Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023064.1 Corchorus olitorius cultivar O-4 contig23097, 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: 72112
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2848 original size:20 final size:20
Alignment explanation
Indices: 2823--2860 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2813 TTGTTATTTC
2823 AAGAATGTGATATCGAAATT
1 AAGAATGTGATATCGAAATT
* *
2843 AAGAATTTGATATTGAAA
1 AAGAATGTGATATCGAAA
2861 GGTTGGCAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.18, T:0.32
Consensus pattern (20 bp):
AAGAATGTGATATCGAAATT
Found at i:4636 original size:22 final size:21
Alignment explanation
Indices: 4584--4637 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
4574 GCTTCTTGGA
4584 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
4605 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
4624 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
4638 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:8285 original size:76 final size:76
Alignment explanation
Indices: 8148--8299 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
8138 ACAAGGACCC
* *
8148 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
8213 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
8224 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
8286 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
8300 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 55 0.85
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:16283 original size:30 final size:30
Alignment explanation
Indices: 16249--16453 Score: 97
Period size: 29 Copynumber: 7.0 Consensus size: 30
16239 TATAATTAAG
16249 ATGACCAAAGA-GAACCTAGAGTATGC-AAAA
1 ATGACCAAA-ATGAACCTAGA-TATGCAAAAA
** *
16279 ATGACCAAAATGCCCCTAGATGTGCAAAAA
1 ATGACCAAAATGAACCTAGATATGCAAAAA
** * * **
16309 ATGACCAAAATGCCCCTGGATGT-TTAAAA
1 ATGACCAAAATGAACCTAGATATGCAAAAA
* *
16338 A-GACCAAAATG-CCCTTGAATATGC-AAAA
1 ATGACCAAAATGAACCTAG-ATATGCAAAAA
* **
16366 ATGACCAAAATG-CCCCCGAATATGC-AAAA
1 ATGACCAAAATGAACCTAG-ATATGCAAAAA
* * * *
16395 ATAACCAAAAT-ACCCCTGGATGTGC-AAAA
1 ATGACCAAAATGA-ACCTAGATATGCAAAAA
** * *
16424 ATGACCAAAATGCCCCTGGATGTGCAAAAA
1 ATGACCAAAATGAACCTAGATATGCAAAAA
16454 TGATCAATTA
Statistics
Matches: 149, Mismatches: 17, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
27 5 0.03
28 18 0.12
29 76 0.51
30 50 0.34
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (30 bp):
ATGACCAAAATGAACCTAGATATGCAAAAA
Found at i:16454 original size:29 final size:29
Alignment explanation
Indices: 16272--16456 Score: 255
Period size: 29 Copynumber: 6.4 Consensus size: 29
16262 ACCTAGAGTA
*
16272 TGCAAAAATGACCAAAATGCCCCTAGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
16301 TGCAAAAAATGACCAAAATGCCCCTGGATG
1 TGC-AAAAATGACCAAAATGCCCCTGGATG
** * * *
16331 TTTAAAAA-GACCAAAATGCCCTTGAATA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* * *
16359 TGCAAAAATGACCAAAATGCCCCCGAATA
1 TGCAAAAATGACCAAAATGCCCCTGGATG
* *
16388 TGCAAAAATAACCAAAATACCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
16417 TGCAAAAATGACCAAAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGATG
16446 TGCAAAAATGA
1 TGCAAAAATGA
16457 TCAATTAAGG
Statistics
Matches: 137, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
28 23 0.17
29 88 0.64
30 26 0.19
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGGATG
Found at i:21253 original size:14 final size:14
Alignment explanation
Indices: 21226--21258 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
21216 TAAACGGCTC
*
21226 CCCA-AAATCGAAA
1 CCCAGAAATCAAAA
21239 CCCAGAAATCAAAA
1 CCCAGAAATCAAAA
21253 CCCAGA
1 CCCAGA
21259 TGTGTGGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.52, C:0.33, G:0.09, T:0.06
Consensus pattern (14 bp):
CCCAGAAATCAAAA
Found at i:23845 original size:15 final size:15
Alignment explanation
Indices: 23782--23850 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
23772 ATCCAAACAA
*
23782 TGAATTTGAAATTAT
1 TGAATTTCAAATTAT
* *
23797 AGAATTTCAAATTAC
1 TGAATTTCAAATTAT
* *
23812 T-AATTTCCAAA-CAA
1 TGAATTT-CAAATTAT
*
23826 AGAATTTCAAATTAT
1 TGAATTTCAAATTAT
23841 TGAA-TTCAAA
1 TGAATTTCAAA
23851 AATCTTGCAT
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
14 16 0.39
15 25 0.61
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (15 bp):
TGAATTTCAAATTAT
Found at i:24233 original size:12 final size:13
Alignment explanation
Indices: 24216--24248 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
24206 GGCGCAACAA
