Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006532.1 Hibiscus syriacus cultivar Beakdansim tig00015922_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 76702
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:7867 original size:45 final size:45
Alignment explanation
Indices: 7818--7903 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
7808 AATGAAGCAA
* *
7818 AAAGGAGGGT-TCAAGATGAAAACTCGAAAAGGGCGTCTTGAAACC
1 AAAGGA-GGTCTCAAGATGAAAACCCGAAAAGGGCGGCTTGAAACC
* *
7863 AAAGGAGGTCTCAAGTTGAAAACCCGTAAAGGGCGGCTTGA
1 AAAGGAGGTCTCAAGATGAAAACCCGAAAAGGGCGGCTTGA
7904 GTTTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 3 0.08
45 33 0.92
ACGTcount: A:0.37, C:0.16, G:0.30, T:0.16
Consensus pattern (45 bp):
AAAGGAGGTCTCAAGATGAAAACCCGAAAAGGGCGGCTTGAAACC
Found at i:8984 original size:55 final size:55
Alignment explanation
Indices: 8863--9552 Score: 1032
Period size: 55 Copynumber: 12.6 Consensus size: 55
8853 AGCATCAAGG
*
8863 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGA-ACGATTGTTGAAAA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
8917 TTGTTCGAGTCTTACACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* * *
8972 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATGGAATA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
9027 TTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
9082 TTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* ** * *
9137 TTGTTAGAGTCTTATACTCTCTGAAGGAATAAAGAGCAGACACGATTGCTAAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
*
9192 TTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
9247 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
9302 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGG
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* *
9357 TTTTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAA-A
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
* * * *
9411 GTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTTGAAGA
1 -TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
** * * * *
9467 TTGTTTAAGTCCTATACTCTTTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
*
9522 ----TCGAGTCCTATACTCTCTGAAGGAATAGGGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGA
9553 ATGAACCTGT
Statistics
Matches: 582, Mismatches: 51, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
51 28 0.05
54 38 0.07
55 515 0.88
56 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (55 bp):
TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
Found at i:9684 original size:55 final size:54
Alignment explanation
Indices: 8863--9684 Score: 894
Period size: 55 Copynumber: 15.0 Consensus size: 54
8853 AGCATCAAGG
* *
8863 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGA-ACGATTGTTGAAAA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
8917 TTGTTCGAGTCTTACACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
8972 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTATGGAATA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
9027 TTGTTCAAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
9082 TTGTTTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* ** ** *
9137 TTGTTAGAGTCTTATACTCTCTGAAGGAATAAAGAGCAGACACGATTGCTAAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* *
9192 TTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
9247 TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCATACACGATTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
* * *
9302 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGG
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACG-TTTTTGAAGA
*
9357 TTTTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAA-A
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTT-TTGAAGA
* * *
9411 GTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTGTTGAAGA
1 -TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTT-TTGAAGA
