGAAAATTG
Found at i:65649 original size:140 final size:140
Alignment explanation
Indices: 65486--65767 Score: 444
Period size: 140 Copynumber: 2.0 Consensus size: 140
65476 TTACAAAAAT
* *
65486 TACTTAGTAAGTTACTGAATTTGTTAATAACCCCATATAG-TTT-TGTTTTTAACCTTTATAACT
1 TACTCAGTAAGTTACTGAATTTGTTAATAACCCCATATAGTTTTCTGTTTTTAACCATTATAAC-
*
65549 AATTTTATAGTAACTTTAGACATGAAATTTGATAACCTTCATTATTTAT-AAAAGTTTACTAATG
65 --TTTTATAGTAACTTTAGACATGAAAGTTGATAACCTTCATTATTTATAAAAAGTTTACTAATG
65613 TAAAGTTATACAA
128 TAAAGTTATACAA
* *
65626 TACTCAGTAAGTTACTGAATTTGTTAATAACCCCTTATAGTTTTTCTTTTTTTAACCATTATAAC
1 TACTCAGTAAGTTACTGAATTTGTTAATAACCCCATATAG-TTTTCTGTTTTTAACCATTATAAC
* *
65691 TTTTATAGTAACTTTAGATATGAAAGTTGATAACCTTCATTATTTATAAAAAGTTTACTGATGTA
65 TTTTATAGTAACTTTAGACATGAAAGTTGATAACCTTCATTATTTATAAAAAGTTTACTAATGTA
65756 AAGTTATACAA
130 AAGTTATACAA
65767 T
1 T
65768 TTTCTTATCG
Statistics
Matches: 131, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
140 83 0.63
141 28 0.21
142 3 0.02
143 17 0.13
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (140 bp):
TACTCAGTAAGTTACTGAATTTGTTAATAACCCCATATAGTTTTCTGTTTTTAACCATTATAACT
TTTATAGTAACTTTAGACATGAAAGTTGATAACCTTCATTATTTATAAAAAGTTTACTAATGTAA
AGTTATACAA
Found at i:66595 original size:7 final size:7
Alignment explanation
Indices: 66583--66607 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
66573 AAGTATGCAC
66583 ATTATAT
1 ATTATAT
66590 ATTATAT
1 ATTATAT
66597 ATTATAT
1 ATTATAT
66604 ATTA
1 ATTA
66608 AGTATAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTATAT
Found at i:69833 original size:17 final size:18
Alignment explanation
Indices: 69811--69844 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
69801 ACTAATTAAT
*
69811 TTATTATTTAA-AAAATA
1 TTATTATCTAAGAAAATA
69828 TTATTATCTAAGAAAAT
1 TTATTATCTAAGAAAAT
69845 TCAATTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TTATTATCTAAGAAAATA
Found at i:70576 original size:19 final size:20
Alignment explanation
Indices: 70529--70589 Score: 97
Period size: 19 Copynumber: 3.0 Consensus size: 20
70519 ATCGCTGTTC
70529 TAATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
*
70549 TACATAATCTAATCTGTACAG
1 TA-ATAATCTCATCTGTACAG
70570 T-ATAATCTCATCTGTACAG
1 TAATAATCTCATCTGTACAG
70589 T
1 T
70590 TGCCAAACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 18 0.47
20 2 0.05
21 18 0.47
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
TAATAATCTCATCTGTACAG
Found at i:79952 original size:15 final size:16
Alignment explanation
Indices: 79928--79967 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
79918 AGAGGTTGAA
*
79928 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
79943 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
79959 AGAAAACAA
1 AGAAAACAA
79968 AGCAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:85220 original size:436 final size:437
Alignment explanation
Indices: 84340--85343 Score: 1200
Period size: 436 Copynumber: 2.3 Consensus size: 437
84330 TTTGACTTTT
*
84340 ATTTTTGTTT-TT-TTT-TTCTATTTATCCGATTATAAGGTGATTCAAGTGTCTATTAAAAGGTT
1 ATTTTT-TTTATTCTTTGTTCTATTTATCCGATTA-AA-GTGATTCAAGTGTCTATTAAAAGGTA
* * * * * * * *
84402 ATTTCATGATCTACAATTTTCATTAAGAACTTAAAAGCCAATTATAATGTTTTGATTCTAAAAAA
63 ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAA
* * * *
84467 TGCTTCCGAAAGTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCCACAT
128 TGCTTCCGAAAGTTTGTCGTTTTGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCCACAT
* * * * * * * * *
84532 GTCCGATTGAAGTTATTGAAGTGTCGGTTAAATGGTTATTGCATGATTTACGACTTTTATAAGGA
193 GTCCAATTAAAGTTATTCAACTGTCGGTTAAAAGGTTACTGCATGATCTACGACTTTCATAAGAA
* * * *
84597 TCCGAAAGCTAAACTTGATCTACGAGTTTCGTGGAGGGTTCAAAAGGGAATTTTTATATTTCAAG
258 GCCGAAAGCTAAACTTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATATTTCAAG
** * * *
84662 ATCTTTATTAACAAACATTTTCTTATTTGCATTATTTATCAAATGACCCTCATACTTTTCTACTT
323 ATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTT
* * * * *