24216 TATTAGTAT-TAG
1 TATTAGTATATAG
24228 TATTAGTATATAG
1 TATTAGTATATAG
24241 TATATAGT
1 TAT-TAGT
24249 GTATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 6 0.32
14 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTAGTATATAG
Found at i:28619 original size:16 final size:15
Alignment explanation
Indices: 28568--28619 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
28558 AGAGGTTGAA
*
28568 AGAAAGCAATTAAAC
1 AGAAAACAATTAAAC
28583 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
*
28598 AGAAAACAATTATAC
1 AGAAAACAATTAAAC
28613 TAGAAAA
1 -AGAAAA
28620 TAAAACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 28 0.82
16 6 0.18
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:37280 original size:15 final size:16
Alignment explanation
Indices: 37256--37295 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37246 ATAGGTTGAA
*
37256 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
37271 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
37287 AGAAAACAA
1 AGAAAACAA
37296 AACAAAGCAA
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:41799 original size:2 final size:2
Alignment explanation
Indices: 41792--41830 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
41782 AAACATTTAC
41792 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41831 TTGCACTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51843 original size:9 final size:9
Alignment explanation
Indices: 51829--51865 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
51819 CGTTTGTTCC
51829 CTTTTTTCT
1 CTTTTTTCT
*
51838 CTTTTTTTT
1 CTTTTTTCT
51847 C-TTTTTCT
1 CTTTTTTCT
51855 CTTTTTTCT
1 CTTTTTTCT
51864 CT
1 CT
51866 GTTTAACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (9 bp):
CTTTTTTCT
Found at i:55599 original size:178 final size:178
Alignment explanation
Indices: 55284--55628 Score: 446
Period size: 178 Copynumber: 1.9 Consensus size: 178
55274 TGGTTATCCG
* * *
55284 ATTGAGGTGATTTAAGTGTCTATTAAAAGATTGTTCCATCATCTACAGCTTTCATGAAGGACTCG
1 ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
* * *** *
55349 AAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCTGAAAAATTTGTTGTTTTGGTTAACGG
66 AAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCAATTAAAGG
* *
55414 GAATAGACGATCCACTTAATATTATATAACTTT-TGCTCCAGATGTCTA
131 AAATAGACGATCCACTTAATATTACATAA-TTTGTGCTCCAGATGTCTA
* * * * *
55462 ATTGAGATGATTCAAGTGTCTCTTGAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGGCTCG
1 ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
* *
55527 AAAACTAAATTTAATG-TTCGAGGTAT-AAAAGTTGCTT-TCAAAGAATTAGTTGTTTCAATTAA
66 AAAACTAAATTTAATGTTTC-AAGTATCAAAA-ATGCTTCTCAAA-AATTAGTTGTTTCAATTAA
* *
55589 AGGAAATAGACGGTCTACTTAATATTACATAATTTGTGCT
128 AGGAAATAGACGATCCACTTAATATTACATAATTTGTGCT
55629 TATGGTGGAA
Statistics
Matches: 143, Mismatches: 20, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
177 14 0.10
178 129 0.90
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (178 bp):
ATTGAGATGATTCAAGTGTCTATTAAAAGATTGTTCCATCATCTACAACTTTCATGAAGGACTCG
AAAACTAAATTTAATGTTTCAAGTATCAAAAATGCTTCTCAAAAATTAGTTGTTTCAATTAAAGG
AAATAGACGATCCACTTAATATTACATAATTTGTGCTCCAGATGTCTA
Found at i:56644 original size:28 final size:27
Alignment explanation
Indices: 56602--56656 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
56592 ACTGAGACTA
*
56602 GACTCGAAACTGACTCGAAAAAACAAACT
1 GACTCGAAACCGACTC--AAAAACAAACT
56631 GACTC-AAACCGACTCAAAAACAAACT
1 GACTCGAAACCGACTCAAAAACAAACT
56657 CAAATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAACT
Found at i:59262 original size:20 final size:20
Alignment explanation
Indices: 59220--59262 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
59210 ATTATTATTG
*
59220 ATATATTAGTAATTAATAAT
1 ATATATTAGTAATTAAAAAT
*
59240 ATATATTATTAA-TAAAAAT
1 ATATATTAGTAATTAAAAAT
59259 -TATA
1 ATATA
59263 AAGATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATATTAGTAATTAAAAAT
Found at i:59309 original size:17 final size:17
Alignment explanation
Indices: 59210--59309 Score: 58
Period size: 17 Copynumber: 6.3 Consensus size: 17
59200 TTATTATTTA
* *
59210 ATTATTATTGATATATT
1 ATTATTAATAATATATT
*
59227 AGTAATTAATAATATA-T
1 A-TTATTAATAATATATT
59244 ATTATTAATAA-A-A--
1 ATTATTAATAATATATT
59257 ATTA-TAA-AGATA-A-T
1 ATTATTAATA-ATATATT
59271 ATTATTAATAATATATT
1 ATTATTAATAATATATT
* *
59288 TTTATTAA-AATTTAATT
1 ATTATTAATAATAT-ATT
59305 ATTAT
1 ATTAT
59310 ATATAATTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 4 0.06
13 6 0.09
14 5 0.07
15 7 0.10
16 15 0.22
17 18 0.27