** * * *
9467 TTGTTTAAGTCCTATACTCTTTGAAGGAATAGGGAGCGGACACGTTTGTTGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTT-TTGAAGA
*
9522 ----TCGAGTCCTATACTCTCTGAAGGAATAGGGA--ATGA-ACCTGTTTTATGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCA-GACA-C-GTTTT-TGAAGA
* * * * * *
9573 TTGTTTGAGTTTTATACTCCCTGAAGCAGTAGGGAAC-GA-ATC-TATTTTCAGAAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA-CGT-TTTT--GAAGA
* * * * * * * *
9628 TTGTTCAAATCCTATACTCCCTGAAAGAATAGGGAGCGGACATGTTTTCTGGAGA
1 TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTT-TGAAGA
9683 TT
1 TT
9685 TTTCAGGTCT
Statistics
Matches: 677, Mismatches: 70, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.00
50 4 0.01
51 38 0.06
53 2 0.00
54 43 0.06
55 580 0.86
56 6 0.01
57 3 0.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (54 bp):
TTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTTTGAAGA
Found at i:11670 original size:2 final size:2
Alignment explanation
Indices: 11663--11694 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
11653 TGCTATATCG
*
11663 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
11695 AATAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12015 original size:2 final size:2
Alignment explanation
Indices: 11914--12003 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
11904 ATCATATGTA
11914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11956 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11998 AT AT AT
1 AT AT AT
12004 GATTGCTATA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14037 original size:54 final size:54
Alignment explanation
Indices: 13949--14080 Score: 192
Period size: 54 Copynumber: 2.4 Consensus size: 54
13939 CCTTAGACAA
* * *
13949 CCAGACGTCCTCATCACGAAGGAACCGTATTATCTCAAATATCTTTAAAGATGG
1 CCAGATGTCCTCATCACGAAGGAACCGTATTATCTCAAATATCTTCAAAAATGG
* * * *
14003 TCAGATGTCCTCATCACGAAGGTACTGTGTTATCTCAAATATCTTCAAAAATGG
1 CCAGATGTCCTCATCACGAAGGAACCGTATTATCTCAAATATCTTCAAAAATGG
*
14057 CCAGATGGCCTCATCACGAAGGAA
1 CCAGATGTCCTCATCACGAAGGAA
14081 TAATGTCATC
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
CCAGATGTCCTCATCACGAAGGAACCGTATTATCTCAAATATCTTCAAAAATGG
Found at i:14228 original size:54 final size:54
Alignment explanation
Indices: 14142--14272 Score: 217
Period size: 54 Copynumber: 2.4 Consensus size: 54
14132 TTAGACAACT
14142 AGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCC
1 AGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCC
* * * *
14196 AGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATCTCTTTAAAGATGGCT
1 AGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCC
*
14250 AGACATCCTCATCACGAAGGAAC
1 AGACGTCCTCATCACGAAGGAAC
14273 AATGTCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 71 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
AGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCC
Found at i:14408 original size:191 final size:190
Alignment explanation
Indices: 13813--14409 Score: 876
Period size: 191 Copynumber: 3.1 Consensus size: 190
13803 CTTAGACAAC
* * *
13813 CAGACGTCCTCATCACGAAGGAA-TCGTGTTATCTTAAATATCTTTAAAAATGGTTAGATGTCCT
1 CAGATGTCCTCATCACGAAGGAACT-GTGTTATCTCAAATATCTTTAAAAATGGCTAGATGTCCT
13877 CATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCACATCATCCT
65 CATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCACATCATCCT
13942 TAGACAACCAGACGTCCTCATCACGAAGGAACCGTA-TTATCTCAAATATCTTTAAAGATGGT
130 TAGACAA-CAGACGTCCTCATCACGAAGGAACCG-AGTTATCTCAAATATCTTTAAAGATGGT
* * * *
14004 CAGATGTCCTCATCACGAAGGTACTGTGTTATCTCAAATATCTTCAAAAATGGCCAGATGGCCTC
1 CAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTAAAAATGGCTAGATGTCCTC
*
14069 ATCACGAAGGAATAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCACATCATCCTT
66 ATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCACATCATCCTT
* *
14134 AGACAACTAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGC
131 AGACAAC-AGACGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTTAAAGATGGT
* * **
14195 CAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATCTCTTTAAAGATGGCTAGACATCCTC
1 CAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTAAAAATGGCTAGATGTCCTC
* *** * * *
14260 ATCACGAAGGAACAATGTCATCCATTGATTAGAATTCCTCATCATAAAGGAGT-AGCATCATCCT
66 ATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCA-CATCATCCT
* * * *
14324 TAGATAGTCAGATGTCCTCGTCACGAAGGAACCGAGTTATCTCAAATATCTTTAAAGATGGT
130 TAGACA-ACAGACGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTTAAAGATGGT
* *
14386 TATATGTCCTCATCACGAAGGAAC
1 CAGATGTCCTCATCACGAAGGAAC
14410 AATGTCATAC
Statistics
Matches: 367, Mismatches: 34, Indels: 10
0.89 0.08 0.02
Matches are distributed among these distances:
190 2 0.01
191 363 0.99
192 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (190 bp):
CAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTAAAAATGGCTAGATGTCCTC
ATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTCACATCATCCTT
AGACAACAGACGTCCTCATCACGAAGGAACCGAGTTATCTCAAATATCTTTAAAGATGGT
Found at i:14586 original size:12 final size:12
Alignment explanation
Indices: 14569--14594 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14559 TTTCGTCCCG
14569 TTATTATTTATA
1 TTATTATTTATA
14581 TTATTATTTATA
1 TTATTATTTATA
14593 TT
1 TT
14595 GTATTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:16909 original size:21 final size:23
Alignment explanation
Indices: 16879--16921 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
16869 GTTAAAATTG
16879 AATTTGAAT-ATTTT-ATTTTAT
1 AATTTGAATAATTTTAATTTTAT
*
16900 AATTTTAATAATTTTAATTTTA
1 AATTTGAATAATTTTAATTTTA
16922 ATTGAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 5 0.26
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
AATTTGAATAATTTTAATTTTAT
Found at i:19833 original size:21 final size:20
Alignment explanation
Indices: 19807--19846 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
19797 ACCCCCTGAC
19807 TTTTTCTTCTTTCTTATTCTT
1 TTTTTCTTC-TTCTTATTCTT
*
19828 TTTTTCTTCTTCTTTTTCT
1 TTTTTCTTCTTCTTATTCT
19847 AAGTTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTCTTCTTCTTATTCTT
Found at i:21606 original size:13 final size:14
Alignment explanation
Indices: 21590--21664 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 14
21580 AAGTTAACAA
21590 AATA-AATTAAGAC
1 AATATAATTAAGAC
21603 AATATAATTAA-AC
1 AATATAATTAAGAC
*
21616 ACAT-T-A-T-AGAA
1 A-ATATAATTAAGAC
* * *
21627 AAAATAATTAAAAA
1 AATATAATTAAGAC
21641 AATA-AATTAAGAC
1 AATATAATTAAGAC
21654 AATATAATTAA
1 AATATAATTAA
21665 AAATAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
10 2 0.04
11 4 0.08
12 2 0.04
13 20 0.42
14 20 0.42
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (14 bp):
AATATAATTAAGAC
Found at i:21609 original size:15 final size:14
Alignment explanation
Indices: 21586--21664 Score: 53
Period size: 14 Copynumber: 5.9 Consensus size: 14
21576 GCACAAGTTA
21586 ACAAAATAAATTAAG
1 ACAAAAT-AATTAAG
*
21601 ACAATATAATTAA-
1 ACAAAATAATTAAG
* *
21614 AC-ACATTA-T-AG
1 ACAAAATAATTAAG
*
21625 AAAAAATAATTAA-
1 ACAAAATAATTAAG
21638 A-AAAATAAATTAAG
1 ACAAAAT-AATTAAG
*
21652 ACAATATAATTAA
1 ACAAAATAATTAA
21665 AAATAAAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
10 1 0.02
11 2 0.04
12 13 0.26
13 10 0.20
14 14 0.28
15 10 0.20
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (14 bp):
ACAAAATAATTAAG
Found at i:22997 original size:301 final size:301
Alignment explanation
Indices: 22455--23037 Score: 862
Period size: 301 Copynumber: 1.9 Consensus size: 301
22445 ACAACTAATT
* * * * *
22455 AAATAAAGGAGAACGAAATACAAATGAGGAATTTTTTACCTCTGAAGTTGTTGTGAGCAATATAC
1 AAATAAAAGAGAACGAAATACAAATGAGGAATCTTTTACCTCTGAAATTGTTGTAACCAATATAC
* * *
22520 AAAAATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATATTTCCTTCCATACTGTTGTTCCA
66 AAAAATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCACACAGTTGTTCCA
* * *
22585 CAATGATATATACCTCAACTCCTTGCACTTGTATAAGCTGCTGGGAATGATACCAGAAATCTGGT
131 CAATGATAAATACCTCAACTCCTTGCACTTGTATAAACTACTGGGAATGATACCAGAAATCTGGT
* * *
22650 TCCCATCCAACCTTAATACTTGCAATTTAGACATGTTATCAAATATTC-CTGACTCAAGATGGCC
196 TCCCATCCAACCTTAATACTTGCAATTTAGAAAGGTTATCAAATATTCTC-GACTCAAGATGACC
22714 TGCAGTGAGATTGTTAATTATAAGATAACTTTTATGTAATGA
260 TGCAGTGAGATTGTTAATTATAAGATAACTTTTATGTAATGA
* * *
22756 AAATAAAAGAGAACGGAATGCAAATGAGGAATCTTTTACCTTTGAAATTGTTGTAACCAATATAC
1 AAATAAAAGAGAACGAAATACAAATGAGGAATCTTTTACCTCTGAAATTGTTGTAACCAATATAC
* *
22821 AAATATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCACAGAGTTGTTCCA
66 AAAAATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCACACAGTTGTTCCA
* * * * * *
22886 CAATGATAAATACCTCAACTCTTTGCTCTTGTATAAACTACTGGGAATGCTACTAGATATTTGGT
131 CAATGATAAATACCTCAACTCCTTGCACTTGTATAAACTACTGGGAATGATACCAGAAATCTGGT
* * * *
22951 TCCCTTCCAAGCTTAATTCTTGCAATTTAGAAAGGTTATCAAATATTCTCGACTCTAGATGACCT
196 TCCCATCCAACCTTAATACTTGCAATTTAGAAAGGTTATCAAATATTCTCGACTCAAGATGACCT
* * *
23016 GCGGTGAGATTTTTAGTTATAA
261 GCAGTGAGATTGTTAATTATAA
23038 AACAGCTTTA
Statistics
Matches: 249, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
301 248 1.00
302 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (301 bp):
AAATAAAAGAGAACGAAATACAAATGAGGAATCTTTTACCTCTGAAATTGTTGTAACCAATATAC
AAAAATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCACACAGTTGTTCCA
CAATGATAAATACCTCAACTCCTTGCACTTGTATAAACTACTGGGAATGATACCAGAAATCTGGT
TCCCATCCAACCTTAATACTTGCAATTTAGAAAGGTTATCAAATATTCTCGACTCAAGATGACCT
GCAGTGAGATTGTTAATTATAAGATAACTTTTATGTAATGA
Found at i:24973 original size:17 final size:18
Alignment explanation
Indices: 24933--24975 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
24923 AAAATGATCT
*
24933 AGGCCCAAATAACCCAGC
1 AGGCCCAAATAACCCAGA
*
24951 AGGCCCAAATAA-CCTGA
1 AGGCCCAAATAACCCAGA
24968 AGGCCCAA
1 AGGCCCAA
24976 CAAGACCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.40, C:0.35, G:0.19, T:0.07
Consensus pattern (18 bp):
AGGCCCAAATAACCCAGA
Found at i:30784 original size:2 final size:2
Alignment explanation
Indices: 30777--30806 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30767 TTAATCATGC
30777 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
30807 TTAGGGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31729 original size:45 final size:45
Alignment explanation
Indices: 31653--31742 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
31643 TCGAACATCG
* *
31653 AATGCATTTTATGCATCGATGCACATACCATGCATCAATGCACTC
1 AATGCATTTGATGCATCGATGCACATACCATGCATCAATACACTC
* *
31698 AATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATACACTC
1 AATGCATTTGATGCATCGATGCA-CATACCATGCATCAATACACTC
31743 TGGCTGTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 38 0.95
46 2 0.05
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.27
Consensus pattern (45 bp):
AATGCATTTGATGCATCGATGCACATACCATGCATCAATACACTC
Found at i:34109 original size:7 final size:7
Alignment explanation
Indices: 34095--34134 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
34085 ATAATATTGT
34095 GGGTTTA
1 GGGTTTA
*
34102 GAGTTTA
1 GGGTTTA
*
34109 GGGTTCA
1 GGGTTTA
34116 GGGTTTA
1 GGGTTTA
34123 GGGTTTA
1 GGGTTTA
*
34130 AGGTT
1 GGGTT
34135 CAAGTTCTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.17, C:0.03, G:0.40, T:0.40
Consensus pattern (7 bp):
GGGTTTA
Found at i:34120 original size:21 final size:21
Alignment explanation
Indices: 34095--34136 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34085 ATAATATTGT
*
34095 GGGTTTAGAGTTTAGGGTTCA
1 GGGTTTAGAGTTTAAGGTTCA
*
34116 GGGTTTAGGGTTTAAGGTTCA
1 GGGTTTAGAGTTTAAGGTTCA
34137 AGTTCTAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.38
Consensus pattern (21 bp):
GGGTTTAGAGTTTAAGGTTCA
Found at i:36386 original size:43 final size:42
Alignment explanation
Indices: 36324--36674 Score: 236
