Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016090.1 Corchorus capsularis cultivar CVL-1 contig16111, 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: 163626
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--31 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1 AT 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 A
32 ACAGATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16652 original size:26 final size:26
Alignment explanation
Indices: 16604--16816 Score: 261
Period size: 27 Copynumber: 8.0 Consensus size: 26
16594 AAATTAGTAT
*
16604 CAGTAATCAGTAAAAAAGAGTAAGAAA
1 CAGTATTCAGT-AAAAAGAGTAAGAAA
16631 CAGTATTCAGTAAAAAGAGTAAGAAAA
1 CAGTATTCAGTAAAAAGAGTAAG-AAA
*
16658 GAGTCA-TCAGTAAATAAGAGTAAGAAA
1 CAGT-ATTCAGTAAA-AAGAGTAAGAAA
*
16685 CAATATTCAGTAAAAAGAGTAAGAAAA
1 CAGTATTCAGTAAAAAGAGTAAG-AAA
* *
16712 GAGCCA-TCAGTAAAAAGAGTAAGAAA
1 CAG-TATTCAGTAAAAAGAGTAAGAAA
*
16738 CAATATTCAGTAAAAAGAGTAAGAAAA
1 CAGTATTCAGTAAAAAGAGTAAG-AAA
*
16765 GAGTCA-TCAGTAAAAAGAGTAAGAAA
1 CAGT-ATTCAGTAAAAAGAGTAAGAAA
*
16791 CAATATTCAGTAAAAAGAGTAAGAAA
1 CAGTATTCAGTAAAAAGAGTAAGAAA
16817 AGCGTAATAG
Statistics
Matches: 162, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.01
26 68 0.42
27 80 0.49
28 12 0.07
ACGTcount: A:0.56, C:0.08, G:0.19, T:0.17
Consensus pattern (26 bp):
CAGTATTCAGTAAAAAGAGTAAGAAA
Found at i:16753 original size:53 final size:53
Alignment explanation
Indices: 16609--16818 Score: 384
Period size: 53 Copynumber: 3.9 Consensus size: 53
16599 AGTATCAGTA
*
16609 ATCAGTAAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 ATCAGT-AAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
*
16663 ATCAGTAAATAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCC
1 ATCAGTAAA-AAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
16717 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
16770 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
16819 CGTAATAGTA
Statistics
Matches: 152, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
53 95 0.62
54 57 0.38
ACGTcount: A:0.57, C:0.08, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
Found at i:18671 original size:24 final size:24
Alignment explanation
Indices: 18638--18693 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
18628 TTGGTTTGTT
18638 GATTGCTAGACACTGTGGGGTTCAA
1 GATTG-TAGACACTGTGGGGTTCAA
18663 GATTGTAGACACTGTGGGGTTCAA
1 GATTGTAGACACTGTGGGGTTCAA
18687 GATTGTA
1 GATTGTA
18694 TCGTAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.30
Consensus pattern (24 bp):
GATTGTAGACACTGTGGGGTTCAA
Found at i:19587 original size:2 final size:2
Alignment explanation
Indices: 19580--19621 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
19570 AATTTCAATA
*
19580 AT AT AT AT AT AT AT AT AT AT AA AT AT ACT AT A- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
19621 A
1 A
19622 CTATTGTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:19634 original size:15 final size:15
Alignment explanation
Indices: 19577--19625 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
19567 TAAAATTTCA
19577 ATAATATATATATA-T
1 ATAATATAT-TATACT
*
19592 ATATATATAAATATACT
1 ATA-ATAT-ATTATACT
19609 ATAATATATTATACT
1 ATAATATATTATACT
19624 AT
1 AT
19626 TGTATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
15 12 0.41
16 12 0.41
17 5 0.17
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATATTATACT
Found at i:20031 original size:16 final size:15
Alignment explanation
Indices: 20002--20049 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19992 TCAAACCCCG
* *
20002 AAACGAAAAAGACCC
1 AAACCAAAATGACCC
*
20017 GAACCAAAATTGACCC
1 AAACCAAAA-TGACCC
*
20033 AAACCCAAATGACCC
1 AAACCAAAATGACCC
20048 AA
1 AA
20050 CATTTGAGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.52, C:0.31, G:0.10, T:0.06
Consensus pattern (15 bp):
AAACCAAAATGACCC
Found at i:20047 original size:15 final size:16
Alignment explanation
Indices: 20012--20049 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20002 AAACGAAAAA
*
20012 GACCCGAACCAAAATT
1 GACCCAAACCAAAATT
*
20028 GACCCAAACCCAAA-T
1 GACCCAAACCAAAATT
20043 GACCCAA
1 GACCCAA
20050 CATTTGAGCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.45, C:0.37, G:0.11, T:0.08
Consensus pattern (16 bp):
GACCCAAACCAAAATT
Found at i:20718 original size:2 final size:2
Alignment explanation
Indices: 20711--20744 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
20701 CTCGTACTTT
20711 TA TA TA TA GTA TA TA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
20745 CACTATAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33052 original size:30 final size:31
Alignment explanation
Indices: 32997--33193 Score: 110
Period size: 32 Copynumber: 5.7 Consensus size: 31
32987 GACTATGCTT