84727 TATACTACTTAGTCCTTTACAAATTCTATCTTAATCTAATGTTAAGCTTT
388 TATACTACTTAGTCCTTTACAAAGTATATATTAATCTAATGTTAAACTTC
* * * * *
84777 A-TTTTTTTATTCTTTGTTCTATTTTTCCGATTAAATTGATTTATGTGTCTATCAAAAGGTAATT
1 ATTTTTTTTATTCTTTGTTCTATTTATCCGATTAAAGTGATTCAAGTGTCTATTAAAAGGTAATT
* *
84841 TCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTCAAAAAAATGC
66 TCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGC
* **
84906 TTCCTAAA-TTTGGTCGTTTTGATTGTTGGTCT-ATTTAATACCATATAA-TTTTCGATCCACAT
131 TTCCGAAAGTTT-GTCGTTTTGATTGCCGGT-TAATTTAATACCATATAATTTTTCG-TCCACAT
* * *
84968 GTCCAATTAAAGTTATTCAACTGTCGGTTAAAAGGTTACTGTATGATCTATGACTTTCATGAATA
193 GTCCAATTAAAGTTATTCAACTGTCGGTTAAAAGGTTACTGCATGATCTACGACTTTCAT-AAGA
* * * *
85033 AGCCGAAAG-TTAATTTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATGTTTTAA
257 AGCCGAAAGCTAAACTTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATATTTCAA
* * *
85097 GATCTCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTTTATT
322 GATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACT
* * *
85162 TTATGCTACTTAGTCCTTTACAAAGTATATATTACTC-GAT-TTAACACTTC
387 TTATACTACTTAGTCCTTTACAAAGTATATATTAATCTAATGTTAA-ACTTC
* * * * * *
85212 ATTTTTTTTTATTTTCTTTGTTCTATGTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAGGTA
1 A-TTTTTTTTA--TTCTTTGTTCTATTTATCCGATTAAAGTGATTCAAGTGTCTATTAAAAGGTA
* * * * * *
85277 ATTTTATGATCTGCAACTTTCATGAAAGATTCAAAAGCTAATTTTTATTTTTTAATTCTAAAAAA
63 ATTTCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAA
85342 TG
128 TG
85344 TTTTTGAAAT
Statistics
Matches: 479, Mismatches: 76, Indels: 22
0.83 0.13 0.04
Matches are distributed among these distances:
434 4 0.01
435 17 0.04
436 315 0.66
437 25 0.05
438 16 0.03
439 102 0.21
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (437 bp):
ATTTTTTTTATTCTTTGTTCTATTTATCCGATTAAAGTGATTCAAGTGTCTATTAAAAGGTAATT
TCATGATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTTAATTCTAAAAAATGC
TTCCGAAAGTTTGTCGTTTTGATTGCCGGTTAATTTAATACCATATAATTTTTCGTCCACATGTC
CAATTAAAGTTATTCAACTGTCGGTTAAAAGGTTACTGCATGATCTACGACTTTCATAAGAAGCC
GAAAGCTAAACTTGATCTACGAGTTTCATGAAGAGTTCAAAAGGGAATTTTTATATTTCAAGATC
TCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATACTTTTCTACTTTAT
ACTACTTAGTCCTTTACAAAGTATATATTAATCTAATGTTAAACTTC
Found at i:93430 original size:42 final size:44
Alignment explanation
Indices: 93379--93473 Score: 115
Period size: 45 Copynumber: 2.2 Consensus size: 44
93369 AGTGCACTAC
* * * *
93379 CTAA-ATTCTA-CTCCATCTCTAGGTAATTTAT-CAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAACTCATAAAAAATAAAG
93420 CTAATATTCTACTCCTCCATCTCTAGATAACTCATAAAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAACTCATAAAAAATAAAG
93466 CTAATATT
1 CTAATATT
93474 AATTGTTGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 18 0.40
46 17 0.38
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (44 bp):
CTAATATTCTACCTCCATCTCTAGATAACTCATAAAAAATAAAG
Found at i:97008 original size:27 final size:27
Alignment explanation
Indices: 96975--97084 Score: 139
Period size: 27 Copynumber: 4.1 Consensus size: 27
96965 ACACACGAAA
* * * *
96975 CCCAACTGCAGGAGTTTTAGCATGAAT
1 CCCAACTGCGGGAGCTTCAGCATGAGT
* *
97002 CCTAACTACGGGAGCTTCAGCATGAGT
1 CCCAACTGCGGGAGCTTCAGCATGAGT
*
97029 CCCAACCGCGGGAGCTTCAGCATGAGT
1 CCCAACTGCGGGAGCTTCAGCATGAGT
* *
97056 CCCAACTGCGGGAGCTCCGGCATGAGT
1 CCCAACTGCGGGAGCTTCAGCATGAGT
97083 CC
1 CC
97085 TTCAGCATGA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (27 bp):
CCCAACTGCGGGAGCTTCAGCATGAGT
Found at i:97150 original size:68 final size:68
Alignment explanation
Indices: 97016--97152 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 68
97006 ACTACGGGAG
* **
97016 CTTCAGCATGAGTCCCAACCGCGGGAGCTTCAGCATGAGTCCCAACTGCGGGAGCTCCGGCATGA
1 CTTCAGCATGAGTCCCAACCGCGGGAGCTTCAGCATGAATCCCAACTGCGGGAGCTCCAACATGA
97081 GTC
66 GTC
* ** * *
97084 CTTCAGCATGAGTCCCAACTGC-GGAGGCTTTGGCATGAATCCCAACTGCGGGAGCTTCAACGTG
1 CTTCAGCATGAGTCCCAACCGCGGGA-GCTTCAGCATGAATCCCAACTGCGGGAGCTCCAACATG
