Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011079.1 Corchorus capsularis cultivar CVL-1 contig11100, 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: 159855
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10836 original size:2 final size:2
Alignment explanation
Indices: 10829--10855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10819 CTAGTTCTCG
10829 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
10856 TAGGTTCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14100 original size:32 final size:32
Alignment explanation
Indices: 14059--14139 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 32
14049 TCAAACGGTA
14059 AATGCCACGTCGGACCAAAAATGCCACGTGAC
1 AATGCCACGTCGGACCAAAAATGCCACGTGAC
* * * *
14091 AATGCCACGTTGGACC-AAAATGTCATGTGGC
1 AATGCCACGTCGGACCAAAAATGCCACGTGAC
* *
14122 AAGGCCACGTCAGACCAA
1 AATGCCACGTCGGACCAA
14140 GGCGCTGACG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 25 0.61
32 16 0.39
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.15
Consensus pattern (32 bp):
AATGCCACGTCGGACCAAAAATGCCACGTGAC
Found at i:17857 original size:31 final size:31
Alignment explanation
Indices: 17807--17978 Score: 182
Period size: 31 Copynumber: 5.5 Consensus size: 31
17797 ACGGTGTCCG
* * *
17807 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGTCATGCCACATGTACCAAAAAGTGAC
* *
17838 ATGTGTCGTGCCACATGTACCAAAAAGTGAC
1 ACGTGTCATGCCACATGTACCAAAAAGTGAC
* * * *
17869 ACATGTCACGCCACGTGTACCAAAATGTGAC
1 ACGTGTCATGCCACATGTACCAAAAAGTGAC
* * *
17900 ACATGTCACGCCACGTGTACCAAAAAGTGAC
1 ACGTGTCATGCCACATGTACCAAAAAGTGAC
* * ** *
17931 ACGTGGCATGCCAGATGTTTCAAAAAATGAC
1 ACGTGTCATGCCACATGTACCAAAAAGTGAC
*
17962 ACGTGGCATGCCACATG
1 ACGTGTCATGCCACATG
17979 CACAAAAGGA
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 120 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (31 bp):
ACGTGTCATGCCACATGTACCAAAAAGTGAC
Found at i:19928 original size:1 final size:1
Alignment explanation
Indices: 19922--19950 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
19912 AGAGAGCAGT
19922 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19951 TTCACAGGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22927 original size:7 final size:7
Alignment explanation
Indices: 22915--22950 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
22905 GACTATTTGC
22915 ATTTTAA
1 ATTTTAA
22922 ATTTTAA
1 ATTTTAA
22929 ATTTTAA
1 ATTTTAA
22936 ATTTT-A
1 ATTTTAA
*
22942 TTTTTAA
1 ATTTTAA
22949 AT
1 AT
22951 AAATTTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTTAA
Found at i:22966 original size:24 final size:24
Alignment explanation
Indices: 22926--22971 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
22916 TTTTAAATTT
*
22926 TAAATTTTAAATTTTATTTTTAAA
1 TAAATTTTAAATGTTATTTTTAAA
22950 TAAATTTT-AATAGTTATTTTTA
1 TAAATTTTAAAT-GTTATTTTTA
22972 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TAAATTTTAAATGTTATTTTTAAA
Found at i:22977 original size:24 final size:24
Alignment explanation
Indices: 22924--22977 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
22914 CATTTTAAAT
*
22924 TTTAAATTTTAAATTTTATTTTTA
1 TTTAAATTTTAAATGTTATTTTTA
**
22948 AATAAATTTT-AATAGTTATTTTTA
1 TTTAAATTTTAAAT-GTTATTTTTA
22972 TTTAAA
1 TTTAAA
22978 AATTAAACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTAAATTTTAAATGTTATTTTTA
Found at i:35337 original size:79 final size:76
Alignment explanation
Indices: 35240--35382 Score: 198
Period size: 76 Copynumber: 1.8 Consensus size: 76
35230 AAAAATATAT
* *
35240 TTAAAAAGTTCTAGTATATCTAAGTTTTGTAATTAGTAAAATGGTAAAAATAAAATAGTTATAAA
1 TTAAAAAGTTCTAATATATCTAAGTTTTGTAA-T--TAAAATGGTAAAAATAAAATAGTTACAAA
35305 GATATTAGATTTAA
63 GATATTAGATTTAA
* * *
35319 TTAAAGAA-TTCTAATATATCTAAGTTTTTTAATTAAAATGGTAAAAATAGATTAGTTACAAAGA
1 TTAAA-AAGTTCTAATATATCTAAGTTTTGTAATTAAAATGGTAAAAATAAAATAGTTACAAAGA
35383 GATCAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
76 28 0.48
78 1 0.02
79 27 0.47
80 2 0.03
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (76 bp):
TTAAAAAGTTCTAATATATCTAAGTTTTGTAATTAAAATGGTAAAAATAAAATAGTTACAAAGAT
ATTAGATTTAA
Found at i:35509 original size:192 final size:191
Alignment explanation
Indices: 35308--35686 Score: 661
Period size: 192 Copynumber: 2.0 Consensus size: 191
35298 TTATAAAGAT
* * *
35308 ATTAGATTTAATTAAAGAATTCTAATATATCTAAGTTTTTTAATTAAAATGGTAAAAATAGATTA
1 ATTAGATTTAATTAAAGAATTCTAATACATCTAAGTTTTTTAATTAAAATGGTAAAAATAAAATA
*
35373 GTTACAAAGAGATCAAAAAGTCTCCAATTCCTTAAAATTAAAAATGGT-AAAAATAAAATATTTA
66 GTTACAAAGAGATCAAAAAGTCTCCAACTCCTTAAAATT-AAAATGGTAAAAAAT-AAATATTTA
35437 CATAAATATTGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAAG
129 CATAAATATTGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAAG
*
35500 ATTAGATTTAATTAAAGAATTCTAATACATCTAAGTTTTTTAATTACAATGGTAAAAATAAAATA
1 ATTAGATTTAATTAAAGAATTCTAATACATCTAAGTTTTTTAATTAAAATGGTAAAAATAAAATA
*
35565 GTTACAAAGAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAATGGTAAAAAATAAATATTTATA
66 GTTACAAAGAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAATGGTAAAAAATAAATATTTACA
* *
35630 TAAATATTGACTTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACTGTAAAA
131 TAAATATTGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAA
35687 GTTTAAACAA
Statistics
Matches: 178, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
191 73 0.41
192 105 0.59