* *
32997 ACTTCTCTTAATTACGCTGAATTAAGACTTTA
1 ACTTTTCTTAATTAC-CTAAATTAAGACTTTA
33029 ACTTTTCTTAATTACC-AAATTAAGACCTTGACTA
1 ACTTTTCTTAATTACCTAAATTAAGA-CTT---TA
* *
33063 TGCTTACTTCTCTTAATTACCTTGAATTAAGACTTTA
1 -----ACTTTTCTTAATTACC-TAAATTAAGACTTTA
* *
33100 TCTTTTCTTAATTACC-AAATTAAGACTTTGCTTTTCTT
1 ACTTTTCTTAATTACCTAAATTAAGA-----C--TT-TA
* *
33138 ATTTTTCTTAATTACCCTGAATTAAGACTTTA
1 ACTTTTCTTAATTA-CCTAAATTAAGACTTTA
*
33170 ACTTTTCTTAATTACTCTTAATTA
1 ACTTTTCTTAATTAC-CTAAATTA
33194 CAATGAATTA
Statistics
Matches: 129, Mismatches: 14, Indels: 44
0.69 0.07 0.24
Matches are distributed among these distances:
30 16 0.12
31 5 0.04
32 49 0.38
33 2 0.02
34 2 0.02
35 2 0.02
37 4 0.03
38 13 0.10
39 17 0.13
40 11 0.09
41 8 0.06
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.46
Consensus pattern (31 bp):
ACTTTTCTTAATTACCTAAATTAAGACTTTA
Found at i:33175 original size:70 final size:71
Alignment explanation
Indices: 32975--33184 Score: 332
Period size: 71 Copynumber: 3.0 Consensus size: 71
32965 AATCGGAATC
* *
32975 AATTGAGACCTTGACTATGCTTACTTCTCTTAATTACGCTGAATTAAGACTTTAACTTTTCTTAA
1 AATTAAGACCTTGACTATGCTTACTTCTCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAA
33040 TTACCA
66 TTACCA
* *
33046 AATTAAGACCTTGACTATGCTTACTTCTCTTAATTACCTTGAATTAAGACTTTATCTTTTCTTAA
1 AATTAAGACCTTGACTATGCTTACTTCTCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAA
33111 TTACCA
66 TTACCA
* * * * *
33117 AATTAAGACTTTG-CTTTTCTTATTTTTCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAA
1 AATTAAGACCTTGACTATGCTTACTTCTCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAA
33181 TTAC
66 TTAC
33185 TCTTAATTAC
Statistics
Matches: 128, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
70 49 0.38
71 79 0.62
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.45
Consensus pattern (71 bp):
AATTAAGACCTTGACTATGCTTACTTCTCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAA
TTACCA
Found at i:33201 original size:42 final size:40
Alignment explanation
Indices: 33105--33205 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 40
33095 CTTTATCTTT
* **
33105 TCTTAATTACCA--AATTAAGACTTTGCTTTTCTTATTTT
1 TCTTAATTACCATGAATTAAGACTTTACTTTTCTTATTAC
*
33143 TCTTAATTACCCTGAATTAAGACTTTAACTTTTCTTAATTAC
1 TCTTAATTACCATGAATTAAGACTTT-ACTTTTCTT-ATTAC
*
33185 TCTTAATTACAATGAATTAAG
1 TCTTAATTACCATGAATTAAG
33206 GTTTTAACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 11 0.21
40 12 0.23
41 8 0.15
42 22 0.42
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.47
Consensus pattern (40 bp):
TCTTAATTACCATGAATTAAGACTTTACTTTTCTTATTAC
Found at i:39153 original size:21 final size:21
Alignment explanation
Indices: 39114--39162 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
39104 TCAATGCTTT
**
39114 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
39136 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
39157 A-GAAGC
1 AGGAAGC
39163 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:48802 original size:15 final size:16
Alignment explanation
Indices: 48777--48809 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
48767 AAGTAAAGAG
48777 TTTAGAAAACAATCAA
1 TTTAGAAAACAATCAA
48793 TTTA-AAAACAATCAA
1 TTTAGAAAACAATCAA
48808 TT
1 TT
48810 AAGAGATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (16 bp):
TTTAGAAAACAATCAA
Found at i:50340 original size:13 final size:14
Alignment explanation
Indices: 50316--50345 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
50306 TACTTCTACT
50316 AAATGCATGGATGC
1 AAATGCATGGATGC
50330 AAATG-ATGGATGC
1 AAATGCATGGATGC
50343 AAA
1 AAA
50346 GTCCGATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (14 bp):
AAATGCATGGATGC
Found at i:53373 original size:19 final size:20
Alignment explanation
Indices: 53327--53374 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
53317 TGTGGCACGC
*
53327 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
53349 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
53368 CACATGT
1 CACATGT
53375 TACGCCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:53380 original size:53 final size:53
Alignment explanation
Indices: 53294--53396 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
53284 GACGTGGCAC
* * **
53294 GCCACGTGTACCAAAAAGTGATATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
** *
53347 GCCACATGTACCAAAAAGTGACACATGTTACGCCATATGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
53397 GACATGTGGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:54189 original size:20 final size:20
Alignment explanation
Indices: 54164--54202 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54154 AAAAAGAGCA
54164 CCAATTTGCAAATCAAATGT
1 CCAATTTGCAAATCAAATGT
*
54184 CCAATTTGTAAATCAAATG
1 CCAATTTGCAAATCAAATG