18 11 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTATTAATAATATATT
Found at i:64812 original size:662 final size:657
Alignment explanation
Indices: 63531--66360 Score: 2619
Period size: 662 Copynumber: 4.3 Consensus size: 657
63521 CAGGTTTGAT
* * * * * *
63531 CGTTCCGAGACCCCGGGTCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTGAAATATATATAT
1 CGTTCCGAGGCCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT
* *
63596 TCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTGTTTTTTACGAGCATCTAAATCTTG
66 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTG
* * * * * * * * **
63661 TTTCGATTTAATTA-AAATTAATTCGGAAAAGTAGGGAAAACGATATTAGTAGCGTTAAAAAACC
130 TTTCGATTTAATAAGAAATTAATTCAGAAAAATATGAAAAACGATATTA-AAACG-TGAAAAGTC
* * * * * *
63725 CTTCAATATTTTTGGCATTGAATTATATATTGTTTTATGATAATTTTAGTCAAAAATTGAGGAAA
193 CTCCAATCTTTTTGGCATTAAATTATATA-TATTTTATAAGAATTTTAG-CAAAAATTGAGGAAA
* * * * *
63790 TATCTTTCGGGTCAATTTTTGTAAAATGTTAGCCGAAATCGTCTAATAATCATCACAGTTTTTGG
256 -ATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-ATCATCACAGTTTTTGG
* * * * * * * * *
63855 CTAAAAACGCGTTCCAGGA-CCCCGGGTCTGTTTTGCATGATTTTTTGCACCAAGGCTCCTTGAG
319 CTAAAAACACGTACC-GGAGCCACAGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAA
* * * * *
63919 ATATCCATATTCATCTAATCAAATCTCAGTCACATTGCG-TTTTAGGATTTGTTTTTACGAGCAT
383 ATATCTATATTCATCTAACCAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTACAAGCAT
* * ** *
63983 CTTAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAATATGAAAAACGATATGAAAAG
447 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAAATATAT-AGAAG
* ** * * * *
64047 TGTGAAAA-ATCTTCCAACCTTTTTGGCGTTAAATTATAT-ATATTTCATGAGTATTTTAGCCAA
511 CGTGAAAAGCCCTT-CAATCTTTTTGGCGTTGAATTATATAAT-TTTTATGAGTATTGTAGCCAA
* * *
64110 AAATTGAGGAAAAAT-TTTTCAGGTCATTTTTTGCAAAATTTTAGTCAAAATCATGTACGTA-CA
574 AAATTGAGGAAAAATCTTTT-GGGTCAATTTTTGCAAAATTTTAGTCGAAATC-TGTA--TACCA
*
64173 TCACAGTTTTTT-G-AAAAAACG
635 TCACAGTTTTTTAGCTAAAAACG
* * * ** *
64194 CGTTTCGAGGCTC-CGGCTCAGTTTTGCATG-TTTCTTTGCGTCGTGGCTCCTTGAAATATCTAT
1 CGTTCCGAGGC-CACGGCTCAGTTTTGCATGATTT-TTGGCGCCAAGACTCCTTGAAATATCTAT
* * *
64257 ATTC-TCTAATCAAATCTC-GCCACATTGTATTAAAAGATTTGTTTTTATC-AGCATCTGAATCT
64 ATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA-CGAGCATCTGAATCT
* *
64319 TGTTTCTATTTAATAAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAGT
128 TGTTTCGATTTAATAAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAA-CGTGAAAAGT
* *
64384 CCTCCAATCTTTTTGG-AGTTAAATTATATATATTTTATAAGAATTTTAG-ACAAATTTGTGGGA
192 CCTCCAATCTTTTTGGCA-TTAAATTATATATATTTTATAAGAATTTTAGCA-AAAATTG-AGGA
* *
64447 AAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCGAAATCACAGT
254 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-TC---ATCACAGT
* * * * *
64512 TTTTTGCTAAAAACACGTACCGGAGCCACAGTTCTGTGTTGCAT-ATTTTTGGCGCCGAGACTCC
313 TTTTGGCTAAAAACACGTACCGGAGCCACAGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTCC
* * ***
64576 TTGAAATATCTATATTCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTG-TAAAACAA
378 TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAA
* * * *
64640 GCATCTGAAT-TATGTTTTGATTTAATTACAAATTAATTCGGAAAATAATA-GAAAAAATGATAA
443 GCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAAAT-AT-A
* * *
64703 TAGAAGCATGAAAAGCCCTTTAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGG
505 TAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTAG
* * * * * *
64768 CTAAAGATTGAGGAAATATCTTTTGGCTCAATTTTTGTAAAATTTTAGTTGAAATCGTGTTATAA
570 CCAAAAATTGAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATC-TG-TAT-A
*
64833 TCATCACAGTTTTTT-GCTAAAAACG
632 CCATCACAGTTTTTTAGCTAAAAACG
* * ** * * *
64858 CGTTCCGAGGCC-CGGCTAAGTTTTGCATGATTTTTGGCACCAAGACTTTTTCAGATATCTATAC
1 CGTTCCGAGGCCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT
* * *
64922 TCATCTGATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
66 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
64987 TTTGATTTAATTAA-AAATTAATTCAGAAAAATATGATAAACGATATTAAACATGTTAAAAGTCC
131 TTCGATTTAA-TAAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAA-ACGTGAAAAGTCC
*
65051 TCCAATCTTTTTGGCATTAATATATATATATATATATATATATTATGAGTATTTTGGCTAAAAAT
194 TCCAATCTTTTTGGCATTAA-AT-TATATATAT-T-T-TATA--A-GA--ATTTTAGC-AAAAAT
* * *
65116 TGAGGAAAAAATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAC---CATCACGGT
248 TGAGGAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCATCACAGT
* * * * *
65178 TGTTTGGCT-AAAA-ACGTATTCCGGGGTCC-CA-TGTCAGTTTTGCAT-TTTTTTTGTGGCAAC
313 T-TTTGGCTAAAAACACGTA--CCGGAG-CCACAGT-TCAGTTTTGCATGATTTTTTGCGCCAAG