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.34
Consensus pattern (191 bp):
ATTAGATTTAATTAAAGAATTCTAATACATCTAAGTTTTTTAATTAAAATGGTAAAAATAAAATA
GTTACAAAGAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAATGGTAAAAAATAAATATTTACA
TAAATATTGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAAG
Found at i:35758 original size:192 final size:192
Alignment explanation
Indices: 35316--35738 Score: 498
Period size: 192 Copynumber: 2.2 Consensus size: 192
35306 ATATTAGATT
* * * ** * * * * *
35316 TAATTAAAGAATTCTAATATATCTAAGTTTTTTAATTAAAATGGTAAAAATAGATTAGTTACAAA
1 TAATGAAAGAATTCTAAAAAATCTAAGTAATATAACTACAATGGTAAAAATAAAATAGTTACAAA
*
35381 GAGATCAAAAAGTCTCCAATTCCTTAAAATTAAAAATGGTAAAAATAAAATATTTACATAAATAT
66 GAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAAATGGTAAAAATAAAATATTTACATAAATAT
* * * *
35446 TGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAAGATTAGATT
131 TGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAACAATACATG
* * * ** * *
35508 TAATTAAAGAATTCTAATACATCTAAGTTTTTTAATTACAATGGTAAAAATAAAATAGTTACAAA
1 TAATGAAAGAATTCTAAAAAATCTAAGTAATATAACTACAATGGTAAAAATAAAATAGTTACAAA
*
35573 GAGATCAAAAAGTCTCCAACTCCTTAAAATT-AAAATGGTAAAAA-ATAAATATTTATATAAATA
66 GAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAAATGGTAAAAATA-AAATATTTACATAAATA
* *
35636 TTGACTTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACTGTAAAAGTTTAAACAATATC
130 TTGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAA----AAACAATA-C
35701 ATG
190 ATG
* *
35704 TAA-GAAATATATT-TAAAAAAT-TTA-TAATATAACTA
1 TAATGAAAGA-ATTCTAAAAAATCTAAGTAATATAACTA
35739 AGTTTTGTAA
Statistics
Matches: 203, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
190 1 0.00
191 78 0.38
192 91 0.45
193 7 0.03
194 2 0.01
195 16 0.08
196 8 0.04
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.34
Consensus pattern (192 bp):
TAATGAAAGAATTCTAAAAAATCTAAGTAATATAACTACAATGGTAAAAATAAAATAGTTACAAA
GAGATCAAAAAGTCTCCAACTCCTTAAAATTAAAAATGGTAAAAATAAAATATTTACATAAATAT
TGAATTTAATTAAATAAAAATAGAGTTTGTAGTATAATAAAACGGTAAAAAAACAATACATG
Found at i:35916 original size:85 final size:85
Alignment explanation
Indices: 35716--35919 Score: 311
Period size: 84 Copynumber: 2.4 Consensus size: 85
35706 AGAAATATAT
* * * *
35716 TTAAAAAATTTATAATATAACTAAGTTTTGTAATTAAAATAGTAAAAATATTAAAAATAAAATAG
1 TTAAAAAATTT-TAATATATCTAATTTTTTTAATTAAAATAGTAAAAATAGTAAAAATAAAATAG
*
35781 TTATAAAGAGATTAGATTTAA
65 TTATAAAGAGATTAAATTTAA
*
35802 TTAAAAAATTTTAATATATCTAATTTTTTTAATTAAAATAGT-AAAATGGTAAAAATAAAATAGT
1 TTAAAAAATTTTAATATATCTAATTTTTTTAATTAAAATAGTAAAAATAGTAAAAATAAAATAGT
35866 TATAAAGAGATTAAATTTAA
66 TATAAAGAGATTAAATTTAA
* *
35886 TTAAAGAATTTTAGTATTATCTAATTTTTTTAAT
1 TTAAAAAATTTTAATA-TATCTAATTTTTTTAAT
35920 ATGGTAAAAC
Statistics
Matches: 109, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
84 53 0.49
85 45 0.41
86 11 0.10
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (85 bp):
TTAAAAAATTTTAATATATCTAATTTTTTTAATTAAAATAGTAAAAATAGTAAAAATAAAATAGT
TATAAAGAGATTAAATTTAA
Found at i:37003 original size:5 final size:5
Alignment explanation
Indices: 36968--37031 Score: 78
Period size: 5 Copynumber: 13.0 Consensus size: 5
36958 TACTTTTTAA
* *
36968 TATAG TATAG ATATA- CATAT TATAG -ATAG TATAG TATAG TATAG TATAG
1 TATAG TATAG -TATAG TATAG TATAG TATAG TATAG TATAG TATAG TATAG
*
37017 TATAG TATAT TATAG
1 TATAG TATAG TATAG
37032 ATTAAAATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
4 7 0.14
5 40 0.78
6 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
TATAG
Found at i:40972 original size:41 final size:41
Alignment explanation
Indices: 40915--40995 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
40905 TTATGTCTTG
* *
40915 GTTAAGGATTTCGGTTATCGTGGACTTATATATAGGAACAT
1 GTTAAAGATTTCGGTTATCATGGACTTATATATAGGAACAT
40956 GTTAAAGATTTCGGTTATCATGGACTTATATATAGGAACA
1 GTTAAAGATTTCGGTTATCATGGACTTATATATAGGAACA
40996 GAGGGAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (41 bp):
GTTAAAGATTTCGGTTATCATGGACTTATATATAGGAACAT
Found at i:54801 original size:2 final size:2
Alignment explanation
Indices: 54794--54819 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54784 ATAACAGAAC
54794 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
54820 CATTAATCAT
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:55013 original size:20 final size:20
Alignment explanation
Indices: 54974--55014 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54964 GTTTGCTGCC
* *
54974 ATACAAATGTGATAAGTGCA
1 ATACAAATGTGACAAATGCA
*
54994 ATACAAGTGTGACAAATGCA
1 ATACAAATGTGACAAATGCA
55014 A
1 A
55015 ACATGGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (20 bp):
ATACAAATGTGACAAATGCA
Found at i:58460 original size:29 final size:29
Alignment explanation
Indices: 58418--58480 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
58408 CACTCGTATG
* * *
58418 ATTTTGACGTTTTACCTCTTAAACTTTCA
1 ATTTGGACATTTTACCTCTTAAACTTGCA
* *
58447 ATTTGGACATTTTATCTCTTGAACTTGCA
1 ATTTGGACATTTTACCTCTTAAACTTGCA
58476 ATTTG
1 ATTTG
58481 AAACCTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (29 bp):
ATTTGGACATTTTACCTCTTAAACTTGCA
Found at i:64299 original size:19 final size:19
Alignment explanation
Indices: 64262--64299 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
64252 AAGTGAAAGG
*
64262 AAAAGAGAGAGGAAAAAAA
1 AAAAGAGAGAAGAAAAAAA
*
64281 AAAAGAG-GAAGAAAGAAA
1 AAAAGAGAGAAGAAAAAAA
64299 A
1 A