54203 CCTTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGT
Found at i:54759 original size:27 final size:27
Alignment explanation
Indices: 54699--54774 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
54689 AAGTGACCTT
*** **
54699 AAAATGACCAAAATGCCCCCAAAATGTG
1 AAAATGACCAAAATG-CCCTTGAATGCA
54727 AAAATGACCAAAATGCCCTTGAATGCA
1 AAAATGACCAAAATGCCCTTGAATGCA
* *
54754 AAAATGACTAAAATGGCCTTG
1 AAAATGACCAAAATGCCCTTG
54775 GATGACCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 26 0.63
28 15 0.37
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCTTGAATGCA
Found at i:57852 original size:33 final size:33
Alignment explanation
Indices: 57810--57905 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
57800 CTAATTTGCA
* **
57810 TGTTGTTTGTGATGACATTAAATCTGTTTTAGG
1 TGTTGTTTGTGATGAAACAAAATCTGTTTTAGG
57843 TGTTGTTTGTGATGAAACAAAATCTGTTTT-GG
1 TGTTGTTTGTGATGAAACAAAATCTGTTTTAGG
* **
57875 ATGCTAATTGTGATGAAA-ACAAATCTGTTTT
1 -TGTTGTTTGTGATGAAACA-AAATCTGTTTT
57906 GGTTGATCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.05
33 52 0.95
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGTGATGAAACAAAATCTGTTTTAGG
Found at i:60886 original size:30 final size:30
Alignment explanation
Indices: 60850--60912 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
60840 CATCTTCAAG
*
60850 TCCATGATAAGTCCTT-GGCGTATCATTCCC
1 TCCATGATAAG-CCTTGGGCGCATCATTCCC
60880 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGGGCGCATCATTCCC
60910 TCC
1 TCC
60913 CCTTGAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.19, C:0.33, G:0.17, T:0.30
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCGCATCATTCCC
Found at i:61254 original size:33 final size:33
Alignment explanation
Indices: 61208--61293 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
61198 TTCTTTTCAC
*
61208 CCAAAACATAATTATTTTCAATGCTATGATAAA
1 CCAAAACAAAATTATTTTCAATGCTATGATAAA
* * *
61241 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAAAATTATTTTCAATGCTATGATAAA
61274 CCAAAACAAAATTATTTTCA
1 CCAAAACAAAATTATTTTCA
61294 TCACAATTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.30
Consensus pattern (33 bp):
CCAAAACAAAATTATTTTCAATGCTATGATAAA
Found at i:61387 original size:33 final size:33
Alignment explanation
Indices: 61309--61413 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
61299 ATTAGCATCC
* * * *
61309 AAAATAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACACCT
*
61342 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTATCATCGCAAACAACACCT
** * * **
61374 CAAATTAGGTTTAGTATCATTGCAAACAACTTCT
1 -AAAACAGATTTAGTATCATCGCAAACAACACCT
61408 AAAACA
1 AAAACA
61414 CTCTTTGCAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
32 2 0.03
33 54 0.93
34 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACCT
Found at i:64436 original size:21 final size:18
Alignment explanation
Indices: 64398--64438 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
64388 GGAATATTCT
64398 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
64416 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
64437 TG
1 TG
64439 GTCTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Found at i:70869 original size:21 final size:18
Alignment explanation
Indices: 70831--70871 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 18
70821 GGAATATTCT
70831 TGCTTCCAATGACTTCAA
1 TGCTTCCAATGACTTCAA
70849 TGCTCTCCAATTGATCTTCAA
1 TGCT-TCCAA-TGA-CTTCAA
70870 TG
1 TG
70872 GTCTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 3 0.15
21 8 0.40
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (18 bp):
TGCTTCCAATGACTTCAA
Found at i:75043 original size:19 final size:18
Alignment explanation
Indices: 75008--75050 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
74998 TTTAAAGAAT
75008 AAAAAAATCAAAAATTTGA
1 AAAAAAATCAAAAATTT-A
*
75027 AAAAAAAT-AAAGGATTTA
1 AAAAAAATCAAA-AATTTA
75045 AAAAAA
1 AAAAAA
75051 TCCGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.19
Consensus pattern (18 bp):
AAAAAAATCAAAAATTTA
Found at i:78681 original size:26 final size:26
Alignment explanation
Indices: 78652--78783 Score: 99
Period size: 26 Copynumber: 5.0 Consensus size: 26
78642 TTACTTATTC
*
78652 TGCAATTTTGAAATTTGTATACTCTT
1 TGCAATTCTGAAATTTGTATACTCTT
*
78678 TGCAATTCTGAAATTTGTATACTCTC
1 TGCAATTCTGAAATTTGTATACTCTT
* * * ** *
78704 T-AAATTCAGCAA-TTG-ACCCTTTTATT
1 TGCAATTCTGAAATTTGTA---TACTCTT
* *
78730 ATGCAATTCTGAAACTAGTATACTCTT
1 -TGCAATTCTGAAATTTGTATACTCTT
* *
78757 TGCAATTATGAAATTTATATACTCTT
1 TGCAATTCTGAAATTTGTATACTCTT
78783 T
1 T
78784 ATATTCTACA
Statistics
Matches: 79, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
23 1 0.01
24 3 0.04
25 8 0.10
26 51 0.65
27 5 0.06
28 8 0.10
29 2 0.03
30 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (26 bp):