Period size: 43 Copynumber: 8.3 Consensus size: 42
36314 GTTTGAGAAT
* *
36324 AAAAAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTG
1 AAAAAACGCCGCAAAAGGTC-ATATCTA-TAGCGGCGTTTTTAG
* * * *
36367 AACAAATGCCGCAAAAGGTCGATATCTATATCGGCGTTTTTGG
1 AAAAAACGCCGCAAAAGGTC-ATATCTATAGCGGCGTTTTTAG
* * * * *
36410 AATAAACGCCGCAAAAAGTTATGATATATAGCGGCGTTTCTAG
1 AAAAAACGCCGCAAAAGGTCAT-ATCTATAGCGGCGTTTTTAG
*
36453 AAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCG---TT-G
1 AAAAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTAG
*
36491 ATAAAAACGCCGCAAAAGAG--A-AGGCATATA-CTGGCGTTTTTAG
1 A-AAAAACGCCGCAAAAG-GTCATA-TC-TATAGC-GGCGTTTTTAG
* * * * *
36534 AACAAACGCCGCAAAAGGTCAGACCTATAGCGGTGTTTTTGG
1 AAAAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTAG
* * * * * *
36576 ACACAAACGCCGCAAAAGGTTAGACCTATAACGGCGTTTGT-G
1 A-AAAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTAG
* * * * * *
36618 AACTCAAACGCCGTAAAAAGTCAGACCTATAGCGGCGTTTTTGG
1 AA--AAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTAG
*
36662 ATACAAACGCCGC
1 A-AAAAACGCCGC
36675 TAATTACCTT
Statistics
Matches: 254, Mismatches: 34, Indels: 40
0.77 0.10 0.12
Matches are distributed among these distances:
37 1 0.00
38 5 0.02
39 25 0.10
40 1 0.00
41 2 0.01
42 49 0.19
43 167 0.66
44 3 0.01
45 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.23
Consensus pattern (42 bp):
AAAAAACGCCGCAAAAGGTCATATCTATAGCGGCGTTTTTAG
Found at i:36464 original size:86 final size:84
Alignment explanation
Indices: 36353--36674 Score: 334
Period size: 86 Copynumber: 3.8 Consensus size: 84
36343 CAATATCTAT
* * * * * *
36353 TACGGCGTTTTTTGAACAAATGCCGCAAAAGGTCGATATCTATATCGGCGTTTTTGGA-ATAAAC
1 TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAAC
*
36417 GCCGCAAAAAGTTATGATATA
65 GCCGCAAAAAGTTA-GACATA
* * * * *
36438 TAGCGGCGTTTCTAGAAAAAACGCCGCAAAAGGTCAGATCTATAGCGGCG---TT-GATAAAAAC
1 TA-CGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
* *
36499 GCCGCAAAAGAG-AAGGCATA
65 GCCGCAAAA-AGTTAGACATA
*
36519 TACTGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGTGTTTTTGGACACAAAC
1 TAC-GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
* *
36584 GCCGCAAAAGGTTAGACCTA
65 GCCGCAAAAAGTTAGACATA
* * * *
36604 TAACGGCGTTTGT-GAACTCAAACGCCGTAAAAAGTCAGACCTATAGCGGCGTTTTTGGATACAA
1 T-ACGGCGTTTTTAGAA--CAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAA
36668 ACGCCGC
63 ACGCCGC
36675 TAATTACCTT
Statistics
Matches: 200, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
80 1 0.00
81 50 0.25
82 17 0.09
83 2 0.01
84 6 0.03
85 45 0.22
86 79 0.40
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (84 bp):
TACGGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACG
CCGCAAAAAGTTAGACATA
Found at i:36539 original size:167 final size:166
Alignment explanation
Indices: 36356--36656 Score: 408
Period size: 167 Copynumber: 1.8 Consensus size: 166
36346 TATCTATTAC
* * * * * *
36356 GGCGTTTTTTGAACAAATGCCGCAAAAGGTCGATATCTATATCGGCGTTTTTGGA-ATAAACGCC
1 GGCGTTTTTAGAACAAACGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAACGCC
* * * *
36420 GCAAAAAGTTATGATATATAGCGGCGTTTCTAGAA-AAAACGCCGCAAAAGGTCAGATCTATAGC
65 GCAAAAAGTTA-GACATATAACGGCGTTTCT-GAACAAAACGCCGCAAAAAGTCAGACCTATAGC
36484 GGCGTTGATAAAAACGCCGCAAAAGAGAAGGCATATACT
128 GGCGTTGATAAAAACGCCGCAAAAGAGAAGGCATATACT
*
36523 GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGTGTTTTTGGACACAAACGCCG
1 GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCG
* * * * *
36588 CAAAAGGTTAGACCTATAACGGCGTTTGTGAACTCAAACGCCGTAAAAAGTCAGACCTATAGCGG
66 CAAAAAGTTAGACATATAACGGCGTTTCTGAAC-AAAACGCCGCAAAAAGTCAGACCTATAGCGG
36653 CGTT
130 CGTT
36657 TTTGGATACA
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
165 3 0.03
166 34 0.30
167 78 0.68
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (166 bp):
GGCGTTTTTAGAACAAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACGCCG
CAAAAAGTTAGACATATAACGGCGTTTCTGAACAAAACGCCGCAAAAAGTCAGACCTATAGCGGC
GTTGATAAAAACGCCGCAAAAGAGAAGGCATATACT
Found at i:40022 original size:41 final size:41
Alignment explanation
Indices: 39948--40246 Score: 312
Period size: 41 Copynumber: 7.3 Consensus size: 41
39938 TTGTAAACTT
* * *
39948 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAACGCCACTAAAGTACAAGTCTATA
* * * ** *
39991 ACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
** ** *
40032 GCGGAATTTGTATAAAAACGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * *
40073 GCGGCGTTTGTATAAAAACGCCACTATAGTACATGTGTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * *
40114 ACGGCGTTTGTATAAAAACGCCATTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * *
40155 GCGGCGTTTGTATAAAAATGCCACT-AATTACGAGTCTTTA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
* * * * *
40195 GCGGCGTTTGTATAAAAACGCTACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
40236 GCGGCGTTTGT
1 GCGGCGTTTGT
40247 TGAAAAAACA
Statistics
Matches: 212, Mismatches: 43, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
40 34 0.16
41 166 0.78
42 1 0.00
43 11 0.05
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
Found at i:42873 original size:90 final size:90
Alignment explanation
Indices: 42720--42897 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
42710 CCTAACACAC
* * *
42720 CCTTTTATAACCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAACCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
*
42785 ATTTAATTAATTGAAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
42810 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAACCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
42875 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
42898 TTCGGGATTA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (90 bp):
CCTTTTATAACCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:44148 original size:17 final size:17
Alignment explanation
Indices: 44126--44160 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
44116 AACGTCCATG
44126 TTCAACCAACATAATCT
1 TTCAACCAACATAATCT
44143 TTCAACCAACATAATCT
1 TTCAACCAACATAATCT
44160 T
1 T
44161 AAGGCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (17 bp):
TTCAACCAACATAATCT
Found at i:48552 original size:40 final size:40
Alignment explanation
Indices: 48497--48618 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
48487 TGCAGGTTTA
*
48497 TAATACACTTCGGTGTATATGGTGGGAACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
48537 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
48577 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
48617 TA
1 TA
48619 TACGGTGCAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:48787 original size:47 final size:45
Alignment explanation
Indices: 48696--48821 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
48686 GTAAGCATAC
* *
48696 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
* * *
48740 AAATAAGCTTATGAACTTATGGAATTTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATGGGTA
*
48787 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
48822 AGATTTTATG
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 21 0.30
45 11 0.15
46 1 0.01
47 38 0.54
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:49546 original size:35 final size:35
Alignment explanation
Indices: 49473--49547 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
49463 CATCACGTCC
* **
49473 AGTAAGGCCCTGAGCACACAGTCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
49508 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
49543 AGTAA
1 AGTAA
49548 TCTTCCCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:49652 original size:24 final size:24
Alignment explanation
Indices: 49625--49706 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
49615 CATAATTCAA
*
49625 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
49649 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