* * *
65238 ACTCCTTGAAATATCTATATTCATCTAAACAAATCTTAGCCACATTGGATATAAGGATTTGTTTT
373 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * * *
65303 TACGAGCATTTGAATC----AT-GATTTAATTATAAATTAATTTGAAAAAAAATA-GAAAAAATA
438 TACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAAATA
* * * * *** * *
65362 TTATTAGAAACGCGAGAAGCCCTTCAATATTTTTGTTTTTCAATTATATATTTTTTATGAGTATT
503 -TA-TAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATT
* * *
65427 GT-GCCTAAAAATTGA-GAAAGATATTTCGGGTCAATTTTTGCAAAATTTTAG-CTGAAAT-T-T
566 GTAGCC-AAAAATTGAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGTC-GAAATCTGT
** **
65487 GCACCATCATGGTTTTTTAGCTAAAAACG
629 ATACCATCACAGTTTTTTAGCTAAAAACG
* * * * ** *
65516 CGTTCCCAGGCCTCGGGTCAGTTTTGTATGATTTTTGATGCCAAGACTCCTTAAAATATATCTAT
1 CGTTCCGAGGCCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTAT
* * * * * *
65581 ATTCATCTAACCAAATCTCAGTCACATTGTATTTAAAGATATGTTTTTACGAGTATCTGAATCTT
64 ATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTT
* * ** * *
65646 ATTTCGATTTAATCAGAAATTAATTTGGAAATAAATTAGGAAAAACGATATTGGAAACGTGAAAA
129 GTTTCGATTTAATAAGAAATTAATTCAG-AA-AAA-TATGAAAAACGATATT-AAAACGTGAAAA
* * * * * * * * * * *
65711 GGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTAGAAATTG-GGC
190 GTCCTCCAATCTTTTTGGCATTAAATTATATATATTTTATAAGAATTTTAGC-AAAAATTGAGG-
* * * * * *
65775 AAAAATCTTTCGGGACAAGTTTTGCAAAATTTTAGCCGAAATCGTGCACTAACCATCACGGTTTT
253 -AAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-ATCATCACAGTTTT
* * * * * * *
65840 CGGCTAAAAACGCGTTCCGG-GGCACGGCTCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTG
316 TGGCTAAAAACACGTACCGGAGCCACAGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTG
* * * * * *
65904 AAATATCTATATTCATCTAACAAAATATCAGCCAAATTGGGTTTAAGAATTTATTTTTACAAGCA
381 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCA
* * *
65969 TCTGAATCTTGTTTCGATTTAAATAGAAATTAATTCGAAAAAAAATTATGTGAAACAATAT-TAT
446 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAA-TA--TGAAAAAATATATAG
* * *** * *
66033 AAGCGTTAAAAGCCCTTCAAGCTTTTTTATGTCGAA-T-TATAATTTTTATGAGTATTTTAGCCA
508 AAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTAGCCA
**
66096 AAAATTGAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATC-GTATACCATCA
573 AAAATTGAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCTGTATACCATCA
* *
66160 CGGTTTTTTGGCTAAAAACG
638 CAGTTTTTTAGCTAAAAACG
* * * * * * *
66180 CGTTAC-AGGGCCATGTCTCTGTTTTGCATGATTTTTGGCGCCGAGACTCTTTGAAATATCTTTA
1 CGTTCCGA-GGCCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATA
* * * * ** * ** *
66244 TTAATCTAATCAAATATAAACTGCATTGGATTTAAGGATTTATTTTTACGTCCATCTGAATGTTG
65 TTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* *
66309 TTTCCATTTAATTAGAAATTAATTCAGTAAAAATATGAAAAACGATATTAAA
130 TTTCGATTTAATAAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAA
66361 GTCCTCCAAT
Statistics
Matches: 1770, Mismatches: 305, Indels: 188
0.78 0.13 0.08
Matches are distributed among these distances:
653 2 0.00
654 15 0.01
655 42 0.02
656 2 0.00
657 29 0.02
658 159 0.09
659 73 0.04
660 90 0.05
661 185 0.10
662 343 0.19
663 331 0.19
664 170 0.10
665 119 0.07
666 21 0.01
667 105 0.06
668 16 0.01
669 2 0.00
670 4 0.00
672 1 0.00
673 2 0.00
675 52 0.03
676 6 0.00
677 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (657 bp):
CGTTCCGAGGCCACGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATAAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAACGTGAAAAGTCCTC
CAATCTTTTTGGCATTAAATTATATATATTTTATAAGAATTTTAGCAAAAATTGAGGAAAATATT
TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCATCACAGTTTTTGGCTAAAAA
CACGTACCGGAGCCACAGTTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTAT
ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTT
GTTTCGATTTAATTAGAAATTAATTCGAAAAAAAATATGAAAAAATATATAGAAGCGTGAAAAGC
CCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTAGCCAAAAATTGAGGAAA
AATCTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCTGTATACCATCACAGTTTTTTAGCT
AAAAACG
Found at i:65897 original size:994 final size:980
Alignment explanation
Indices: 63544--66180 Score: 2739
Period size: 994 Copynumber: 2.7 Consensus size: 980
63534 TCCGAGACCC
* *
63544 CGGGTCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTGAAATATA--TATATTCATCTAATCA
1 CGGGTCAGTTTTGCAT-ATTTTTGGCGCCAAGACTCCTT-AAATATATCTATATTCATCTAACCA
*
63607 AATCTCAGACACATTGGATTTAAGGATTTGTTTTTTACGAGCATCTAAATCTTGTTTCGATTTAA
64 AATCTCAGACACATT-GATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* * * * * *