TGCAATTCTGAAATTTGTATACTCTT
Found at i:89792 original size:30 final size:30
Alignment explanation
Indices: 89756--89816 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
89746 CAAAGGATCA
89756 AATGGCATCTTTGGTACGATTCCTCCATCC
1 AATGGCATCTTTGGTACGATTCCTCCATCC
**
89786 AATGGCATCTTTGGTGTGATTCCTCCATCC
1 AATGGCATCTTTGGTACGATTCCTCCATCC
89816 A
1 A
89817 TTGATGTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (30 bp):
AATGGCATCTTTGGTACGATTCCTCCATCC
Found at i:89827 original size:30 final size:30
Alignment explanation
Indices: 89756--89835 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
89746 CAAAGGATCA
* **
89756 AATGGCATCTTTGGTACGATTCCTCCATCC
1 AATGACATCTTTGGTGTGATTCCTCCATCC
*
89786 AATGGCATCTTTGGTGTGATTCCTCCATCC
1 AATGACATCTTTGGTGTGATTCCTCCATCC
* **
89816 ATTGATGTCTTTGGTGTGAT
1 AATGACATCTTTGGTGTGAT
89836 CCCATCTCCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (30 bp):
AATGACATCTTTGGTGTGATTCCTCCATCC
Found at i:91013 original size:16 final size:14
Alignment explanation
Indices: 90979--91008 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
90969 GTGACCCATT
90979 AAGCACACAACGCA
1 AAGCACACAACGCA
90993 AAGCACACAACGCA
1 AAGCACACAACGCA
91007 AA
1 AA
91009 AAGCAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.33, G:0.13, T:0.00
Consensus pattern (14 bp):
AAGCACACAACGCA
Found at i:96238 original size:30 final size:30
Alignment explanation
Indices: 96201--96276 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
96191 TGATCAAATC
96201 ACATCTTTGGTGCGATTCCTCCATCCAATG
1 ACATCTTTGGTGCGATTCCTCCATCCAATG
* *
96231 GCATCTTTGGTGCGATTCCTCCATCCATTG
1 ACATCTTTGGTGCGATTCCTCCATCCAATG
**
96261 ATGTCTTTGGTGCGAT
1 ACATCTTTGGTGCGAT
96277 CCCATCTCCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (30 bp):
ACATCTTTGGTGCGATTCCTCCATCCAATG
Found at i:98079 original size:2 final size:2
Alignment explanation
Indices: 98072--98105 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
98062 AATTAAGAAG
98072 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
98106 GTGTGTGCGC
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:98528 original size:17 final size:18
Alignment explanation
Indices: 98503--98536 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
98493 GTCGAGTTTT
*
98503 TTGATTGAGTTT-TATAG
1 TTGAGTGAGTTTATATAG
98520 TTGAGTGAGTTTATATA
1 TTGAGTGAGTTTATATA
98537 TCACCTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (18 bp):
TTGAGTGAGTTTATATAG
Found at i:105975 original size:17 final size:16
Alignment explanation
Indices: 105953--106003 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
105943 GATCACCCCC
105953 AGATCACTAGTGATCTA
1 AGATCACTAGTGATC-A
*
105970 AGATCACTAGTAATGCA
1 AGATCACTAGTGAT-CA
**
105987 AGATCACCGGTGATCA
1 AGATCACTAGTGATCA
106003 A
1 A
106004 AGATTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (16 bp):
AGATCACTAGTGATCA
Found at i:114463 original size:30 final size:28
Alignment explanation
Indices: 114422--114482 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
114412 GAGTTTTTTA
114422 CCCAAATATAACA-TTTGGAAAACTTATTT
1 CCCAAATATAACACTTT--AAAACTTATTT
*
114451 CCCAAAGTATAACACTTTTAAACTTATTT
1 CCCAAA-TATAACACTTTAAAACTTATTT
114480 CCC
1 CCC
114483 TAATTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 19 0.66
30 7 0.24
31 3 0.10
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (28 bp):
CCCAAATATAACACTTTAAAACTTATTT
Found at i:115865 original size:30 final size:30
Alignment explanation
Indices: 115744--116190 Score: 506
Period size: 30 Copynumber: 14.6 Consensus size: 30
115734 AGTCTCCAAA
* *
115744 TGACACCAGAAGTTGTCATGATAAATCT-CCAT
1 TGACACCAGAAGTTGTCATGAT--CT-TACAAT
* *
115776 TAACACCAGAAGTTGTCAAT-AGTGTTACAAT
1 TGACACCAGAAGTTGTC-ATGA-TCTTACAAT
* *
115807 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* * *
115838 TGACACCATAAGTTGTCATGGTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
115868 TGACACCAGAAGTTGTCATGATGTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
115898 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* * *
115929 AGACACTAGAAGTTGTCATGATTTTACAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
115959 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATCTTACAAT
* * *
115990 TGACACTAGAAGTTGTCATGCTCTTACAAA
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* * *
116020 TGACACCAGAAGTAGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
* *
116050 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
116080 TGACACCAGAAGTTGTCATGAT-TTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTA--CAAT
* *
116111 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATCTTACAAT
*
116141 TGACACCAAAAGTTGTCATGAT-TTATTCAAT
1 TGACACCAGAAGTTGTCATGATCTTA--CAAT