49673 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
*
49696 GTCAGGTATCA
1 GTCAAGTATCA
49707 TAACATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.41
24 30 0.59
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:52135 original size:31 final size:30
Alignment explanation
Indices: 52099--52163 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
52089 TCAAAGTTGT
52099 GGTCAACGCTAGTC-AACGGGTCAACGGGTCG
1 GGTCAACG--AGTCGAACGGGTCAACGGGTCG
**
52130 GGTCAACGAGTCGGGTCGGGTCAACGGGTCG
1 GGTCAACGAGTC-GAACGGGTCAACGGGTCG
52161 GGT
1 GGT
52164 TATGACCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.13
31 26 0.87
ACGTcount: A:0.18, C:0.23, G:0.42, T:0.17
Consensus pattern (30 bp):
GGTCAACGAGTCGAACGGGTCAACGGGTCG
Found at i:52146 original size:18 final size:18
Alignment explanation
Indices: 52123--52163 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
52113 AACGGGTCAA
52123 CGGGTCGGGTCAACGAGT
1 CGGGTCGGGTCAACGAGT
*
52141 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGAGT
52159 CGGGT
1 CGGGT
52164 TATGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGAGT
Found at i:52163 original size:13 final size:13
Alignment explanation
Indices: 52115--52146 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
52105 CGCTAGTCAA
*
52115 CGGGTCAACGGGT
1 CGGGTCAACGAGT
52128 CGGGTCAACGAGT
1 CGGGTCAACGAGT
52141 CGGGTC
1 CGGGTC
52147 GGGTCAACGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGAGT
Found at i:53575 original size:18 final size:19
Alignment explanation
Indices: 53552--53587 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53542 TTAAGAAAAT
53552 AAATTTT-AAATCGTTTTC
1 AAATTTTGAAATCGTTTTC
*
53570 AAATTTTGAAATGGTTTT
1 AAATTTTGAAATCGTTTT
53588 AGAAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (19 bp):
AAATTTTGAAATCGTTTTC
Found at i:54208 original size:2 final size:2
Alignment explanation
Indices: 54201--54228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54191 TAAAGTATTC
54201 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
54229 CAGGAGAGTA
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):
AT
Found at i:57338 original size:20 final size:20
Alignment explanation
Indices: 57221--57349 Score: 124
Period size: 20 Copynumber: 6.6 Consensus size: 20
57211 AAATGACCAA
*
57221 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
*
57240 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
57260 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
* *
57279 CCAATTTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
57300 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
57319 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
57339 -AATTTCGCAAC
1 CAAATTCGCAAC
57350 AAGTTTTAGT
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
19 43 0.48
20 45 0.50
21 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:58111 original size:12 final size:12
Alignment explanation
Indices: 58094--58127 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58084 ACCACATTTC
*
58094 CAATATCGAACA
1 CAATATCAAACA
58106 CAATATCAAACA
1 CAATATCAAACA
*
58118 CAATCTCAAA
1 CAATATCAAA
58128 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:60555 original size:18 final size:18
Alignment explanation
Indices: 60532--60567 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
60522 AAGCAAAAAG
*
60532 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
60550 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
60568 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:60919 original size:20 final size:20
Alignment explanation
Indices: 60896--60936 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
60886 GCGTTGCGAT
60896 AGTCAAATTCGCAACACGAA
1 AGTCAAATTCGCAACACGAA
*
60916 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACACGAA
60936 A
1 A
60937 TAAGCAACGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.17, T:0.15