63672 TTAAAATTAATTCGG-AAAAGTAGGGAAAACGATATTAGTAGCGTTAAAAAACCCTTCAATATTT
127 TTAAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCG-TGAAAAGCCTTTCAATATTT
* *
63736 TTGGCATTGAATTATATATTGTTTTATGA-TAATTTTAGTCAAAAATTGAGGAAATATCTTTCGG
191 TTGGCGTTGAATTATATATT-TTTTATGAGT-ATTTTAG-CTAAAATTGAGGAAATATCTTTCGG
*
63800 GTCAATTTTTGTAAAATGTTAGCCGAAATCGT-CTAATAATCATCACAGTTTTTGGCTAAAAACG
253 GTCAATTTTTGTAAAATTTTAGCCGAAATCGTGC--ATAATCATCACAGTTTTTGGCTAAAAACG
** * * * *
63864 CGTTCCAGGACCCCGGGTCTGTTTTGCATGATTTTTTGCACCAAGGCTCCTTGAGATATCCATAT
316 CGTTCC-GGGGCCCGGCTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAGATATCTATAT
* * * * *
63929 TCATCTAATCAAATCTCAGTCACATTGCGTTTTAGGATTTGTTTTTACGAGCATCTTAATCTTGT
380 TCATCT-ATCAAATCTCAGCCACATTGAGTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
* * * *
63994 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAA-AGTGTGAAAAATC
444 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGATAAACGATATTAAACA-TGTTAAAAGTC
* * *
64058 TTCCAACCTTTTTGGC--GTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATTGAGGAA
507 CTCCAACCTTTTTGGCTTATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAA
* * * * * * * *
64121 AAATTTTTCAGGTCATTTTTTGCAAAATTTTAGTCAAAATCATGTACGTACATCACAGTTTTTTG
572 AAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC---CATCACGGTTTTTGG
* * * * ****
64186 -AAAAAACGCGTTTCGAGGCTCCGGCTCAGTTTTGCATGTTTCTTTGCGTCGTGGCTCCTTGAAA
634 CTAAAAACGCATTCCGAGGCTCCGGCTCAGTTTTGCATGTTTCTTTGCGGCAACACTCCTTGAAA
* * *
64250 TATCTATATTCTCTAATCAAATCTCGCCACATTGTATTAAAAGATTTGTTTTTATCAGCATCTGA
699 TATCTATATTCTCTAAACAAATCTAGCCACATTGGATTAAAAGATTTGTTTTTATCAGCATCTGA
* * * *
64315 ATCTTGTTTCTATTTAATAAGAAATTAATTCAGAAAAATATGAAAAATGATATTAAAAGCGTGAA
764 ATCATG----TATTTAATAAGAAATTAATTAAAAAAAATATGAAAAATGATATTAAAAGCGCGAA
* * * ** *
64380 AAGTCCTCCAATCTTTTTGGAGTTAAATTATATATATTTTATAAGAATTTTAGACAAATTTGTGG
825 AAGCCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATAAGAATTGTAGACAAAAATGTGA
* *
64445 GAAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCGAAATCACA
890 GAAAATATTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATC-TGTA-GTCAG-C-AAATCACA
*
64510 GTTTTTTGCTAAAAACACGTACCGGAGCCA
951 GTTTTTTGCTAAAAACACGTACCAGAGCCA
* * * * * * *
64540 CAGTTCTGTGTTGCATATTTTTGGCGCCGAGACTCCTTGAA-ATATCTATATTCTTCTAACCAAA
1 CGGGTCAGTTTTGCATATTTTTGGCGCCAAGACTCCTTAAATATATCTATATTCATCTAACCAAA
* *** * *
64604 TCTCAGCCACATTAGATTTAAGGATTTG-TAAAACAAGCATCTGAAT-TATGTTTTGATTTAATT
66 TCTCAGACACATT-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTTAATT
* * * * *
64667 ACAAATTAATTCGGAAAATAATAGAAAAAATGATAATAGAAGCATGAAAAGCCCTTT-AATCTTT
129 A-AAATTAATTCGGAAAA-AATAGGAAAAACGATATTAGAAGCGTGAAAAG-CCTTTCAATATTT
* * * * *
64731 TTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAGATTGAGGAAATATCTTTTGGCT
191 TTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAA-ATTGAGGAAATATCTTTCGGGT
** * *
64796 CAATTTTTGTAAAATTTTAGTTGAAATCGTGTTATAATCATCACAGTTTTTTGCTAAAAACGCGT
255 CAATTTTTGTAAAATTTTAGCCGAAATCGTG-CATAATCATCACAGTTTTTGGCTAAAAACGCGT
* * * ** * *
64861 TCCGAGGCCCGGCTAAGTTTTGCATGATTTTTGGCACCAAGACTTTTTCAGATATCTATACTCAT
319 TCCGGGGCCCGGCTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAGATATCTATATTCAT
* *
64926 CTGATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTTG
384 CT-ATCAAATCTCAGCCACATTGAGTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCG
*
64991 ATTTAATTAAAAATTAATTCAGAAAAATATGATAAACGATATTAAACATGTTAAAAGTCCTCCAA
448 ATTTAATTAGAAATTAATTCAGAAAAATATGATAAACGATATTAAACATGTTAAAAGTCCTCCAA
* * *
65056 TCTTTTTGGCATTAATATATATATATATATATATATATTATGAGTATTTTGGCTAAAAATTGAGG
513 CCTTTTTGGC-TT-AT-TA-A-AT-TATATATAT-T-TTATGAGTATTTTAGCCAAAAATTGAGG
*
65121 AAAAA-ATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACCATCACGGTTGTTTGG
570 AAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTT-TTTGG
* * * * *
65185 CTAAAAACGTATTCCG-GGGTCCCATG-TCAGTTTTGCAT-TTTTTTTGTGGCAACACTCCTTGA
634 CTAAAAACGCATTCCGAGGCT-CC-GGCTCAGTTTTGCATGTTTCTTTGCGGCAACACTCCTTGA
*
65247 AATATCTATATTCATCTAAACAAATCTTAGCCACATTGGA-TATAAGGATTTGTTTTTA-CGAGC
697 AATATCTATATTC-TCTAAACAAATC-TAGCCACATTGGATTA-AAAGATTTGTTTTTATC-AGC
* * *
65310 ATTTGAATCATG-ATTTAATTATAAATTAATTTGAAAAAAAATA-GAAAAAAT-ATTATTAGAAA
758 ATCTGAATCATGTATTTAATAAGAAATTAA-TT-AAAAAAAATATG-AAAAATGA-TATTA-AAA
* * *** * * * * *
65372 -CGCGAGAAGCCCTTCAATATTTTTGTTTTTCAATTATATATTTTTTATGAGTATTGT-GCCTAA
818 GCGCGAAAAGCCCTCCAATATTTTTGGAGTTAAATTATATATATTTTATAAGAATTGTAGAC-AA
* * *
65435 AAAT-TGAGAAAGATATTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAAT-T-T-G-CA-C-CA