97148 AGTC
65 AGTC
97152 C
1 C
97153 CAACCGCGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
67 3 0.05
68 57 0.95
ACGTcount: A:0.21, C:0.31, G:0.28, T:0.20
Consensus pattern (68 bp):
CTTCAGCATGAGTCCCAACCGCGGGAGCTTCAGCATGAATCCCAACTGCGGGAGCTCCAACATGA
GTC
Found at i:97153 original size:27 final size:27
Alignment explanation
Indices: 97084--97213 Score: 109
Period size: 27 Copynumber: 4.7 Consensus size: 27
97074 GGCATGAGTC
*
97084 CTTCAGCATGAGTCCCAACTGC-GGAGG
1 CTTCAACATGAGTCCCAACTGCGGGA-G
*** *
97111 CTTTGGCATGAATCCCAACTGCGGGAG
1 CTTCAACATGAGTCCCAACTGCGGGAG
* * *
97138 CTTCAACGTGAGTCCCAACCGCGAGAG
1 CTTCAACATGAGTCCCAACTGCGGGAG
* * *
97165 CTTCATAGCGTAAGTCCCAACTTCGGGAG
1 CTTCA-A-CATGAGTCCCAACTGCGGGAG
* *
97194 TTTCAGCATGAGTCCCAACT
1 CTTCAACATGAGTCCCAACT
97214 ACAGAGCATC
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
27 57 0.70
28 4 0.05
29 21 0.26
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (27 bp):
CTTCAACATGAGTCCCAACTGCGGGAG
Found at i:97206 original size:56 final size:54
Alignment explanation
Indices: 97084--97212 Score: 145
Period size: 56 Copynumber: 2.4 Consensus size: 54
97074 GGCATGAGTC
* *
97084 CTTCAGCATGAGTCCCAACTGCGGAGGCTTTGGCATGAATCCCAACTGCGGGAG
1 CTTCAGCATGAGTCCCAACCGCGGAGGCTTTAGCATGAATCCCAACTGCGGGAG
* * * *
97138 CTTCAACGTGAGTCCCAACCGC-GAGAGCTTCATAGCGT-AAGTCCCAACTTCGGGAG
1 CTTCAGCATGAGTCCCAACCGCGGAG-GCTT--TAGCATGAA-TCCCAACTGCGGGAG
*
97194 TTTCAGCATGAGTCCCAAC
1 CTTCAGCATGAGTCCCAAC
97213 TACAGAGCAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
53 3 0.05
54 23 0.37
55 2 0.03
56 34 0.55
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (54 bp):
CTTCAGCATGAGTCCCAACCGCGGAGGCTTTAGCATGAATCCCAACTGCGGGAG
Found at i:97653 original size:42 final size:42
Alignment explanation
Indices: 97594--97727 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 42
97584 AGTGTCGTTA
* **
97594 TCCTTCTCTCTAACCGCAACAACAGTCTCAACTATGGGAATG
1 TCCTTCTCCCTAACCGCAACAACAGTCTCAACTGCGGGAATG
* *
97636 TCCTTCTCCCTAACCGCAACAACAGTCTTAACTGCGAGAATG
1 TCCTTCTCCCTAACCGCAACAACAGTCTCAACTGCGGGAATG
** * * * *
97678 TTTTTCTCCCTAACCGCAACATCAATGTCAACTGCGGGAGTG
1 TCCTTCTCCCTAACCGCAACAACAGTCTCAACTGCGGGAATG
97720 TCCTTCTC
1 TCCTTCTC
97728 TATAGCCGCA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (42 bp):
TCCTTCTCCCTAACCGCAACAACAGTCTCAACTGCGGGAATG
Found at i:98783 original size:24 final size:24
Alignment explanation
Indices: 98756--98846 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 24
98746 CTTAAGCACC
*
98756 ATTTTGCGGCAGAAGTTAACCACA
1 ATTTTGCGGCAGAAGTCAACCACA
* * * *
98780 ATTTTACCGCAGAAGTCAAGCACC
1 ATTTTGCGGCAGAAGTCAACCACA
** * *
98804 ATTCCGCGGCAGAAGCCAACCATA
1 ATTTTGCGGCAGAAGTCAACCACA
* * *
98828 ATTTTACCGTAGAAGTCAA
1 ATTTTGCGGCAGAAGTCAA
98847 GTACCATGCT
Statistics
Matches: 48, Mismatches: 19, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (24 bp):
ATTTTGCGGCAGAAGTCAACCACA
Found at i:98825 original size:48 final size:48
Alignment explanation
Indices: 98749--98853 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 48
98739 CACCAATCTT
** **
98749 AAGCACCATTTTGCGGCAGAAGTTAACCACAATTTTACCGCAGAAGTC
1 AAGCACCATTCCGCGGCAGAAGCCAACCACAATTTTACCGCAGAAGTC
* *
98797 AAGCACCATTCCGCGGCAGAAGCCAACCATAATTTTACCGTAGAAGTC
1 AAGCACCATTCCGCGGCAGAAGCCAACCACAATTTTACCGCAGAAGTC
*
98845 AAGTACCAT
1 AAGCACCAT
98854 GCTGCCGCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (48 bp):
AAGCACCATTCCGCGGCAGAAGCCAACCACAATTTTACCGCAGAAGTC
Found at i:102615 original size:14 final size:14
Alignment explanation
Indices: 102596--102623 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
102586 TTTCTTTCTT
102596 AATTTTGGGTGATG
1 AATTTTGGGTGATG
102610 AATTTTGGGTGATG
1 AATTTTGGGTGATG
102624 CTCTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
AATTTTGGGTGATG
Found at i:105170 original size:246 final size:246
Alignment explanation
Indices: 104736--105228 Score: 923
Period size: 246 Copynumber: 2.0 Consensus size: 246