64300 TGGCAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AAAAGAGAGAAGAAAAAAA
Found at i:75735 original size:21 final size:22
Alignment explanation
Indices: 75711--75753 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
75701 AAAATGGGGA
75711 TTACAAAATACCGCCC-CCTTT
1 TTACAAAATACCGCCCTCCTTT
* **
75732 TTACTAGGTACCGCCCTCCTTT
1 TTACAAAATACCGCCCTCCTTT
75754 GGACAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.21, C:0.37, G:0.09, T:0.33
Consensus pattern (22 bp):
TTACAAAATACCGCCCTCCTTT
Found at i:86350 original size:24 final size:24
Alignment explanation
Indices: 86318--86372 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
86308 GTAAACCAAC
*
86318 TCCACTATGATTCCATCTTTTCTT
1 TCCACTATGATTCCATCTTTCCTT
*
86342 TCCAGTATGATTCCATCTTTCCTT
1 TCCACTATGATTCCATCTTTCCTT
86366 TCCACTA
1 TCCACTA
86373 ATCTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.18, C:0.31, G:0.05, T:0.45
Consensus pattern (24 bp):
TCCACTATGATTCCATCTTTCCTT
Found at i:87747 original size:49 final size:49
Alignment explanation
Indices: 87680--87780 Score: 166
Period size: 49 Copynumber: 2.1 Consensus size: 49
87670 TAACAATGGT
*
87680 TTCCTCCATTCACAAGACTCGAACCCGAAATCTTGTTTAAGTGGAACAA
1 TTCCTCCATTCACAAGACTCGAACCCGAAATCTTGTTTAAATGGAACAA
* * *
87729 TTCCTTCATTCACAAGACTCGAACTCGAGATCTTGTTTAAATGGAACAA
1 TTCCTCCATTCACAAGACTCGAACCCGAAATCTTGTTTAAATGGAACAA
87778 TTC
1 TTC
87781 ACAAGACTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (49 bp):
TTCCTCCATTCACAAGACTCGAACCCGAAATCTTGTTTAAATGGAACAA
Found at i:87817 original size:41 final size:41
Alignment explanation
Indices: 87736--87818 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
87726 CAATTCCTTC
* *
87736 ATTCACAAGACTCGAACTCGAGATCTTGTTTAAATGGAACA
1 ATTCACAAGACTCGAACTCGAGACCTTGTTTAAAGGGAACA
87777 ATTCACAAGACTCGAACAT-GAGACCTTGTTT-AAGGAGAACA
1 ATTCACAAGACTCGAAC-TCGAGACCTTGTTTAAAGG-GAACA
87818 A
1 A
87819 ATGTCAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 3 0.08
41 34 0.89
42 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (41 bp):
ATTCACAAGACTCGAACTCGAGACCTTGTTTAAAGGGAACA
Found at i:96827 original size:2 final size:2
Alignment explanation
Indices: 96820--96854 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
96810 ATTTCTGGGC
96820 AT AT 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 AT AT A
96855 GTAGTACTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:99827 original size:250 final size:249
Alignment explanation
Indices: 99386--99886 Score: 993
Period size: 250 Copynumber: 2.0 Consensus size: 249
99376 GTCCTTTACA
99386 AAATTCAATCCAATTATCTTATTTTTAAGAATCATCAAACTTATTCAACTTAATCCATACAATGT
1 AAATTCAATCCAATTATCTTATTTTTAAGAATCATCAAACTTATTCAACTTAATCCATACAATGT
99451 ACTTAAATATTGTGTATACAATACATAATACAAACTTTGACACAACATCTCACCAAATGACACAC
66 ACTTAAATATTGTGTATACAATACATAATACAAACTTTGACACAACATCTCACCAAATGACACAC
99516 CTCTAAATTACTTTTGTTTTCGGGGAAAAATAATCTCAAACTTTTAAGTTTCCCATCATAAACAT
131 CTCTAAATTACTTTTGTTTTCGGGGAAAAATAATCTCAAACTTTTAAGTTTCCCATCATAAACAT
99581 ATTCTAATTAGTGCCAAAAAAATCATATTCTAATTAAAAAAAGTTTTTTTTGGCC
196 ATTCTAATTAGTGCCAAAAAAA-CATATTCTAATTAAAAAAAGTTTTTTTTGGCC
99636 AAATTCAATCCAATTATCTTATTTTTAAGAATCATCAAACTTATTCAACTTAATCCATACAATGT
1 AAATTCAATCCAATTATCTTATTTTTAAGAATCATCAAACTTATTCAACTTAATCCATACAATGT
99701 ACTTAAATATTGTGTATACAATACATAATACAAACTTTGACACAACATCTCACCAAATGACACAC
66 ACTTAAATATTGTGTATACAATACATAATACAAACTTTGACACAACATCTCACCAAATGACACAC
99766 CTCTAAATTACTTTTGTTTTCGGGGAAAAATAATCTCAAACTTTTAAGTTTCCCATCATAAACAT
131 CTCTAAATTACTTTTGTTTTCGGGGAAAAATAATCTCAAACTTTTAAGTTTCCCATCATAAACAT
99831 ATTCTAATTAGTGCCAAAAAAACATATTCTAATTAAAAAAAGTTTTTTTTGGCC
196 ATTCTAATTAGTGCCAAAAAAACATATTCTAATTAAAAAAAGTTTTTTTTGGCC
99885 AA
1 AA
99887 CATTTACTTA
Statistics
Matches: 251, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
249 34 0.14
250 217 0.86
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (249 bp):
AAATTCAATCCAATTATCTTATTTTTAAGAATCATCAAACTTATTCAACTTAATCCATACAATGT
ACTTAAATATTGTGTATACAATACATAATACAAACTTTGACACAACATCTCACCAAATGACACAC
CTCTAAATTACTTTTGTTTTCGGGGAAAAATAATCTCAAACTTTTAAGTTTCCCATCATAAACAT
ATTCTAATTAGTGCCAAAAAAACATATTCTAATTAAAAAAAGTTTTTTTTGGCC
Found at i:106018 original size:13 final size:13
Alignment explanation
Indices: 106000--106026 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
105990 TTTAGTTGGG
106000 AATAGATAAGAGA
1 AATAGATAAGAGA
106013 AATAGATAAGAGA
1 AATAGATAAGAGA
106026 A
1 A
106027 TAAATGTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (13 bp):
AATAGATAAGAGA
Found at i:133190 original size:91 final size:91
Alignment explanation
Indices: 133035--133217 Score: 305
Period size: 91 Copynumber: 2.0 Consensus size: 91
133025 CAAAGTATAA
*
133035 TACCAAGGACACGTGGCGTAATTTGGTGGTTGAGGCACAATGGGGCATCAAAAATGGGGCAGAGG
1 TACCAAGGACACGTGGCGTAATTTGGTAGTTGAGGCACAATGGGGCATCAAAAATGGGGCAGAGG
133100 ATTTTGATTCAGTTTATTGGAGGACT
66 ATTTTGATTCAGTTTATTGGAGGACT
* * * *
133126 TACCAGGGACACGTGGTGTAATTTGGTAGTTG-GGTTACAATGGGGCATCAAAAATGGGGTAGAG
1 TACCAAGGACACGTGGCGTAATTTGGTAGTTGAGG-CACAATGGGGCATCAAAAATGGGGCAGAG
133190 GATTTTGATTCAGTTTATTGGAGGACT
65 GATTTTGATTCAGTTTATTGGAGGACT
133217 T
1 T
133218 GCAAGTGCCT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
90 2 0.02
91 84 0.98
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (91 bp):
TACCAAGGACACGTGGCGTAATTTGGTAGTTGAGGCACAATGGGGCATCAAAAATGGGGCAGAGG
ATTTTGATTCAGTTTATTGGAGGACT