882 AAATGTGAGAAA-ATATTTCGGGTCAATTTTTGCAAAATATTAGCCGAAATCTGTAGTCAGCAAA
** * * *
65493 TCATGGTTTTTTAGCTAAAAACGCGTTCCCAG-GCCT
946 TCACAGTTTTTT-GCTAAAAACACG-TACCAGAGCCA
* **
65529 CGGGTCAGTTTTGTATGATTTTTGATGCCAAGACTCCTTAAAATATATCTATATTCATCTAACCA
1 CGGGTCAGTTTTGCAT-ATTTTTGGCGCCAAGACTCCTT-AAATATATCTATATTCATCTAACCA
* * * * *
65594 AATCTCAGTCACATTGTATTTAAAGATATGTTTTTACGAGTATCTGAATCTTATTTCGATTTAAT
64 AATCTCAGACACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * * *
65659 CAGAAATTAATTTGGAAATAAATTAGGAAAAACGATATTGGAAACGTGAAAAGGCTTTCAATTTT
128 TA-AAATTAATTCGGAAA-AAA-TAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATT
* *
65724 TTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTAGAAATTG-GGCAAAAATCTTTCGG
190 TTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTA-AAATTGAGG-AAATATCTTTCGG
* * * * * *
65788 GACAAGTTTTGCAAAATTTTAGCCGAAATCGTGCACTAACCATCACGGTTTTCGGCTAAAAACGC
253 GTCAATTTTTGTAAAATTTTAGCCGAAATCGTGCA-TAATCATCACAGTTTTTGGCTAAAAACGC
* ** *
65853 GTTCCGGGGCACGGCTCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATTC
317 GTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAGATATCTATATTC
* * * * * *
65918 ATCTAACAAAATATCAGCCAAATTGGGTTTAAGAATTTATTTTTACAAGCATCTGAATCTTGTTT
382 ATCTATC-AAATCTCAGCCACATTGAGTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTT
* * *
65983 CGATTTAAATAGAAATTAATTCGAAAAAAAATTATG-TGAAACAATATTATAAGC--GTTAAAAG
446 CGATTTAATTAGAAATTAATTC--AGAAAAA-TATGAT-AAACGATATTA-AA-CATGTTAAAAG
* * * *
66045 CCCTTCAAGC-TTTT---TTATGTCGAATTATA-AT-TTTTATGAGTATTTTAGCCAAAAATTGA
505 TCCTCCAACCTTTTTGGCTTAT-T-AAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* * * *
66104 GGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTATACCATCACGGTTTTTT
568 GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGG-TTTTT
66169 GGCTAAAAACGC
632 GGCTAAAAACGC
66181 GTTACAGGGC
Statistics
Matches: 1365, Mismatches: 215, Indels: 132
0.80 0.13 0.08
Matches are distributed among these distances:
985 31 0.02
986 61 0.04
987 3 0.00
988 13 0.01
989 29 0.02
990 26 0.02
991 7 0.01
992 94 0.07
993 215 0.16
994 372 0.27
995 98 0.07
996 62 0.05
997 43 0.03
998 114 0.08
999 43 0.03
1000 48 0.04
1001 76 0.06
1002 30 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (980 bp):
CGGGTCAGTTTTGCATATTTTTGGCGCCAAGACTCCTTAAATATATCTATATTCATCTAACCAAA
TCTCAGACACATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAA
AATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTTGGC
GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAATTGAGGAAATATCTTTCGGGTCAATTT
TTGTAAAATTTTAGCCGAAATCGTGCATAATCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGG
CCCGGCTCAGTTTTGCATGATTTTTTGCACCAAGACTCCTTGAGATATCTATATTCATCTATCAA
ATCTCAGCCACATTGAGTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATT
AGAAATTAATTCAGAAAAATATGATAAACGATATTAAACATGTTAAAAGTCCTCCAACCTTTTTG
GCTTATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATATTTCGGGTC
AATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCACGGTTTTTGGCTAAAAACGCATTCCGA
GGCTCCGGCTCAGTTTTGCATGTTTCTTTGCGGCAACACTCCTTGAAATATCTATATTCTCTAAA
CAAATCTAGCCACATTGGATTAAAAGATTTGTTTTTATCAGCATCTGAATCATGTATTTAATAAG
AAATTAATTAAAAAAAATATGAAAAATGATATTAAAAGCGCGAAAAGCCCTCCAATATTTTTGGA
GTTAAATTATATATATTTTATAAGAATTGTAGACAAAAATGTGAGAAAATATTTCGGGTCAATTT
TTGCAAAATATTAGCCGAAATCTGTAGTCAGCAAATCACAGTTTTTTGCTAAAAACACGTACCAG
AGCCA
Found at i:65974 original size:333 final size:328
Alignment explanation
Indices: 63531--66429 Score: 2501
Period size: 333 Copynumber: 8.8 Consensus size: 328
63521 CAGGTTTGAT
* * * * * *
63531 CGTTCCGAGACCCCGGGTCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTGAAATATATATAT
1 CGTTCCG-GGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATAT
* *
63596 TCATCTAATCAAATCTCAGACACATTGGATTTAAGGATTTGTTTTTTACGAGCATCTAAATCTTG
65 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTG-TTTTTACGAGCATCTGAATCTTG
* * * * * * * *
63661 TTTCGATTTAATTA-AAATTAATTC-GGAAAAGTAGGGAAAACGATATTAGTAGCGTTAAAAAAC
128 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAAACG-TGAAAAGC
* *
63724 CCTTCAATATTTTTGGCATTGAATTATATATTGTTTTATGA-TAATTTTAG-TCAAAAATTGAGG
192 CCTTCAATCTTTTTGGCGTTGAATTATATATT-TTTTATGAGT-ATTTTAGCT-AAAAATTGAGG
* * * * * *
63787 AAATATCTTTCGGGTCAATTTTTGTAAAATGTTAGCCGAAATCGTCTAATAATCATCACAGTTTT
254 AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT-GACT-ACCATCACAGTTTT
63852 TGGCTAAAAACG
317 TGGCTAAAAACG
* * * * * * *
63864 CGTTCCAGGACCCCGGGTCTGTTTTGCATGATTTTTTGCACCAAGGCTCCTTGAGATATCCATAT
1 CGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATAT
* * *
63929 TCATCTAATCAAATCTCAGTCACATTGCG-TTTTAGGATTTGTTTTTACGAGCATCTTAATCTTG
65 TCATCTAA-CAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
63993 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATGA-AAAGTGTGAAAA-A
128 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAGC
* * * * * *
64056 TCTTCCAACCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTTAGCCAAAAATTGAGGAA
192 CCTT-CAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAA
* * * * * * *
64121 AAATTTTTCAGGTCATTTTTTGCAAAATTTTAGTCAAAATCATGTACGTA-CATCACAGTTTTTT
256 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-AC-TACCATCACAGTTTTTG
*
64185 G-AAAAAACG
319 GCTAAAAACG
* * * ** *
64194 CGTTTCGAGGCTCCGGCTCAGTTTTGCATG-TTTCTTTGCGTCGTGGCTCCTTGAAATATCTATA
1 CGTTCCG-GGCCCCGGCTCAGTTTTGCATGATTT-TTTGCGCCAAGACTCCTTGAAATATCTATA
* * *
64258 TTC-TCTAATCAAATCTC-GCCACATTGTATTAAAAGATTTGTTTTTATC-AGCATCTGAATCTT
64 TTCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA-CGAGCATCTGAATCTT
* * *
64320 GTTTCTATTTAATAAGAAATTAATTCAG-AAAAATATGAAAAATGATATTA-AAAGCGTGAAAAG
127 GTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAAA-CGTGAAAAG
* * * * * * * * * *
64383 TCCTCCAATCTTTTTGGAGTTAAATTATATATATTTTATAAGAATTTTAG--ACAAATTTGTGGG
191 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTA-AAAATTGAGGA
* * * *
64446 AAAATATTTCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACGTTAGTCGAAATCACAG
255 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-AC--TA--C--CATCACAG
* *
64511 TTTTTTGCTAAAAACA
313 TTTTTGGCTAAAAACG
* * * * * * * *
64527 CGTACCGGAGCCACAGTTCTGTGTTGCAT-ATTTTTGGCGCCGAGACTCCTTGAAATATCTATAT
1 CGTTCCGG-GCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATAT
* * *** *
64591 TCTTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTG-TAAAACAAGCATCTGAAT-TATG
65 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TG
* * * * * * *
64654 TTTTGATTTAATTACAAATTAATTCGGAAAATAATA-GAAAAAATGATAATAGAAGCATGAAAAG
128 TTTCGATTTAATTAGAAATTAATTCAGAAAA-AATATG-AAAAACGATATTAGAAACGTGAAAAG
* * * * *
64718 CCCTTTAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAGATTGAGGAA
191 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAA
* * * * ** *
64783 ATATCTTTTGGCTCAATTTTTGTAAAATTTTAGTTGAAATCGTGTTA-TAATCATCACAGTTTTT
256 AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG--ACT-ACCATCACAGTTTTT
*
64847 TGCTAAAAACG
318 GGCTAAAAACG
* * * ** * * *
64858 CGTTCCGAGG-CCCGGCTAAGTTTTGCATGATTTTTGGCACCAAGACTTTTTCAGATATCTATAC
1 CGTTCCG-GGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATAT
* * *
64922 TCATCTGATCAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
65 TCATCT-AACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
64987 TTTGATTTAATTAAAAATTAATTCAG-AAAAATATGATAAACGATATTA-AACATGTTAAAAGTC
129 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAA-ACGTGAAAAGCC
* * * *
65050 CTCCAATCTTTTTGGCATTAATATATATATATATATATATATATTATGAGTATTTTGGCTAAAAA
193 CTTCAATCTTTTTGGC-GT--T-GA-AT-TATATAT-T-T-T-TTATGAGTATTTTAGCTAAAAA
* * *
65115 TTGAGGAAAAA-ATTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTG--TACCATCACGG
248 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACTACCATCACAG
65177 TTGTTTGGCTAAAAACG
313 TT-TTTGGCTAAAAACG
** ** * * * *
65194 TATTCCGGGGTCCCATG-TCAGTTTTGCAT-TTTTTTTGTGGCAACACTCCTTGAAATATCTATA
1 CGTTCC-GGG-CCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATA
* * *
65257 TTCATCTAAACAAATCTTAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATTTGAATC---
64 TTCATCT-AACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * * ** * *
65319 -AT-GATTTAATTATAAATTAATT-TGAAAAAAAATAGAAAAAATATTATTAGAAACGCGAGAAG
128 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATAT-GAAAAACGA-TATTAGAAACGTGAAAAG
* *** * *
65381 CCCTTCAATATTTTTGTTTTTCAATTATATATTTTTTATGAGTATTGT-GCCTAAAAATTGA-GA
191 CCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAG-CTAAAAATTGAGGA
* * * * ** *
65444 AAGATATTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAAT-TTG-C-ACCATCATGGTTTTTTA
255 AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACTACCATCACAG-TTTTTG
65506 GCTAAAAACG
319 GCTAAAAACG
* * * * * *
65516 CGTTCCCAGGCCTCGGGTCAGTTTTGTATGA-TTTTTGATGCCAAGACTCCTTAAAATATATCTA
1 CGTT-CCGGGCCCCGGCTCAGTTTTGCATGATTTTTTG-CGCCAAGACTCCTT-GAA-ATATCTA
* * * * *
65580 TATTCATCTAACCAAATCTCAGTCACATTGTATTTAAAGATATGTTTTTACGAGTATCTGAATCT
62 TATTCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* * ** * *
65645 TATTTCGATTTAATCAGAAATTAATTTGGAAATAAATTAGGAAAAACGATATTGGAAACGTGAAA