104726 TCCAAATCTA
* *
104736 TCTATACTATATATAAAAGTACGAATAATGGAGAACTTTATGTTTCCGATTGTACCCTTTTTTCA
1 TCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTCCGATTGTACCATTTTTTCA
*
104801 AATATTTTTCTAAATTGACATTATTAAAATTTATTATTTAAGAATTAATTATAAAATTTCAATTT
66 AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAGAATTAATTATAAAATTTCAATTT
*
104866 AAACTGAATTATAAGTTTGTAAAATTGATTTTCATTGATGAACATGCAAATTTTTACGAATAATG
131 AAACTGAATTATAAGTTTGTAAAATTGAATTTCATTGATGAACATGCAAATTTTTACGAATAATG
* *
104931 GGAAACTTTATGTTTTCCGATTGTACCCTTTTTTCAAATATATTTTTAAAT
196 GGAAACTTTATGTTTTCCAATTGTACCCTTTTTCCAAATATATTTTTAAAT
104982 TCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTCCGATTGTACCATTTTTTCA
1 TCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTCCGATTGTACCATTTTTTCA
105047 AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAGAATTAATTATAAAATTTCAATTT
66 AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAGAATTAATTATAAAATTTCAATTT
*
105112 AGACTGAATTATAAGTTTGTAAAATTGAATTTCATTGATGAACATGCAAATTTTTACGAATAATG
131 AAACTGAATTATAAGTTTGTAAAATTGAATTTCATTGATGAACATGCAAATTTTTACGAATAATG
105177 GGAAACTTTATGTTTTCCAATTGTACCCTTTTTCCAAATATATTTTTAAAT
196 GGAAACTTTATGTTTTCCAATTGTACCCTTTTTCCAAATATATTTTTAAAT
105228 T
1 T
105229 GCCATTATTA
Statistics
Matches: 240, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
246 240 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (246 bp):
TCTATACTATATATAAAAGTACGAATAATGGAAAACTTTATGTTTCCGATTGTACCATTTTTTCA
AATATATTTCTAAATTGACATTATTAAAATTTATTATTTAAGAATTAATTATAAAATTTCAATTT
AAACTGAATTATAAGTTTGTAAAATTGAATTTCATTGATGAACATGCAAATTTTTACGAATAATG
GGAAACTTTATGTTTTCCAATTGTACCCTTTTTCCAAATATATTTTTAAAT
Found at i:105309 original size:22 final size:22
Alignment explanation
Indices: 105272--105511 Score: 157
Period size: 22 Copynumber: 10.9 Consensus size: 22
105262 TTTTATAGAA
*
105272 GGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATAGAGT
105293 GGTTATCAAAATTTCATAGAGTT
1 GGTTATCAAAATTTCATAGAG-T
* *
105316 CAGATTATCAAAATTT-ATA-AGAA
1 --GGTTATCAAAATTTCATAGAG-T
* * * *
105339 GATTTTCAAAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGAGT
** * * *
105361 TATTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATAGAGT
*
105383 GGTTATCAAAATTACATA-ATGT
1 GGTTATCAAAATTTCATAGA-GT
* *
105405 GATTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAGAGT
* * * *
105427 GGTCAACAAAATTTTATAGAGA
1 GGTTATCAAAATTTCATAGAGT
* *
105449 GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGAGT
* * *
105471 GGTTATCGAATTTTCA-AAATGT
1 GGTTATCAAAATTTCATAGA-GT
* *
105493 GATTACCAAAATTTCATAG
1 GGTTATCAAAATTTCATAG
105512 TGGTATTTCT
Statistics
Matches: 170, Mismatches: 39, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
21 23 0.14
22 125 0.74
23 6 0.04
24 3 0.02
25 13 0.08
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGAGT
Found at i:105410 original size:44 final size:45
Alignment explanation
Indices: 105274--105510 Score: 195
Period size: 44 Copynumber: 5.4 Consensus size: 45
105264 TTATAGAAGG
* *
105274 TTATC-AAATCTCAT-AGAGTGGTTATCAAAATTTCATAGA-GTTCAGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATG-T--GA
* * * * *
105320 TTATCAAAATTT-ATAAGA-AGATTTTCAAAATTTTATAGTGTTA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* *
105363 TTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
105407 TTATCAAAATTTCAT-AGAGGGGTCAACAAAATTTTATAGA-GAGG
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATA-ATGTGA
* * *
105451 TTATCAAAATTTCATAA-AGAGGTTATCGAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
*
105495 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
105511 GTGGTATTTC
Statistics
Matches: 150, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
43 17 0.11
44 99 0.66
45 3 0.02
46 23 0.15
47 8 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:105437 original size:88 final size:88
Alignment explanation
Indices: 105345--105511 Score: 228