116172 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
116191 ATACACCATG
Statistics
Matches: 363, Mismatches: 41, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.01
30 191 0.53
31 145 0.40
32 20 0.06
33 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATCTTACAAT
Found at i:115879 original size:61 final size:60
Alignment explanation
Indices: 115740--116190 Score: 505
Period size: 61 Copynumber: 7.4 Consensus size: 60
115730 TCAAAGTCTC
* * * *
115740 CAAATGACACCAGAAGTTGTCATGATAAATCT-CCATTAACACCAGAAGTTGTCAAT-AGTGTTA
1 CAAATGACACCAGAAGTTGTCATGAT--CT-TACAATTGACACCAGAAGTTGTC-ATGA-TCTTA
* * * * *
115803 CAATTGACACCAGAAGTTGTCAATAATCTTACAAATGACACCATAAGTTGTCATGGTCTTA
1 CAAATGACACCAGAAGTTGTC-ATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTA
* *
115864 CAAATGACACCAGAAGTTGTCATGATGTTACAATTGACACCAGAAGTTGTCAATAATCTTA
1 CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATGATCTTA
* * * *
115925 CAAAAGACACTAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATAATCTTA
1 CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTC-ATGATCTTA
* * * * * *
115986 CAAATGACACTAGAAGTTGTCATGCTCTTACAAATGACACCAGAAGTAGTCATGATTTTG
1 CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTA
* * *
116046 CAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGAT-TTA
1 CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTA
* * * *
116105 TTCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAAAAGTTGTCATGAT-TTA
1 --CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTA
*
116166 TTCAATTGACACCAGAAGTTGTCAT
1 --CAAATGACACCAGAAGTTGTCAT
116191 ATACACCATG
Statistics
Matches: 346, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.01
60 81 0.23
61 221 0.64
62 18 0.05
63 20 0.06
64 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (60 bp):
CAAATGACACCAGAAGTTGTCATGATCTTACAATTGACACCAGAAGTTGTCATGATCTTA
Found at i:115911 original size:91 final size:91
Alignment explanation
Indices: 115740--116189 Score: 561
Period size: 91 Copynumber: 4.9 Consensus size: 91
115730 TCAAAGTCTC
* * *
115740 CAAATGACACCAGAAGTTGTCATGATAAATCT-CCATTAACACCAGAAGTTGTCAAT-AGTGTTA
1 CAAATGACACCAGAAGTTGTCATGAT---TTTACAATTGACACCAGAAGTTGTC-ATGA-TGTTA
115803 CAATTGACACCAGAAGTTGTCAATAATCTTA
61 CAATTGACACCAGAAGTTGTCAATAATCTTA
* * * *
115834 CAAATGACACCATAAGTTGTCATGGTCTTACAAATGACACCAGAAGTTGTCATGATGTTACAATT
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATGTTACAATT
115899 GACACCAGAAGTTGTCAATAATCTTA
66 GACACCAGAAGTTGTCAATAATCTTA
* * * * *
115925 CAAAAGACACTAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCAATAATCTTACAAA
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTC-ATGATGTTACAAT
* **
115990 TGACACTAGAAGTTGTC-ATGCTCTTA
65 TGACACCAGAAGTTGTCAATAATCTTA
* * * *
116016 CAAATGACACCAGAAGTAGTCATGATTTTGCAATTGACACCAGAAGTTGTCATGATTTTGCAATT
1 CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATGTTACAATT
*
116081 GACACCAGAAGTTGTC-ATGAT-TTA
66 GACACCAGAAGTTGTCAATAATCTTA
* * *
116105 TTCAATTGACACCAGAAGTTGTCATGATTTTGCAATTGACACCAAAAGTTGTCATGAT-TTATTC
1 --CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATGTTA--C
116169 AATTGACACCAGAAGTTGTCA
62 AATTGACACCAGAAGTTGTCA
116190 TATACACCAT
Statistics
Matches: 315, Mismatches: 33, Indels: 17
0.86 0.09 0.05
Matches are distributed among these distances:
89 3 0.01
90 31 0.10
91 191 0.61
92 66 0.21
94 24 0.08
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (91 bp):
CAAATGACACCAGAAGTTGTCATGATTTTACAATTGACACCAGAAGTTGTCATGATGTTACAATT
GACACCAGAAGTTGTCAATAATCTTA
Found at i:116451 original size:118 final size:118
Alignment explanation
Indices: 116243--116455 Score: 417
Period size: 118 Copynumber: 1.8 Consensus size: 118
116233 ATAACTAATT
116243 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
116308 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCAATCTTTCTTGGGAATTTA
66 GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCAATCTTTCTTGGGAATTTA
116361 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
1 CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
*
116426 GTTGGATTTTAAGTGAGACTGTTTGTGACT
66 GTTGGATTTTAAGTGAGACCGTTTGTGACT
116456 AGGAATTTAC
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 94 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (118 bp):
CCCATTTGACACTAGAAGTTGTCATTGTGCTTTAATTACATGTCTAGGCAAATTCTGTCTAAGGA
GTTGGATTTTAAGTGAGACCGTTTGTGACTCCTCAATCTTTCTTGGGAATTTA
Found at i:118331 original size:39 final size:39
Alignment explanation
Indices: 118277--118357 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
118267 TTTATCGAGG
118277 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
1 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
118316 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
1 AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