126 TGTTTCGATTTAATTAGAAATTAATTCAGAAA-AAA-TATGAAAAACGATATTAGAAACGTGAAA
* * * * *
65710 AGGCTTTCAATTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCGCTAGAAATTG-GG
189 AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGG
* * *
65774 CAAAAATCTTTCGGGACAAGTTTTGCAAAATTTTAGCCGAAATCGTGCACTAACCATCACGGTTT
254 -AAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-ACT-ACCATCACAGTTT
*
65839 TCGGCTAAAAACG
316 TTGGCTAAAAACG
* * *
65852 CGTTCCGGGGCACGGCTCAGTTTTGCATGATTTTTTGTGCCAAGACTCCTTGAAATATCTATATT
1 CGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATATT
* * * * * *
65917 CATCTAACAAAATATCAGCCAAATTGGGTTTAAGAATTTATTTTTACAAGCATCTGAATCTTGTT
66 CATCTAAC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
* * ** * * * *
65982 TCGATTTAAATAGAAATTAATTCGAAAAAAAATTATGTGAAACAATATTATAAGCGTTAAAAGCC
130 TCGATTTAATTAGAAATTAATTC-AGAAAAAA-TATGAAAAACGATATTAGAAACGTGAAAAGCC
* *** * *
66047 CTTCAAGCTTTTTTATGTCGAATTATA-A-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
193 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAA
* * *
66110 ATCTTTTGGGTCAATTTTTGCAAAATTTTAACCGAAATCGT-A-TACCATCACGGTTTTTTGGCT
258 ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACTACCATCACAG-TTTTTGGCT
66173 AAAAACG
322 AAAAACG
* ** * * * * * *
66180 CGTTACAGGGCCATGTCTCTGTTTTGCATGATTTTTGGCGCCGAGACTCTTTGAAATATCTTTAT
1 CGTT-CCGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATAT
* * * * ** * ** *
66245 TAATCTAATCAAATATAAACTGCATTGGATTTAAGGATTTATTTTTACGTCCATCTGAATGTTGT
65 TCATCTAA-CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
66310 TTCCATTTAATTAGAAATTAATTCAGTAAAAATATGAAAAACGATATT--AAA-GT-------CC
129 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGCCC
* * * * * *
66365 TCCAATCTTTTTGGCGTTGAATTATATATGTTTTATGAGTATTTTTGCCAAAAATTAAGAAAAAA
194 TTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAA
66430 AAAATCTTTC
Statistics
Matches: 2097, Mismatches: 371, Indels: 210
0.78 0.14 0.08
Matches are distributed among these distances:
317 22 0.01
318 1 0.00
319 32 0.02
321 3 0.00
322 51 0.02
323 73 0.03
324 7 0.00
325 64 0.03
326 50 0.02
327 103 0.05
328 92 0.04
329 147 0.07
330 125 0.06
331 272 0.13
332 253 0.12
333 370 0.18
334 54 0.03
335 112 0.05
336 173 0.08
337 25 0.01
338 4 0.00
339 34 0.02
340 30 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
CGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCCTTGAAATATCTATATT
CATCTAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
CGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGCCCTT
CAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATC
TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACTACCATCACAGTTTTTGGCTAAAA
ACG
Found at i:66959 original size:32 final size:31
Alignment explanation
Indices: 66901--66979 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
66891 GCATTTTTTA
** *
66901 ACACGTGGCGTGCCACATGTTTTTTTTTTTGT
1 ACACGTGGCGTGCCACATG-TCATTTTTTGGT
* **
66933 ACATGTGGCGTGCCAGGTGTCATTTTTTGGT
1 ACACGTGGCGTGCCACATGTCATTTTTTGGT
*
66964 ACACGTGGCATGCCAC
1 ACACGTGGCGTGCCAC
66980 GTCGGACGCC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 22 0.58
32 16 0.42
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.37
Consensus pattern (31 bp):
ACACGTGGCGTGCCACATGTCATTTTTTGGT
Found at i:67790 original size:16 final size:16
Alignment explanation
Indices: 67769--67800 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
67759 GAGCCTCTGA
*
67769 TTTTCGGGTTCGGGTC
1 TTTTCGGATTCGGGTC
67785 TTTTCGGATTCGGGTC
1 TTTTCGGATTCGGGTC
67801 ATTTAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.34, T:0.44
Consensus pattern (16 bp):
TTTTCGGATTCGGGTC
Found at i:70930 original size:19 final size:19
Alignment explanation
Indices: 70906--70944 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
70896 TTCATTTTCT
70906 AACTCTCAAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
*
70925 AACTCTCTAAACTTCTTCA
1 AACTCTCAAAACTTCTTCA
70944 A
1 A
70945 GAATATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (19 bp):
AACTCTCAAAACTTCTTCA
Found at i:71131 original size:33 final size:34
Alignment explanation
Indices: 71058--71131 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
71048 AAATGGCAGT
71058 GCCGCCCCAGGGGGGACGGCACCGCCATGGCTAC
1 GCCGCCCCAGGGGGGACGGCACCGCCATGGCTAC
* * *
71092 GGCGCCCCCGGGGGG-CGGCACCGCTATGG-TGAC
1 GCCGCCCCAGGGGGGACGGCACCGCCATGGCT-AC
71125 GCCGCCC
1 GCCGCCC
71132 AAGTTGGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.11, C:0.42, G:0.41, T:0.07
Consensus pattern (34 bp):
GCCGCCCCAGGGGGGACGGCACCGCCATGGCTAC
Done.