Period size: 88 Copynumber: 1.9 Consensus size: 88
105335 AGAAGATTTT
* ** * *
105345 CAAAATTTTATAGTGTTATTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
*
105409 ATCAAAATTTCATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * * *
105433 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCGAATTTTCAAAATGTGATTA
1 CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
105498 CCAAAATTTCATAG
66 CCAAAATTTCATAG
105512 TGGTATTTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
88 66 0.97
89 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (88 bp):
CAAAATTTTATAGAGAGATTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:105477 original size:66 final size:66
Alignment explanation
Indices: 105274--105883 Score: 221
Period size: 66 Copynumber: 9.2 Consensus size: 66
105264 TTATAGAAGG
* *
105274 TTATC-AAATCTCATAGAGTGGTTATCAAAATTTCATAGAGTTCAGATTATCAAAATTT-AT-AA
1 TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAG---AGGTTATCAAAATTTCATAAA
105336 GAAGA
63 G-AGA
* * * ** * * * * *
105341 TTTTCAAAATTTTATAGTGTTATTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTG
1 TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAG
105406 A
66 A
* * * *
105407 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAG
1 TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAG
*
105472 G
66 A
* * * * *
105473 TTATCGAATTTTCA-AAATGTGATTACCAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAA
1 TTATCAAAATTTCATAGA-GTGGTTATCAAAATTTCATA---G-A--------GAGGTTATCA-A
*
105537 AATTTCAT--AGTATGG
52 AATTTCATAAAG-A-GA
* * * * * * * ***
105552 TTA-CCAAA-TT-A-GGA-AGGTTATTAAACTTTTATTATG-GA-GTAATCAAAATTTCAGGCAG
1 TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCA-TA-GAGAGGTTATCAAAATTTCATAAAG
105610 A-A
64 AGA
* ** *
105612 -TATCAAAATTTCATATGA-AGGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCAT-AAG
1 TTATCAAAATTTCATA-GAGTGGTTATCAAAATTTCATAG-AGAGGTTATCAAAATTTCATAAAG
*
105673 AGGG
64 A-GA
* * * ** * *
105677 TTATCAAAATTTCATAGTA-T-GTAGATCAAAATTTCATAGGGAGATTAAAAAAACTTCATAATG
1 TTATCAAAATTTCATAG-AGTGGT-TATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAG
*
105740 AGG
64 AGA
** * * * * *
105743 TTATCAAAAAATCATAGGGAGGTTATCAAAA-TT--T-G-TA-GTTATCAAGATTTCATAAGGAG
1 TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAG
*
105802 G
66 A
* * * * **
105803 TTATCAAAATTTTATAGGAAG-GTTTATCAAAATTTCATAGCGAGGTTATCACAATTTCATAGTG
1 TTATCAAAATTTCATA-G-AGTGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAG
*
105867 TGA
64 AGA
105870 TTATCAAAATTTCA
1 TTATCAAAATTTCA
105884 GAGTGTGATT
Statistics
Matches: 402, Mismatches: 95, Indels: 92
0.68 0.16 0.16
Matches are distributed among these distances:
59 2 0.00
60 34 0.08
61 22 0.05
62 13 0.03
63 10 0.02
64 31 0.08
65 22 0.05
66 149 0.37
67 41 0.10
68 28 0.07
69 1 0.00
70 1 0.00
73 1 0.00
74 11 0.03
75 2 0.00
76 2 0.00
77 4 0.01
78 14 0.03
79 14 0.03
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAGAGTGGTTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAG
A
Found at i:105833 original size:23 final size:21
Alignment explanation
Indices: 105612--106164 Score: 253
Period size: 22 Copynumber: 25.4 Consensus size: 21
105602 TCAGGCAGAA
*
105612 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATA-GGAGGT
*
105634 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATAG--GAGGT
* *
105656 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGA-GGT
* *
105678 TATCAAAATTTCATAGTATGT
1 TATCAAAATTTCATAGGAGGT
* *
105699 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATA-GGAGGT
** * *
105722 TAAAAAAACTTCATAATGAGGT
1 TATCAAAATTTCAT-AGGAGGT
**
105744 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATA-GGAGGT
*
105766 TATCAAAA-TT--T-GTA-GT
1 TATCAAAATTTCATAGGAGGT
*
105782 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCAT-AGGAGGT
*
105804 TATCAAAATTTTATAGGAAGGTT
1 TATCAAAATTTCATAGG-AGG-T
105827 TATCAAAATTTCATAGCGAGGT
1 TATCAAAATTTCATAG-GAGGT
* * *