Found at i:138442 original size:321 final size:322
Alignment explanation
Indices: 137671--142393 Score: 4027
Period size: 321 Copynumber: 14.6 Consensus size: 322
137661 GCCACAACTT
* * * * * *
137671 AGTTTTGCATGATTTTTGGCGTAAAGACTCATTGAAGTATCTATATTCATCGAACCTAATCCCAG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAA
* * * * * * *
137736 CCACATTCGATTTAAGAATTTGATTTTACGAGCATCTGAATCTGGTTTCGATTTGATTAGAAATT
66 CCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATT
* * * * * *
137801 AATTCAG-AAAAAAATGGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATCTTTTTGGCATT
131 AATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-GCCATCAATATTTTTGGCGTT
** * * * * * *
137865 GAATTATATA-TTTTTCTTTGTACTGTGACAAAGAATTGAGGAAAAATTTTTCGGATCAGATTTT
195 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAACTTTTCGGGT-A-A--GT
* * * ** * *
137929 TGCAAAACTTTAGCCGAAATCGTTTAC--A-CATCAC-GGTTTTTGTTTAAAAACACGTTCCAGG
255 T-------TTTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTC-GG
*
137990 GG-TCCGACTC
312 GGCCCCGACTC
* * * *
138000 AGTTTTGCATGATTTTTGACGTAAAGAATCCTTGAAATATCTATATTCATCGATA-CAAATCCCA
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGA-ACCAAATCTCA
* * * * * *
138064 ACCACATTCGATTTAA-TGATTTATTTTTACGAGCATCTCAATCTTATTT-GAATTTAATTAGAA
65 ACCACATTGGATATAAGT-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCG-ATTTAATTAGTA
138127 ATTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATATTTTTGGC
128 ATTAATTCGG-AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATATTTTTGGC
* * * * *
138192 ATTGAATTA-ATATTTTTTATGAGTATTGTGCCAAAAACTTGAGATAACACTTTTCGGGTAAGTT
192 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA-AAAACTTTTCGGGTAAGTT
* * * ** **
138256 TTCAGCTGAAATCG-GTACTAATCATTCACGGTTTTTTTGCTAAAAACGCGTAACGGGGCTTCGA
256 TTTAGCTGAAATCGTGTACTAATCA-TCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA
138320 CTC
320 CTC
* * * *
138323 AG-TTTGCAT-TTTTTTGGCATAACGACTCCTCGAAATATCTATATTCATCTAACCAAATCTCAA
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAA
* *
138386 CCACATTGGATATAAGTATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-AAAT
66 CCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATT
* * * * * * **
138450 AGATTTGG-AAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATCTTTTTGGAAT
131 A-ATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAGCCATCAATATTTTTGGCGT
* ** ** **
138514 TGAATTATATATTTTTTATGAGTATT-TTACAATAAAATT-AGAAAAAAATTTCGGGTCGGTTTT
194 TGAATTATATATTTTTTCTGAGTATTGTGGCAA-AAAATTGAGAAAAACTTTTCGGGTAAGTTTT
* * *
138577 TAGCAGAAATCGTGTACTAACCATCACAGTTTTTGTGG-TAAAAACGCGTTTCGGGACCCCGACT
258 TAGCTGAAATCGTGTACTAATCATCACAGTTTTT-TGGCTAAAAACGCGTTTCGGGGCCCCGACT
138641 C
322 C
* * * ** **
138642 AATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCAACGGGCCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAA
* ** * * *
138707 CAATGTTGGAGCA-AAGGT-TTTGTTTTTACGAGCATCTCAATCTTGTTT-GAATTTAATTAGAA
66 CCACATTGGA-TATAA-GTATTTGTTTTTACGAGCATCTGAATCTTGTTTCG-ATTTAATTAGTA
* * * * *
138769 ATTAATTCGGAAAAAATATGGGAAAATGATATTAGAAGCGTGAAAACCCTGTCAATATTTTTGGC
128 ATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCC-ATCAATATTTTTGGC
* * * * *
138834 GTTGAATTATATATTTCTT-TAAGTATTGTGGCAAAAAATTAATGAAAAACTATTCGGCTAAGTT
192 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAACTTTTCGGGTAA---
* * * * * *
138898 TTTGTAAAATTTTAG-TAGAAATTGTGAACTAACCAT-ATCACGATTTTATGGCAAAAAACGTG-
253 ---GT----TTTTAGCT-GAAATCGTGTACTAATCATCA-CA-G-TTTTTTGGCTAAAAACGCGT
**
138960 TTCTGTTGCCCCGACTC
307 TTC-GGGGCCCCGACTC
* ** * * * * * *
138977 AATTTTGCATGATTTTTGGCGCAAAGAATCCTCGAAATATCTAAATTCTTCTG-ACCAAATTTCC
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATC-GAACCAAATCTCA
* * * *
139041 ACCACATTTGATCA-AAGGT-TTGGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAA
65 ACCACATTGGAT-ATAA-GTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTA
* * *
139104 ATTAATTC-G--AAAAAATGG-AAAACGATATTAGAAGCGTGAAAAGTCCGTCACTGTTTTTGGC
128 ATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CCATCAATATTTTTGGC
* * * *
139165 ATTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAACTTGAGAAAACACTTTTTGGGTCAGTT
192 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTTCGGGTAAGTT
* *
139230 TTCT-GCTAAAATCGTGTACTAATCATCACAG-TTTTTGGCTAAAGACGCGTTTCGGGGCCCCGA
256 TT-TAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA
139293 CTC
320 CTC
* * * *
139296 AGTTTTGCATTG-TTTTTGACATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCA
1 AGTTTTGCA-TGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA
** * *
139360 GTCACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTCTCGATTTAATTAGTAAT
65 ACCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAAT
* * * * * *
139425 AAATTTGGGGAAAAAAAA-AGAAAAATGATATTAGAAGCGTGAAAATCTCTTCAATATTTTTGGC
130 TAA-TT-CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGC-CATCAATATTTTTGGC
* * * * * *
139489 GTTGAATTATATA-TTTTTCCGAGTATTTTGGCAAAAAATTCTAGAAAAAATGTTCGGGTCAGTT
192 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAGAAAAACTTTTCGGGTAAGTT
* * ** * *
139553 TTTAGCCGAAATCGTGTACTAATCAGTAACCATCACAATTTTGGGGCTAAAAAACGTGCTTCGGG
256 TTTAGCTGAAATCGTGTACT-A--A-T---CATCACAGTTTTTTGGCT-AAAAACGCGTTTCGGG
** * *
139618 ATCTCGGCTC
313 GCCCCGACTC
* * * *
139628 AGTTTTGCATGATTTTTGGCATAAAGACTCGTTGAAATATCTGTATTTATCGAACCAAATCTCTG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC-A