118355 AAA
1 AAA
118358 ATACTGAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (39 bp):
AAACCAAGTTGCCCTGATATGGCACAAAATAAAGAGAGC
Found at i:122565 original size:16 final size:16
Alignment explanation
Indices: 122485--122588 Score: 59
Period size: 16 Copynumber: 6.4 Consensus size: 16
122475 GGCAGTTTTC
**
122485 TCGGGTCATTTGGGTT
1 TCGGGTCATTCAGGTT
* *
122501 TTGGGTCA-TCTGGGTT
1 TCGGGTCATTC-AGGTT
*
122517 T-GGGTTATTCAGGTCAT
1 TCGGGTCATTCAGGT--T
* * *
122534 TCGGTTCATACGGGTT
1 TCGGGTCATTCAGGTT
*
122550 TCGGGTCGTTCAGGTT
1 TCGGGTCATTCAGGTT
* * *
122566 CCGGGTCATTCAGATC
1 TCGGGTCATTCAGGTT
122582 TCGGGTC
1 TCGGGTC
122589 TATCGGGGGT
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
15 9 0.14
16 46 0.70
17 2 0.03
18 9 0.14
ACGTcount: A:0.11, C:0.18, G:0.34, T:0.38
Consensus pattern (16 bp):
TCGGGTCATTCAGGTT
Found at i:123455 original size:16 final size:15
Alignment explanation
Indices: 123435--123528 Score: 71
Period size: 16 Copynumber: 5.9 Consensus size: 15
123425 CTTGGGTTAT
123435 TCGGGTTTCGGGTCA
1 TCGGGTTTCGGGTCA
*
123450 TACGGGTCTCGGGTCA
1 T-CGGGTTTCGGGTCA
* * *
123466 CTCGGGTTACAGGTAA
1 -TCGGGTTTCGGGTCA
*
123482 TTCAGGTTTCGGGTCA
1 -TCGGGTTTCGGGTCA
* *
123498 TCTGGGTTACAGGTCA
1 TC-GGGTTTCGGGTCA
*
123514 TTCGGGTATCGGGTC
1 -TCGGGTTTCGGGTC
123529 GGACGGGTTC
Statistics
Matches: 59, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
15 3 0.05
16 53 0.90
17 3 0.05
ACGTcount: A:0.14, C:0.20, G:0.35, T:0.31
Consensus pattern (15 bp):
TCGGGTTTCGGGTCA
Found at i:123471 original size:32 final size:31
Alignment explanation
Indices: 123435--123528 Score: 107
Period size: 32 Copynumber: 3.0 Consensus size: 31
123425 CTTGGGTTAT
* * * *
123435 TCGGGTTTCGGGTCATACGGGTCTCGGGTCA
1 TCGGGTTACAGGTCATTCGGGTATCGGGTCA
* * *
123466 CTCGGGTTACAGGTAATTCAGGTTTCGGGTCA
1 -TCGGGTTACAGGTCATTCGGGTATCGGGTCA
123498 TCTGGGTTACAGGTCATTCGGGTATCGGGTC
1 TC-GGGTTACAGGTCATTCGGGTATCGGGTC
123529 GGACGGGTTC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 2 0.04
32 50 0.96
ACGTcount: A:0.14, C:0.20, G:0.35, T:0.31
Consensus pattern (31 bp):
TCGGGTTACAGGTCATTCGGGTATCGGGTCA
Found at i:125571 original size:747 final size:749
Alignment explanation
Indices: 123927--125601 Score: 2935
Period size: 751 Copynumber: 2.2 Consensus size: 749
123917 CCATACTATT
123927 GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
1 GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
* *
123992 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAAGGGATTACTTGGAGGCTAAGTTAATGCTAGT
66 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAATGGATTACTTGGAGGCTAAGTTTATGCTAGT
*
124057 ATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAAGATGTAGTCTAAGGGTTA
131 ATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAAGATGTAGTCTAAGGGATA
** * *
124122 GATTTAGATGGAGACACCCCATAGGGGAAAAGGATGGTCCTTATGTGTGCATGTGAGATTGTTTG
196 GATTTAGATGGAGACACCCCATAGGACAAAAGGATGGTCCTTATGGGTGCATGTGAAATTGTTTG
*
124187 GTTTGATGTTTGGTTTTGTTGATGTGATGATTGGTTTGTAGAGACTGAGCGAGAGTGCTCAAGAT
261 GTTTGATGTTTGGTTTTGTTGATGTGATGATTGGTTTGTAGAGACTGAGCAAGAGTGCTCAAGAT
*
124252 TGTTTGGGTTTGTTTGTTTCTTGTGTGGATGTTTATTATTTTGGTTGCTTCCGCTTGCATGATTA
326 TGTTTGGGTTTGGTTGTTTCTTGTGTGGATGTTTATTATTTTGGTTGCTTCCGCTTGCATGATTA
*
124317 ATTTTATAGATTATAGTTTGGGATATCCAGATTATACAAAAATTGATATCCGAGCTCAGGTTGAA
391 ATTTGATAGATTATAGTTTGGGATATCCAGATTATACAAAAATTGATATCCGAGCTCAGGTTGAA
*
124382 TGGATTGGAGGTTTCCCGATAGCCCAAACTTGTGATATGGGTCGGTAGGTAGATTTGGTTGTTAT
456 TGGATTGGAGGTTGCCCGATAGCCCAAACTTGTGATATGGGT--GTAGGTAGATTTGGTTGTTAT
*
124447 GGAGATTGCCAAATTTCACTGCTTGATGATTGTTTTGAAGATTGCTCAGATTTGGATGAAAAACA
519 GGAGATTGCCAAATTTCACTGCTTGATGATTGTTTTGAAAATTGCTCAGATTTGGATGAAAAACA
* *
124512 AGATCGAATTCGGAATTTAAGTTGAAGATGATGAAGTGAAGATGAAGACACACAAGAGAAGATTG
584 AGATCGAATTCAGAATTAAAGTTGAAGATGATGAAGTGAAGATGAAGACACACAAGAGAAGATTG
* *
124577 CTTGAAGATTGGAAGACTTTCATCGTAGGTGGAGCCATGCATGTCCTTGAAGCTTGAAGATTGAA
649 CCTGAAGATTGGAAGAATTTCATCGTAGGTGGAGCCATGCATGTCCTTGAAGCTTGAAGATTGAA
124642 GATTTGATGGAATTTGAGTCAAGGTGGAGATTGTTA
714 GATTTGATGGAATTTGAGTCAAGGTGGAGATTGTTA
*
124678 GGATTTTGACTCAAATCCTAGTTAGATTTGCATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
1 GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
*
124743 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAACT-GATTACTTGGAGACTAAGTTTATGCTAG
66 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAA-TGGATTACTTGGAGGCTAAGTTTATGCTAG
124807 TATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAAGATGTAGTCTAAGGGAT
130 TATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAAGATGTAGTCTAAGGGAT
* *
124872 AGATTTGGATGGAGACACCCCATAGGACAAAAGGATGGTCCTTATGGGTGCGTGTGAAATTGTTT
195 AGATTTAGATGGAGACACCCCATAGGACAAAAGGATGGTCCTTATGGGTGCATGTGAAATTGTTT