105849 TATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAG-GAGGT
* * *
105871 TATCAAAATTTCAGAGTGTGAT
1 TATCAAAATTTCATAG-GAGGT
* *
105893 TA-CTAACAA-TTCATATGAATGT
1 TATC-AA-AATTTCATA-GGAGGT
* * * * * *
105915 TTTTAAATTTTAATAACGTGGT
1 TATCAAAATTTCAT-AGGAGGT
* *
105937 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATA-GGAGGT
* * *
105959 TATCAACATGTCATAGTGTTGGT
1 TATCAAAATTTCATAG-G-AGGT
* *
105982 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCA-TAGGAGGT
106004 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAG-GAGGT
* *
106026 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCAT-AGGAGGT
* * *
106048 TAACAAAATTTTATAAGAAGGT
1 TATCAAAATTTCAT-AGGAGGT
* * **
106070 TA-AAAAATTTTATAAAAAGGT
1 TATCAAAATTTCAT-AGGAGGT
* * * * *
106091 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGA-GGT
* * *
106113 AATTAAAATTTCATAGGAAGAT
1 TATCAAAATTTCATAGG-AGGT
*
106135 TATCAAAATTTCATAAGGAGAT
1 TATCAAAATTTCAT-AGGAGGT
*
106157 CATCAAAA
1 TATCAAAA
106165 ATAGTGTAAT
Statistics
Matches: 401, Mismatches: 95, Indels: 70
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
19 2 0.00
20 1 0.00
21 37 0.09
22 295 0.74
23 50 0.12
24 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAGGT
Found at i:105984 original size:45 final size:45
Alignment explanation
Indices: 105933--106021 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
105923 TTTAATAACG
* * *
105933 TGGTTATCAATATATCATAT-GGAGGTTATCAACATGTCATAGTGT
1 TGGTTATCAAAATATCAT-TGGGAAGTTATCAAAATGTCATAGTGT
* *
105978 TGGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATATCATTGGGAAGTTATCAAAATGTCATAGTG
106022 AGGTCTTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATTGGGAAGTTATCAAAATGTCATAGTGT
Found at i:106078 original size:21 final size:22
Alignment explanation
Indices: 106039--106091 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
106029 CAAAATTCCT
*
106039 TAAGGAGGTTAACAAAATTTTA
1 TAAGAAGGTTAACAAAATTTTA
106061 TAAGAAGGTTAA-AAAATTTTA
1 TAAGAAGGTTAACAAAATTTTA
*
106082 TAAAAAGGTT
1 TAAGAAGGTT
106092 CTCGAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.32
Consensus pattern (22 bp):
TAAGAAGGTTAACAAAATTTTA
Found at i:108935 original size:39 final size:39
Alignment explanation
Indices: 108891--108970 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
108881 TTTATGGTGC
108891 ACCACCCTTATTTATAATTTTCCCTATACATTTTGAGAG
1 ACCACCCTTATTTATAATTTTCCCTATACATTTTGAGAG
*
108930 ACCACCCTTATTTGTAATTTTCCCTATACATTTTGAGAG
1 ACCACCCTTATTTATAATTTTCCCTATACATTTTGAGAG
108969 AC
1 AC
108971 TATATCAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (39 bp):
ACCACCCTTATTTATAATTTTCCCTATACATTTTGAGAG
Found at i:109357 original size:25 final size:25
Alignment explanation
Indices: 109323--109372 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
109313 ACTATGTCAG
109323 CAATACCATTTTAAAGGGAGTAAAA
1 CAATACCATTTTAAAGGGAGTAAAA
109348 CAATACCATTTTAAAGGGAGTAAAA
1 CAATACCATTTTAAAGGGAGTAAAA
109373 TAGGTCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (25 bp):
CAATACCATTTTAAAGGGAGTAAAA
Found at i:110758 original size:2 final size:2
Alignment explanation
Indices: 110751--110776 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110741 ATTGACACCA
110751 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
110777 TCTAATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115675 original size:2 final size:2
Alignment explanation
Indices: 115668--115705 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
115658 AGTAAAGGGG
115668 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
115706 GAACCTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118441 original size:49 final size:48
Alignment explanation
Indices: 118366--118506 Score: 164
Period size: 49 Copynumber: 3.0 Consensus size: 48
118356 ACAACAATCT
* *
118366 TTTACATTTCC-TGCACTTTTTCTCAATTTTTACA-CCAAAATTGAATC-
1 TTTACTTTTCCTTGCACTTTTTCTCAATTTTTA-AGACAAAATTG-ATCA
*
118413 TTTATTTTTCCTTGCACCTTTTTCTCAATTTTTAAGACAAAATTGATCA