* * * * * * * * *
139693 A-CACGTTGGATCACATGT-TTTGGTTATACAAGCATCTCAATTTTGTTTCGATTTAATAAGTAA
65 ACCACATTGGAT-ATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAA
* * * ** * * *
139756 TTAACTCGGAAAAAAAA-AGAAAAATGATAAAAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCG
129 TTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CCATCAATATTTTTGGCG
* * * *
139820 TTGAATTATATATTTTTTCTGAGTATTGTAG-AAAAAACTAGGGAAAACACTTTTCGGATAAGTT
193 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA-TTGAGAAAA-ACTTTTCGGGTAAGTT
* * * *
139884 TTCAGCTGAAATCGTGTACTAATCATCAC-GATTTTTGGGTAAAAATGCGTTTCGGGGCCCCGAC
256 TTTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGAC
139948 TC
321 TC
* * * *
139950 AGTTTTGCATTG-TTTTTGACATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCA
1 AGTTTTGCA-TGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA
** * *
140014 GTCACATTGGATATAAGTATTTATTTTTACGAGCATGTGAATCTTGTTTCGATTTAATTAGTAAT
65 ACCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAAT
* * * * * ** * *
140079 AAATTTGGGGAAAAAAA-GAAAAAATGATATTAGAAGCGTGAAAATATCTTCAATCTTTTTGGCG
130 TAA-TTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA-GCCATCAATATTTTTGGCG
* * * *
140143 TTGAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCTAGAAAAAATTTTCGGGTTAGTTT
193 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAGAAAAACTTTTCGGGTAAGTTT
* * * ** * ** * *
140208 TTAGCCGAAATCGTGTACTAACCATCACAATTTTGGGGCTAAGAAACGTGCTTT-GGGATCTCGG
257 TTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAA-AAACGCG-TTTCGGGGCCCCGA
140272 CTC
320 CTC
* * * * *
140275 AGTTTTGCATAATTTTTGGCATAAAGACTCCTTGAAATATCTGTATTCGTCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT-CA
* * * * * * * *
140340 A-CGCGTTGGATCACAGGT-TTTGTTTATACGAGCATCTCAATCTAGTTTCGATTTAATAAGTAA
65 ACCACATTGGAT-ATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAA
* * * *
140403 TTAACTCGG----AAAA---AAAAACGATATTAGAAGTGTTAAAAGCCTATCAATATTTTTAGCG
129 TTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCC-ATCAATATTTTTGGCG
* * * *
140461 TTGAATTATATATTTTTTCTTAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGCTAAGTTT
193 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTTCGGGTAAGTTT
* * * *
140526 TTAGCTGAAATCGTG-ACTAATCATCAC-GATTTTTGGGTAAAAATGCGTTTCTGGGCCCCGACT
257 TTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACT
*
140589 T
322 C
* * * *
140590 AGTTTTACATTG-TTTTTGGCATAATGACTCCTTG-AA-A-CTATATTCATCTAACAAAATCTCA
1 AGTTTTGCA-TGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA
** * * *
140651 GTCACATTGGATATAAGTATTTATTTTTACTAGCATGTGAATCTTGTTTCGATTTAATTAGTAAT
65 ACCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAAT
* * * * * * * * *
140716 AAATTTGGGGAATAAAAA--GAAAAATGATATTAGAAGCATGCAAATCTCTTCAATCTTTTTGGC
130 TAA-TT-CGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGC-CATCAATATTTTTGGC
* * * * *
140779 GTTGAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCTAGAAAAAATGTTCGTGTAAGTT
192 GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAGAAAAACTTTTCGGGTAAGTT
* * ** * * ** *
140844 TTTAGCCGAAATCGTGTACTAACCATCAC-GATTTTGGGGCTAAAAAACGTGCTTCGGGATCTCG
256 TTTAGCTGAAATCGTGTACTAATCATCACAG-TTTTTTGGCT-AAAAACGCGTTTCGGGGCCCCG
*
140908 GCTC
319 ACTC
* * *
140912 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTGTATTCATCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT-CA
* * * * * *
140977 A-CACGTTGGATCACAGGT-TTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAA
65 ACCACATTGGAT-ATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAA
** * * *
141040 TTAATTCGGACAAAAAAAAAAGAAAAACGATATTAGAAGTGTGAAAATCCATTCAATATTTTTAG
129 TTAATTCGG--AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCA-TCAATATTTTTGG
* * * *
141105 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAGAACTAGAGAAAACACTTTTCGGATAAGT
191 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTTCGGGTAAGT
* * * *
141170 TTTCAGCTGAAATCGTGTACTAATCATTACAG-TTTTTGGCTAAAAATGCGTTTCGGGACCCCGA
255 TTTTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA
141234 CTC
320 CTC
** ** * * *
141237 AGTTTTGCATTTTTTTTGGCATATTGACTCCTTGAAATATCTATATTCATCAAACAAAATCTCAG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAA
* * * * * *
141302 CAACATTTGATATAGGTATTTATTTTTACGAGCATGTGAATCTTGTTTCGATTTAATTAGTAATA
66 CCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATT
* * * *
141367 AATTTGAGAAAAGAAA---AAAAATGATATTAGAAGC-----ATG--ATCAATATTTTTGGCGTT
131 AATTCG-GAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATATTTTTGGCGTT
* * * * * *
141422 GAATTATATATTTTTTCTGAGTATTTTGGTAAAAAATTATAGAAAAAATTTTCAGGTCAGTTTTT
195 GAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT-GAGAAAAACTTTTCGGGTAAGTTTTT
* * * * ** ** ** * *
141487 AGCCGAATTCGTGTATTAACCATCACAGTTTTGGGGCTAAAAAACATGCATCGGGACCCCAACTC
259 AGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCT-AAAAACGCGTTTCGGGGCCCCGACTC
* * *
141552 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCT-CA
* * * * * * *
141617 A-CACGTTGGATCACATGT-TTTGTTTATACGAGCATGTCAATCTTGTTTCGATTTAATAAGTAA
65 ACCACATTGGAT-ATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAA
* * * ** * *
141680 TTAACTCGG--AAAAAATGGGAAAATGATATTAGAATTGTGAAAAGCCTGTCAATATTTTTAGCG
129 TTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCC-ATCAATATTTTTGGCG
* * * *
141743 TTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCAGGTAAGTTT
193 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-ACTTTTCGGGTAAGTTT
* * * *
141808 TCAGCTGAAATCGTGTACTAATCATCAC-GGTTATTGGCTAAAAACGCGTTTCGTGGCCCC-ATC
257 TTAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA-C
141871 TC
321 TC
* * * * *
141873 AGTTTTGCATTG-TTTTTGGTATAATA-ACTCATTGAAATATCTATATTCATCTAACAAAATGTC
1 AGTTTTGCA-TGATTTTTGGCATAA-AGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
* * *
141936 AGCCACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
64 AACCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAA
* * * * * * * * *
142001 TAAATTTGG-AAAAAAATGGAAAAACAATATTAG-TGCGTGAAAAAACAATTAATCTTTTTGGCA
129 TTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAGCCATCAATATTTTTGGCG
* * * * **** **
142064 TTGAATTATATATTTTTTCTGAGTATTTTAGCAAAAAAATCAGAAAAAAAAATCGGGTCGGTTTT
193 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTAAGTTTT
* * *** * * *
142129 TAGCTGAAATAGTGTACTAACCATCACAGTTTCGGGGCT---AACGCGTTTTGGGACCCCGGCTC
258 TAGCTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTC
* * * * * *
142191 AATTTTGTAAT-ATTTTTGGCAGAAATACTCCTTGAAATATCTATATTTATCGGAA-CAAATCTT
1 AGTTTTG-CATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATC-GAACCAAATCTC
** * * * * *
142254 TGCGACGTTGGATCA-AAGGT-TTTGTTTTTACGAGCATCTCAATCTTGTTTGGATTTAATTAGA
64 AACCACATTGGAT-ATAA-GTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGT
* * ** *** * *
142317 AATTAATTTGGAAGAATTATGGAAAATTTATATTAGAAGCGAGAAAAGCCCGTCAATATTTTTGG
127 AATTAATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAG-CCATCAATATTTTTGG
142382 CGTTGAATTATA
191 CGTTGAATTATA
142394 CTCTCTCAGT
Statistics
Matches: 3546, Mismatches: 678, Indels: 349
0.78 0.15 0.08
Matches are distributed among these distances:
311 5 0.00
312 71 0.02
313 88 0.02
314 22 0.01
315 183 0.05
316 15 0.00
317 19 0.01
318 234 0.07
319 352 0.10
320 158 0.04
321 453 0.13
322 315 0.09
323 310 0.09
324 106 0.03
325 319 0.09
326 33 0.01
327 112 0.03
328 4 0.00
329 126 0.04
330 138 0.04
331 149 0.04
332 161 0.05
333 29 0.01
334 8 0.00
335 134 0.04
336 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (322 bp):
AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAA
CCACATTGGATATAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATT
AATTCGGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATATTTTTGGCGTTG
AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTCGGGTAAGTTTTTAG
CTGAAATCGTGTACTAATCATCACAGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTC
Found at i:139389 original size:654 final size:642
Alignment explanation
Indices: 137671--142393 Score: 4932
Period size: 654 Copynumber: 7.3 Consensus size: 642
137661 GCCACAACTT
* * * * *
137671 AGTTTTGCATGATTTTTGGCGTAAAGACTCATTGAAGTATCTATATTCATCGAACCTAATC-CCA
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCC-
* * * ** ** * * * * *
137735 GCCACATTCGATTTAAGAATTTGATTT-TACGAGCATCTGAATCTGGTTTCGATTTGATTAGAAA
65 GACACGTTGGATCAAAGGTTTTG-TTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAA
* * * * * *
137799 TTAATTCAGAAAAAAATGGAAAAACGATATTAGAAGTGTGAAAACCCCTTCAATCTTTTTGGCAT
129 TTAATTCGGAAAAAAAT-GAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGT
** * * * * *
137864 TGAATTATATA-TTTTTCTTTGTACTGTGACAAAGAA-TTGAGGAAAA-ATTTTTCGGATCAGAT
193 TGAATTATATATTTTTTCTGAGTATTGTGGCAAA-AACTAGA-GAAAACACTTTTCGGAT-A-AG
* * * ** * *
137926 TTTTGCAAAACTTTAGCCGAAATCGTTTAC--A-CATCACGGTTTTTGTTTAAAAACACGTTCCA
254 TTTT------C--T-GCTGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGTTTC-
* * * * *
137988 GGGG-TCCGACTCAGTTTTGCA-TGATTTTTGACGTAAAGAATCCTTGAAATATCTATATTCATC
309 GGGGCCCCGACTCAGTTTTGCATTG-TTTTTGGCATAATGACTCCTTGAAATATCTATATTCATC
* * ** * * * *
138051 GATAC-AAATCCCAACCACATTCGATTTAA-TGATTTATTTTTACGAGCATCTCAATCTTATTT-
373 TA-ACAAAATCTCAGTCACATTGGATATAAGT-ATTTATTTTTACGAGCATCTGAATCTTGTTTC
* * * *
138113 GAATTTAATTAGAAATTAATTCGGAAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGC-C
436 G-ATTTAATTAGTAATAAATT-GG-GAAAAAAA-GGAAAAATGATATTAGAAGCGTGAAAA-CTC
* * * * * * * *
138177 ATCAATATTTTTGGCATTGAATTA-ATATTTTTTATGAGTATTGTGCCAAAAACTT-GAGATAAC
496 TTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGA-AAA
* * * * * ***
138240 ACTTTTCGGGTAAGTTTTCAGCTGAAATCG-GTACTAATCATTCACGGTTTTTTTGCT-AAAAAC
560 AATTTTC-GGTAAGTTTTTAGCCGAAATCGTGTACTAACCA-TCACGATTTTGGGGCTAAAAAAC
* * * *
138303 GCG-TAACGGGGCTTCGACTC
623 GTGCT-TCGGGACCTCGACTC
* * * ** *
138323 AG-TTTGCAT-TTTTTTGGCATAACGACTCCTCGAAATATCTATATTCATCTAACCAAATCT-CA
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
* * * * *
138385 ACCACATTGGAT-ATAA-GTATTTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG-A
66 A-CACGTTGGATCA-AAGGT-TTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTA
* * * * * * * * *
138447 AATAGATTTGGAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATCTTTTTGGA
128 ATTA-ATTCGGAAAAAAATG-AAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGC
* * ** * * * **
138512 ATTGAATTATATATTTTTTATGAGTATT-TTACAATAAAATTAGA-AAAA-A-ATTTCGGGTCGG
191 GTTGAATTATATATTTTTTCTGAGTATTGTGGC-A-AAAACTAGAGAAAACACTTTTCGGATAAG
* * * *
138573 TTTT-TAGCAGAAATCGTGTACTAACCATCACAGTTTTTGTGGTAAAAACGCGTTTCGGGACCCC
254 TTTTCT-GCTGAAATCGTGTACTAATCATCACAGTTTTTG-GCTAAAAACGCGTTTCGGGGCCCC
* * * * *** *
138637 GACTCAATTTTGCA-TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCAACGGGCCAAA
317 GACTCAGTTTTGCATTG-TTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAA
* * * *
138701 TCTCCG-CA-ATGTTGGAGCA-AAGGT-TTTGTTTTTACGAGCATCTCAATCTTGTTT-GAATTT
381 TCTCAGTCACA--TTGGA-TATAA-GTATTTATTTTTACGAGCATCTGAATCTTGTTTCG-ATTT
* * * * *
138761 AATTAGAAATTAATTCGGAAAAAATATGGGAAAATGATATTAGAAGCGTGAAAACCCTGTCAATA
441 AATTAGTAATAAATTGGGAAAAAA-A-GGAAAAATGATATTAGAAGCGTGAAAACTCT-TCAATA
* * * * *
138826 TTTTTGGCGTTGAATTATATATTTCTT-TAAGTATTGTGGCAAAAAATTA-ATGAAAAACTATTC
503 TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATA-GAAAAAATTTTC
** * * **
138889 GGCTAAGTTTTTGTAAAATTTTAGTAGAAATTGTGAACTAACCATATCACGATTTTATGGC-AAA
567 GG-TAA------GT----TTTTAGCCGAAATCGTGTACTAACC--ATCACGATTTTGGGGCTAAA
* *
138953 AAACGTG-TTCTGTTG-CCCCGACTC
619 AAACGTGCTTC-G-GGACCTCGACTC
* ** * * * * * *
138977 AATTTTGCATGATTTTTGGCGCAAAGAATCCTCGAAATATCTAAATTCTTCTGACCAAATTTCC-
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
* * * * * * * *
139041 ACCACATTTGATCAAAGGTTTGGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAAT
66 A-CACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAAT
* * * * * * *
139106 TAATTC-G-AAAAAATGGAAAACGATATTAGAAGCGTGAAAAGTCCGTCACTGTTTTTGGCATTG
130 TAATTCGGAAAAAAATGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTG
* * * *
139169 AATTATATATTTTTTCTGAGTATTGTGGCAAAAACTTGAGAAAACACTTTTTGGGTCAGTTTTCT
195 AATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGATAAGTTTTCT
* *
139234 GCTAAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAGACGCGTTTCGGGGCCCCGACTCAGT
260 GCTGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGT
*
139299 TTTGCATTGTTTTTGACATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTCA
325 TTTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTCA
*
139364 CATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTCTCGATTTAATTAGTAATAAAT
390 CATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATAAA-
*
139429 TTGGGGAAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAATCTCTTCAATATTTTTGGCGTTGA
454 TT-GGG-AAAAAAAGGAAAAATGATATTAGAAGCGTGAAAA-CTCTTCAATATTTTTGGCGTTGA
* * * *
139494 ATTATATA-TTTTTCCGAGTATTTTGGCAAAAAATTCTAGAAAAAATGTTCGGGTCAGTTTTTAG
516 ATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGAAAAAATTTTC-GGTAAGTTTTTAG
* *
139558 CCGAAATCGTGTACTAATCAGTAACCATCACAATTTTGGGGCTAAAAAACGTGCTTCGGGATCTC
580 CCGAAATCGTG---T-A-C--TAACCATCACGATTTTGGGGCTAAAAAACGTGCTTCGGGACCTC
*
139623 GGCTC
638 GACTC
* * * * *
139628 AGTTTTGCATGATTTTTGGCATAAAGACTCGTTGAAATATCTGTATTTATCGAACCAAATCTCTG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
* * * * *
139693 ACACGTTGGATCACATGTTTTGGTTATACAAGCATCTCAATTTTGTTTCGATTTAATAAGTAATT
66 ACACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
* * * **
139758 AACTCGGAAAAAAAAAGAAAAATGATAAAAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTG
131 AATTCGG-AAAAAAATGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTG
* * * *
139823 AATTATATATTTTTTCTGAGTATTGTAGAAAAAACTAGGGAAAACACTTTTCGGATAAGTTTTCA
195 AATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGATAAGTTTTCT
* *
139888 GCTGAAATCGTGTACTAATCATCAC-GATTTTTGGGTAAAAATGCGTTTCGGGGCCCCGACTCAG
260 GCTGAAATCGTGTACTAATCATCACAG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
*
139952 TTTTGCATTGTTTTTGACATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTC
324 TTTTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTC
*
140017 ACATTGGATATAAGTATTTATTTTTACGAGCATGTGAATCTTGTTTCGATTTAATTAGTAATAAA
389 ACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATAAA
* * *
140082 TTTGGGGAAAAAAAGAAAAAATGATATTAGAAGCGTGAAAATATCTTCAATCTTTTTGGCGTTGA
454 -TT-GGGAAAAAAAGGAAAAATGATATTAGAAGCGTGAAAA-CTCTTCAATATTTTTGGCGTTGA
* *
140147 ATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCTAGAAAAAATTTTCGGGTTAGTTTTTAG
516 ATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGAAAAAATTTTC-GGTAAGTTTTTAG
* * * * *
140212 CCGAAATCGTGTACTAACCATCACAATTTTGGGGCTAAGAAACGTGCTTTGGGATCTCGGCTC
580 CCGAAATCGTGTACTAACCATCACGATTTTGGGGCTAAAAAACGTGCTTCGGGACCTCGACTC
* * *
140275 AGTTTTGCATAATTTTTGGCATAAAGACTCCTTGAAATATCTGTATTCGTCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
* * *
140340 ACGCGTTGGATCACAGGTTTTGTTTATACGAGCATCTCAATCTAGTTTCGATTTAATAAGTAATT
66 ACACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
* * **
140405 AACTCGG---AAAA--AAAAACGATATTAGAAGTGTTAAAAGCCTATCAATATTTTTAGCGTTGA
131 AATTCGGAAAAAAATGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTGA
* *
140465 ATTATATATTTTTTCTTAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGCTAAGTTTT-TA
196 ATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGATAAGTTTTCT-
* * * *
140529 GCTGAAATCGTG-ACTAATCATCAC-GATTTTTGGGTAAAAATGCGTTTCTGGGCCCCGACTTAG
260 GCTGAAATCGTGTACTAATCATCACAG-TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAG
*
140592 TTTTACATTGTTTTTGGCATAATGACTCCTTG-AA-A-CTATATTCATCTAACAAAATCTCAGTC
324 TTTTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTC
* *
140654 ACATTGGATATAAGTATTTATTTTTACTAGCATGTGAATCTTGTTTCGATTTAATTAGTAATAAA
389 ACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATAAA
* * *
140719 TTTGGGGAATAAAAA-GAAAAATGATATTAGAAGCATGCAAATCTCTTCAATCTTTTTGGCGTTG
454 -TT-GGGAA-AAAAAGGAAAAATGATATTAGAAGCGTG-AAAACTCTTCAATATTTTTGGCGTTG
* *
140783 AATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTCTAGAAAAAATGTTCGTGTAAGTTTTTA
515 AATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGAAAAAATTTTCG-GTAAGTTTTTA