124937 GGTTTGATGTTTGGTTTTGTTGATGTGATGATTGGTTTGTAGAGACTGAGCAAGAGTGCTCAAGA
260 GGTTTGATGTTTGGTTTTGTTGATGTGATGATTGGTTTGTAGAGACTGAGCAAGAGTGCTCAAGA
125002 TTGTTTGGGTTTGGTTGTTTCTTGTGTGGATGTTTATTATTTTGGTTGCTTCCGCTTGCATGATT
325 TTGTTTGGGTTTGGTTGTTTCTTGTGTGGATGTTTATTATTTTGGTTGCTTCCGCTTGCATGATT
* * *
125067 AATTTGATAGATTATAGTTTGGGATATCCGGATTATACAACAATTGGTATCCGAGCTCAGGTTGA
390 AATTTGATAGATTATAGTTTGGGATATCCAGATTATACAAAAATTGATATCCGAGCTCAGGTTGA
* * *
125132 ATGGATTGGAGGTTGCCCGGTAGCCCAAACTTGTGATAT-GGT-TCGGTAGATTTGGTTGTTGTG
455 ATGGATTGGAGGTTGCCCGATAGCCCAAACTTGTGATATGGGTGTAGGTAGATTTGGTTGTTATG
* *
125195 GAGATTGCCAAATTTCGCTGCTTGATGATTGTTTTGAAAATTGCTCAGATTTGGATGAAAAGC-A
520 GAGATTGCCAAATTTCACTGCTTGATGATTGTTTTGAAAATTGCTCAGATTTGGATGAAAAACAA
125259 GAATCGAATTCAGAATTAAAGTTGAAGATGATGAAGTGAAGATGAAGACACACAAGAGAAGATTG
585 G-ATCGAATTCAGAATTAAAGTTGAAGATGATGAAGTGAAGATGAAGACACACAAGAGAAGATTG
* * * * *
125324 CCTGAAGATTGTAAGAATTTCGTCGTAGGTGTAGCCATGCATGTCCTTGAAGGTTGAAGGTTGAA
649 CCTGAAGATTGGAAGAATTTCATCGTAGGTGGAGCCATGCATGTCCTTGAAGCTTGAAGATTGAA
*
125389 GATTTGATGGAATTTGAGTTAAGGTGGAGATTGTTA
714 GATTTGATGGAATTTGAGTCAAGGTGGAGATTGTTA
*
125425 GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTATTGATTGTTGGACA
1 GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
* *
125490 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAATGGATAACTTGGAGGTTAAGTTTATGCTAGT
66 AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAATGGATTACTTGGAGGCTAAGTTTATGCTAGT
* *
125555 ATAAATAGAAAGTTTCTCTATAGGTTTTTATGTATGCTTGGAGAAAA
131 ATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAA
125602 TGATATCGAA
Statistics
Matches: 880, Mismatches: 41, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
746 3 0.00
747 401 0.46
750 3 0.00
751 473 0.54
ACGTcount: A:0.28, C:0.10, G:0.27, T:0.35
Consensus pattern (749 bp):
GGATTTTGACTCAAATCCTAGTTAGATTTGGATTGGGATTTTTTAGGCCTGTTGATTGTTGGACA
AAAAGTCTTGGTAAACAAGAATCCTAGTAGGAAATGGATTACTTGGAGGCTAAGTTTATGCTAGT
ATAAATAGAGAGTTTCTCTATAGGTTTTTGTGTATGCTTGGAGAAAAGATGTAGTCTAAGGGATA
GATTTAGATGGAGACACCCCATAGGACAAAAGGATGGTCCTTATGGGTGCATGTGAAATTGTTTG
GTTTGATGTTTGGTTTTGTTGATGTGATGATTGGTTTGTAGAGACTGAGCAAGAGTGCTCAAGAT
TGTTTGGGTTTGGTTGTTTCTTGTGTGGATGTTTATTATTTTGGTTGCTTCCGCTTGCATGATTA
ATTTGATAGATTATAGTTTGGGATATCCAGATTATACAAAAATTGATATCCGAGCTCAGGTTGAA
TGGATTGGAGGTTGCCCGATAGCCCAAACTTGTGATATGGGTGTAGGTAGATTTGGTTGTTATGG
AGATTGCCAAATTTCACTGCTTGATGATTGTTTTGAAAATTGCTCAGATTTGGATGAAAAACAAG
ATCGAATTCAGAATTAAAGTTGAAGATGATGAAGTGAAGATGAAGACACACAAGAGAAGATTGCC
TGAAGATTGGAAGAATTTCATCGTAGGTGGAGCCATGCATGTCCTTGAAGCTTGAAGATTGAAGA
TTTGATGGAATTTGAGTCAAGGTGGAGATTGTTA
Found at i:134141 original size:16 final size:16
Alignment explanation
Indices: 134100--134142 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
134090 ACACCTACCC
*
134100 TACTCACCCAATACAG
1 TACTCACCCAATACAA
* * *
134116 CATTCTCCCAATACAA
1 TACTCACCCAATACAA
134132 TACTCACCCAA
1 TACTCACCCAA
134143 CACTCACCCA
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (16 bp):
TACTCACCCAATACAA
Found at i:134149 original size:11 final size:11
Alignment explanation
Indices: 134133--134162 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
134123 CCAATACAAT
134133 ACTCACCCAAC
1 ACTCACCCAAC
134144 ACTCACCCAAC
1 ACTCACCCAAC
134155 ACTCACCC
1 ACTCACCC
134163 TACAATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.57, G:0.00, T:0.10
Consensus pattern (11 bp):
ACTCACCCAAC
Found at i:134191 original size:19 final size:19
Alignment explanation
Indices: 134167--134216 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
134157 TCACCCTACA
134167 ATACTCACTTACAAAGGCC
1 ATACTCACTTACAAAGGCC
*
134186 ATACTCACCTACAAAGGCC
1 ATACTCACTTACAAAGGCC
*
134205 AAACTCACTTAC
1 ATACTCACTTAC
134217 GGTATGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.34, G:0.08, T:0.20
Consensus pattern (19 bp):
ATACTCACTTACAAAGGCC
Found at i:139366 original size:29 final size:29
Alignment explanation
Indices: 139333--139395 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
139323 ACAAACTAAA
* * *
139333 GAATTATGTAATACGTTTATTGGTAGATG
1 GAATTATGTAACACGTATATTGGTAGACG
*
139362 GAATTATGTAGCACGTATATTGGTAGACG
1 GAATTATGTAACACGTATATTGGTAGACG
139391 GAATT
1 GAATT
139396 TTAATGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (29 bp):
GAATTATGTAACACGTATATTGGTAGACG
Found at i:141330 original size:16 final size:16
Alignment explanation
Indices: 141309--141343 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
141299 ACAATTCAGA
141309 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
141325 AAGCAGAAAAGCTCTG
1 AAGCAGAAAAGCTCTG
141341 AAG
1 AAG
141344 TATTTCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGCAGAAAAGCTCTG
Found at i:141543 original size:91 final size:91
Alignment explanation