1 TTTACTTTTCCTTGCA-CTTTTTCTCAATTTTTAAGACAAAATTGATCA
* * * *
118462 TTTACTTTTCATTGCACTTTTTATTAATTTTT-TGACAAAATTGAT
1 TTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTGAT
118507 TGGCACGCTC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
47 21 0.26
48 22 0.27
49 39 0.48
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.50
Consensus pattern (48 bp):
TTTACTTTTCCTTGCACTTTTTCTCAATTTTTAAGACAAAATTGATCA
Found at i:119337 original size:15 final size:15
Alignment explanation
Indices: 119317--119366 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
119307 TGCTACGGTA
*
119317 AATGGTGTAAACAAC
1 AATGGTGTGAACAAC
* *
119332 AATGGTGCGAATAAC
1 AATGGTGTGAACAAC
*
119347 AATGGTGTGAACAAT
1 AATGGTGTGAACAAC
119362 AATGG
1 AATGG
119367 AAATGGTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (15 bp):
AATGGTGTGAACAAC
Found at i:119425 original size:15 final size:15
Alignment explanation
Indices: 119384--119426 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
119374 GCAAGGCATG
* *
119384 GCAATGTTGCATTTC
1 GCAATGCTGCACTTC
* *
119399 GCAAAGCCGCACTTC
1 GCAATGCTGCACTTC
119414 GCAATGCTGCACT
1 GCAATGCTGCACT
119427 ACCACCCCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (15 bp):
GCAATGCTGCACTTC
Found at i:128920 original size:68 final size:68
Alignment explanation
Indices: 128811--128946 Score: 263
Period size: 68 Copynumber: 2.0 Consensus size: 68
128801 TTTTGGACTC
*
128811 CACAAGCGGGTTGAGGAGTTAACACATACTCATTCTCTTAGTTAATTTTGTTTTTAAAATTAAAA
1 CACAAGCAGGTTGAGGAGTTAACACATACTCATTCTCTTAGTTAATTTTGTTTTTAAAATTAAAA
128876 ACT
66 ACT
128879 CACAAGCAGGTTGAGGAGTTAACACATACTCATTCTCTTAGTTAATTTTGTTTTTAAAATTAAAA
1 CACAAGCAGGTTGAGGAGTTAACACATACTCATTCTCTTAGTTAATTTTGTTTTTAAAATTAAAA
128944 ACT
66 ACT
128947 ATTCCCTAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.37
Consensus pattern (68 bp):
CACAAGCAGGTTGAGGAGTTAACACATACTCATTCTCTTAGTTAATTTTGTTTTTAAAATTAAAA
ACT
Found at i:130990 original size:30 final size:28
Alignment explanation
Indices: 130954--131038 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 28
130944 ATCCTCTCTG
* *
130954 ATAATCCTCTTTGGATCTTCTTCTTTGATA
1 ATAATCCTCCTTAGATCTTC-T-TTTGATA
*
130984 ATAATCCTCCTTAGATTTTCTTTTG---
1 ATAATCCTCCTTAGATCTTCTTTTGATA
* * *
131009 ATAATCCTCCTTGGATCTGCTTTTAATA
1 ATAATCCTCCTTAGATCTTCTTTTGATA
131037 AT
1 AT
131039 TGTCCTTGGA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
25 21 0.47
28 6 0.13
29 1 0.02
30 17 0.38
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.48
Consensus pattern (28 bp):
ATAATCCTCCTTAGATCTTCTTTTGATA
Found at i:131017 original size:25 final size:25
Alignment explanation
Indices: 130982--131038 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
130972 TCTTCTTTGA
* *
130982 TAATAATCCTCCTTAGATTTTCTTT
1 TAATAATCCTCCTTAGATCTGCTTT
* *
131007 TGATAATCCTCCTTGGATCTGCTTT
1 TAATAATCCTCCTTAGATCTGCTTT
131032 TAATAAT
1 TAATAAT
131039 TGTCCTTGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (25 bp):
TAATAATCCTCCTTAGATCTGCTTT
Found at i:135656 original size:149 final size:149
Alignment explanation
Indices: 135413--135705 Score: 451
Period size: 149 Copynumber: 2.0 Consensus size: 149
135403 TCACGTGTAT
* * *
135413 ACACGTGGATCCCACTTCATGGTTTCGGACCCTTCGGCATGTTTGTCTCTAGTTGTCTCCTCTAC
1 ACACGTGGATCCCACCTCATGGTTTCGGACCCTTCCGCATGTTTGTCTCCAGTTGTCTCCTCTAC
* * * * *
135478 TTGACATATCACACCATTAGCACTTCCCACCCGACCGGTCCTTGGAGATTGGAGGTCTAGACTAA
66 TTAACATATCACACCATTAGCACTTCCCACCCGACCGGCCCATGGACATTGGAGGCCTAGACTAA
135543 GCTGCTCATTTGTGCGTCC
131 GCTGCTCATTTGTGCGTCC
* * * *
135562 ACACGTGGATCCCGCCTCATGTTTTCGGACCCTTCCGCTTGTTTGTCTCCAGTTGTCTCCTTTAC
1 ACACGTGGATCCCACCTCATGGTTTCGGACCCTTCCGCATGTTTGTCTCCAGTTGTCTCCTCTAC
* *
135627 TTAACATATCACACCATTAGCACTTCCCACCCGACTGGCCCATGGACATTGGAGGCCTAGACTGA
66 TTAACATATCACACCATTAGCACTTCCCACCCGACCGGCCCATGGACATTGGAGGCCTAGACTAA
*
135692 GCTGCTCGTTTGTG
131 GCTGCTCATTTGTG
135706 TGTTAGGCAT
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