* *
140848 GCCGAAATCGTGTACTAACCATCACGATTTTGGGGCTAAAAAACGTGCTTCGGGATCTCGGCTC
579 GCCGAAATCGTGTACTAACCATCACGATTTTGGGGCTAAAAAACGTGCTTCGGGACCTCGACTC
*
140912 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTGTATTCATCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
*
140977 ACACGTTGGATCACAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
66 ACACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
* * **
141042 AATTCGGACAAAAAAAAAAGAAAAACGATATTAGAAGTGTGAAAATCCATTCAATATTTTTAGCG
131 AATTCGG----AAAAAAATGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCG
*
141107 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAGAACTAGAGAAAACACTTTTCGGATAAGTTT
192 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGATAAGTTT
* * * *
141172 TCAGCTGAAATCGTGTACTAATCATTACAGTTTTTGGCTAAAAATGCGTTTCGGGACCCCGACTC
257 TCTGCTGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTC
* * *
141237 AGTTTTGCATTTTTTTTGGCATATTGACTCCTTGAAATATCTATATTCATCAAACAAAATCTCAG
322 AGTTTTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAG
* * *
141302 -CAACATTTGATATAGGTATTTATTTTTACGAGCATGTGAATCTTGTTTCGATTTAATTAGTAAT
387 TC-ACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAAT
* *
141366 AAATTTGAGAAAAGAAA--AAAAATGATATTAGAAGCATG---A----TCAATATTTTTGGCGTT
451 AAA-TTGGGAAAA-AAAGGAAAAATGATATTAGAAGCGTGAAAACTCTTCAATATTTTTGGCGTT
* *
141422 GAATTATATATTTTTTCTGAGTATTTTGGTAAAAAATTATAGAAAAAATTTTCAGGTCAGTTTTT
514 GAATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGAAAAAATTTTC-GGTAAGTTTTT
* * * * * *
141487 AGCCGAATTCGTGTATTAACCATCAC-AGTTTTGGGGCTAAAAAACATGCATCGGGACCCCAACT
578 AGCCGAAATCGTGTACTAACCATCACGA-TTTTGGGGCTAAAAAACGTGCTTCGGGACCTCGACT
141551 C
642 C
*
141552 AGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
1 AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
* * *
141617 ACACGTTGGATCACATGTTTTGTTTATACGAGCATGTCAATCTTGTTTCGATTTAATAAGTAATT
66 ACACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
* * * * * *
141682 AACTCGG-AAAAAATGGGAAAATGATATTAGAATTGTGAAAAGCCTGTCAATATTTTTAGCGTTA
131 AATTCGGAAAAAAAT-GAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTG
141746 AATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCAGG-TAAGTTTTC
195 AATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTC-GGATAAGTTTTC
* * * *
141810 AGCTGAAATCGTGTACTAATCATCACGGTTATTGGCTAAAAACGCGTTTCGTGGCCCC-ATCTCA
259 TGCTGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA-CTCA
* * * * *
141874 GTTTTGCATTGTTTTTGGTATAATAACTCATTGAAATATCTATATTCATCTAACAAAATGTCAGC
323 GTTTTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGT
*
141939 CACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
388 CACATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATAA
* ** * ** * *
142004 ATTTGGAAAAAAATGGAAAAACAATATTAG-TGCGTGAAAAAACAATT-AATCTTTTTGGCATTG
453 ATTGGGAAAAAAA-GGAAAAATGATATTAGAAGCGTG--AAAACTCTTCAATATTTTTGGCGTTG
* *** **
142067 AATTATATATTTTTTCTGAGTATTTTAGCAAAAAA--ATCAGAAAAAAAAATCGGGTCGGTTTTT
515 AATTATATATTTTTTCTGAGTATTTTGGCAAAAAATTAT-AGAAAAAATTTTC-GGTAAGTTTTT
* * * * * * * *
142130 AGCTGAAATAGTGTACTAACCATCAC-AGTTTCGGGGCT----AACGCGTTTTGGGACCCCGGCT
578 AGCCGAAATCGTGTACTAACCATCACGA-TTTTGGGGCTAAAAAACGTGCTTCGGGACCTCGACT
142190 C
642 C
* * * * * * **
142191 AATTTTGTAAT-ATTTTTGGCAGAAATACTCCTTGAAATATCTATATTTATCGGAACAAATCTTT
1 AGTTTTG-CATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCC
* * * *
142255 G-CGACGTTGGATCAAAGGTTTTGTTTTTACGAGCATCTCAATCTTGTTTGGATTTAATTAGAAA
65 GAC-ACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAA
* ** *** * * *
142319 TTAATTTGGAAGAATTATGGAAAATTTATATTAGAAGCGAGAAAAGCCCGTCAATATTTTTGGCG
129 TTAATTCGGAA-AAAAAT-GAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCG
142384 TTGAATTATA
192 TTGAATTATA
142394 CTCTCTCAGT
Statistics
Matches: 3554, Mismatches: 388, Indels: 269
0.84 0.09 0.06
Matches are distributed among these distances:
634 3 0.00
635 14 0.00
636 281 0.08
637 410 0.12
638 25 0.01
639 135 0.04
640 353 0.10
641 216 0.06
642 180 0.05
643 67 0.02
644 52 0.01
645 15 0.00
646 116 0.03
647 249 0.07
648 28 0.01
649 28 0.01
650 267 0.08
651 143 0.04
652 35 0.01
653 142 0.04
654 531 0.15
655 142 0.04
656 108 0.03
657 14 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (642 bp):
AGTTTTGCATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGGACCAAATCTCCG
ACACGTTGGATCAAAGGTTTTGTTTATACGAGCATCTCAATCTTGTTTCGATTTAATAAGTAATT
AATTCGGAAAAAAATGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATATTTTTAGCGTTGA
ATTATATATTTTTTCTGAGTATTGTGGCAAAAACTAGAGAAAACACTTTTCGGATAAGTTTTCTG
CTGAAATCGTGTACTAATCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTT
TTGCATTGTTTTTGGCATAATGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGTCAC
ATTGGATATAAGTATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGTAATAAATT
GGGAAAAAAAGGAAAAATGATATTAGAAGCGTGAAAACTCTTCAATATTTTTGGCGTTGAATTAT
ATATTTTTTCTGAGTATTTTGGCAAAAAATTATAGAAAAAATTTTCGGTAAGTTTTTAGCCGAAA
TCGTGTACTAACCATCACGATTTTGGGGCTAAAAAACGTGCTTCGGGACCTCGACTC
Found at i:144844 original size:20 final size:21
Alignment explanation
Indices: 144819--144860 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
144809 TCTTGGGTTC
144819 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
144839 TACTCTCACGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
144860 T
1 T
144861 TTCTTTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Done.