Indices: 141388--141611 Score: 335
Period size: 91 Copynumber: 2.5 Consensus size: 91
141378 GCTTAAGAAG
* *
141388 ATTGAAAGAAGATCCACGTATGTGGAAAATTCTTCTTTCAAAGAAGACTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
* *
141453 ACTGAAGACCTAGTTATTTGGG-AGTT
66 ACTGAAGACCCAGTTA-TTGGGAAATT
* *
141479 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGA-TCCAATTATTGCAGAAT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACT-CAATTATTGCAGAAT
141543 TACTGAAGACCCAGTTATTGGGAAATT
65 TACTGAAGACCCAGTTATTGGGAAATT
* * *
141570 CTTGAAAGAAGACCCACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
141612 TTATCAAAGA
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
90 6 0.05
91 115 0.95
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGCAGAATT
ACTGAAGACCCAGTTATTGGGAAATT
Found at i:146948 original size:2 final size:2
Alignment explanation
Indices: 146941--146968 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
146931 CAATCTGATT
146941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
146969 AAAGAGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:147987 original size:18 final size:19
Alignment explanation
Indices: 147942--147987 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
147932 ATGGATTCCC
147942 TTGGAGAAATATTCAAAGAA
1 TTGGA-AAATATTCAAAGAA
* *
147962 AT-GCAAATATTCAAA-AA
1 TTGGAAAATATTCAAAGAA
147979 TTGGAAAAT
1 TTGGAAAAT
147988 GGACAATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 1 0.05
20 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
TTGGAAAATATTCAAAGAA
Found at i:149352 original size:18 final size:18
Alignment explanation
Indices: 149329--149378 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 18
149319 ATTAAGTAAG
149329 AATGTAAGATTGTTGAAA
1 AATGTAAGATTGTTGAAA
* * *
149347 AATGTAA-AGTATT--AG
1 AATGTAAGATTGTTGAAA
149362 AATGTAAGATTGTTGAA
1 AATGTAAGATTGTTGAA
149379 TTTGTTGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.33
16 4 0.17
17 4 0.17
18 8 0.33
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (18 bp):
AATGTAAGATTGTTGAAA
Found at i:150399 original size:53 final size:53
Alignment explanation
Indices: 150326--150451 Score: 168
Period size: 53 Copynumber: 2.4 Consensus size: 53
150316 ATGAAGAATA
* * *
150326 TATTTTTTTATG--TTAT-ATTACAAATTATTATGTGATTTATTATATTTATT
1 TATTTTTTTATGATTTATGATTACAAATTAATATATAATTTATTATATTTATT
*
150376 TATTTATTTATGATTTATGATTACAAATTAATATATAATTTATTATATTTATT
1 TATTTTTTTATGATTTATGATTACAAATTAATATATAATTTATTATATTTATT
150429 TATTTGTTTTTTATGATTTATGA
1 TA--T-TTTTTTATGATTTATGA
150452 ACTATTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
50 11 0.17
52 4 0.06
53 33 0.51
55 1 0.02
56 16 0.25
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (53 bp):
TATTTTTTTATGATTTATGATTACAAATTAATATATAATTTATTATATTTATT
Found at i:152900 original size:2 final size:2
Alignment explanation
Indices: 152893--152924 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
152883 CTTTCCTACT
152893 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
152925 CAATTCTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:153321 original size:27 final size:26
Alignment explanation
Indices: 153271--153321 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
153261 ATATAAAACA
*
153271 AAATAATTTTTAAAAATAACACTTAT
1 AAATAATTTTTAAAAATAAAACTTAT
* *
153297 AAATAATTTTTTAAATTACAAACTT
1 AAATAATTTTTAAAAATA-AAACTT
153322 TTCAGCACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAATTTTTAAAAATAAAACTTAT
Found at i:155961 original size:20 final size:20
Alignment explanation
Indices: 155936--155975 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
155926 AGGATTAGTT
*
155936 GAAAACAACACAGATGAGAA
1 GAAAACAACACAGATAAGAA
*
155956 GAAAACAACAGAGATAAGAA
1 GAAAACAACACAGATAAGAA
155976 ACATCAGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.62, C:0.12, G:0.20, T:0.05
Consensus pattern (20 bp):
GAAAACAACACAGATAAGAA
Found at i:161810 original size:26 final size:26
Alignment explanation
Indices: 161774--161825 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
161764 TTGGAGTTTC
161774 GGTGGTGCGGCTGTGCTAAAAAAAAA
1 GGTGGTGCGGCTGTGCTAAAAAAAAA
161800 GGTGGTGCGGCTGTGCTAAAAAAAAA
1 GGTGGTGCGGCTGTGCTAAAAAAAAA
161826 CAATGGTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.19
Consensus pattern (26 bp):
GGTGGTGCGGCTGTGCTAAAAAAAAA
Found at i:161832 original size:27 final size:26
Alignment explanation
Indices: 161776--161832 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
161766 GGAGTTTCGG
**
161776 TGGTGCGGCTGTGCTAAAAAAAAAGG
1 TGGTGCGGCTGTGCTAAAAAAAAAAA
161802 TGGTGCGGCTGTGCTAAAAAAAAACAA
1 TGGTGCGGCTGTGCTAAAAAAAAA-AA
161829 TGGT
1 TGGT
161833 TGGTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (26 bp):
TGGTGCGGCTGTGCTAAAAAAAAAAA
Done.