149 129 1.00
ACGTcount: A:0.18, C:0.31, G:0.20, T:0.31
Consensus pattern (149 bp):
ACACGTGGATCCCACCTCATGGTTTCGGACCCTTCCGCATGTTTGTCTCCAGTTGTCTCCTCTAC
TTAACATATCACACCATTAGCACTTCCCACCCGACCGGCCCATGGACATTGGAGGCCTAGACTAA
GCTGCTCATTTGTGCGTCC
Found at i:135864 original size:71 final size:71
Alignment explanation
Indices: 135748--135881 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 71
135738 TTTAGTCTCT
*
135748 GCTTCTCCGCATCCTTCTACCCAATCACATTTACCATTACGTCTGGTATTTGCATGTATCAACGT
1 GCTTCTCCGCATCCTTCTACCCAATCACATTTACCATTACCTCTGGTATTTGCATGTATCAACGT
135813 TTGAGA
66 TTGAGA
* *
135819 GCTTCTCTGCATCCTTCTACCCAGTCACATTTACCATTACCTCTGGTATTTGCATGTATCAAC
1 GCTTCTCCGCATCCTTCTACCCAATCACATTTACCATTACCTCTGGTATTTGCATGTATCAAC
135882 ATTCCCAGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.36
Consensus pattern (71 bp):
GCTTCTCCGCATCCTTCTACCCAATCACATTTACCATTACCTCTGGTATTTGCATGTATCAACGT
TTGAGA
Found at i:136569 original size:149 final size:149
Alignment explanation
Indices: 136292--136587 Score: 484
Period size: 149 Copynumber: 2.0 Consensus size: 149
136282 TCACGTGTAT
*
136292 ACACGTGGATCCCACCTCATGTTTTCGGACCCTTCGGCTTGTTTGTCTCCAGTTGTCTCATTTAA
1 ACACGTGGATCCCACCTCATGTTTTCGGACCCTTCGGCTTGTTTGTCTCCAGTTGTCTCATCTAA
* *
136357 TTGACATATCACACCATTAGCACTTCCCACCCGACCGTCCATTGGACATTGGAGGTCTGGACTGA
66 TTGACATATCACACCATTAGCACTTCCCACCCGACCGGCCATTGGACATTGGAGGTCTAGACTGA
*
136422 GCTGCTCGTTTGTGCGTCC
131 GCTGCTCGTTTGAGCGTCC
** * * *
136441 ACACGTGGATCCCGGCTTATGTTTTCGGACCCTTCGGCTTGTTTGTCTCCAGTTGTCTCCTCTAC
1 ACACGTGGATCCCACCTCATGTTTTCGGACCCTTCGGCTTGTTTGTCTCCAGTTGTCTCATCTAA
* * *
136506 TTGACATATCACACCATTAGCACTTCCCACCTGACCGGCCCTTGGACATTGGAGTTCTAGACTGA
66 TTGACATATCACACCATTAGCACTTCCCACCCGACCGGCCATTGGACATTGGAGGTCTAGACTGA
136571 GCTGCTCGTTTGAGCGT
131 GCTGCTCGTTTGAGCGT
136588 TAGGCGTCCT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
149 135 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (149 bp):
ACACGTGGATCCCACCTCATGTTTTCGGACCCTTCGGCTTGTTTGTCTCCAGTTGTCTCATCTAA
TTGACATATCACACCATTAGCACTTCCCACCCGACCGGCCATTGGACATTGGAGGTCTAGACTGA
GCTGCTCGTTTGAGCGTCC
Found at i:137813 original size:2 final size:2
Alignment explanation
Indices: 137806--137848 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
137796 TATAAGTTAG
137806 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
137846 AT A
1 AT A
137849 CTACATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:137830 original size:17 final size:16
Alignment explanation
Indices: 137806--137848 Score: 72
Period size: 15 Copynumber: 2.8 Consensus size: 16
137796 TATAAGTTAG
137806 ATATATATATATATAT
1 ATATATATATATATAT
137822 ATATA-ATATATATAT
1 ATATATATATATATAT
137837 ATATAT-TATATA
1 ATATATATATATA
137849 CTACATATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATATATATATAT
Found at i:137860 original size:17 final size:17
Alignment explanation
Indices: 137809--137848 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
137799 AAGTTAGATA
137809 TATATATATATATATAT
1 TATATATATATATATAT
*
137826 AATATATATATATATAT
1 TATATATATATATATAT
137843 TATATA
1 TATATA
137849 CTACATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:141505 original size:11 final size:11
Alignment explanation
Indices: 141462--141499 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
141452 TTCCTATATA
*
141462 AAATAAATTAT
1 AAATTAATTAT
141473 CAAA-TAATTAT
1 -AAATTAATTAT
141484 AAATTAATTAT
1 AAATTAATTAT
141495 AAATT
1 AAATT
141500 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:141723 original size:17 final size:17
Alignment explanation
Indices: 141697--141742 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
141687 AATTTCTCCC
*
141697 CTTCTGCATATTTTCTT
1 CTTCTCCATATTTTCTT
141714 CTTCTCCATATTTTCTT
1 CTTCTCCATATTTTCTT
141731 CTTCTCCATATT
1 CTTCTCCATATT
141743 CTATTGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.13, C:0.28, G:0.02, T:0.57
Consensus pattern (17 bp):
CTTCTCCATATTTTCTT
Done.