Consensus pattern (20 bp):
AGTCAAATTCGCAACACGAA
Found at i:61283 original size:24 final size:24
Alignment explanation
Indices: 61232--61284 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
61222 TTTCATATGT
* * *
61232 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
61256 AATTTGAGTTTGAATTTTAATATA
1 AATTTGAGTTTGAATTTAAATATA
61280 AATTT
1 AATTT
61285 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:61628 original size:39 final size:39
Alignment explanation
Indices: 61585--61671 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
61575 TCCGATGCTC
61585 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
* * *
61624 ATCAAAATTCAAATCTCATATGGTGCCAAGCAAAAGGAT
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
61663 ATCAAAATC
1 ATCAAAATC
61672 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:62016 original size:14 final size:14
Alignment explanation
Indices: 61997--62036 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
61987 ATAATTCTTA
61997 TTTACAAATCAACT
1 TTTACAAATCAACT
62011 TTTACAAATCAACT
1 TTTACAAATCAACT
62025 TTTACAAATCAA
1 TTTACAAATCAA
62037 TTAATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:63490 original size:21 final size:21
Alignment explanation
Indices: 63466--63561 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
63456 GGCGGGACCA
* *
63466 CTTGAACGATGACAGGGGCCT
1 CTTGAATGATGAGAGGGGCCT
* * * *
63487 CTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGAGAGGGGCCT
63508 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAATGATGAGAGGGGCCT
*
63529 CTTGAATGAT-AGGAGGCGCCT
1 CTTGAATGATGA-GAGGGGCCT
63550 CTTGAATGATGA
1 CTTGAATGATGA
63562 TAAGTGCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
CTTGAATGATGAGAGGGGCCT
Found at i:63544 original size:42 final size:42
Alignment explanation
Indices: 63466--63561 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
63456 GGCGGGACCA
* * * * *
63466 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
* *
63508 CTTCG-ATGATGAGAGGGGCCTCTTGAATGATAGGAGGCGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
63550 CTTGAATGATGA
1 CTTGAATGATGA
63562 TAAGTGCATC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 43 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:65914 original size:22 final size:22
Alignment explanation
Indices: 65886--65942 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
65876 GATGGAGATA
65886 GACGGATTTCGCCGGAAATGGG
1 GACGGATTTCGCCGGAAATGGG
* *
65908 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAAATGGG
*
65930 GACGGATGTCGCC
1 GACGGATTTCGCC
65943 ATAGAGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAAATGGG
Found at i:66089 original size:20 final size:20
Alignment explanation
Indices: 66064--66112 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
66054 GCATGAAAAC
*
66064 ATTTGACTTTCGTGTTACAA
1 ATTTGACTTTCGCGTTACAA
* * *
66084 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTACAA
66104 ATTTGACTT
1 ATTTGACTT
66113 CTGTGTTGCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTACAA
Found at i:66120 original size:20 final size:20
Alignment explanation
Indices: 66064--66123 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
66054 GCATGAAAAC
* *
66064 ATTTGACTT-TCGTGTTACAA
1 ATTTGACTTCT-GTGTTGCGA
*
66084 ATTTGACTATC-GCGTTGCGA
1 ATTTGACT-TCTGTGTTGCGA
66104 ATTTGACTTCTGTGTTGCGA
1 ATTTGACTTCTGTGTTGCGA
66124 TTTACAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 30 0.91
21 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTGACTTCTGTGTTGCGA
Found at i:66221 original size:20 final size:20
Alignment explanation
Indices: 66172--66225 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
66162 CGATTTACAT
66172 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
66192 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
66212 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
66226 TTTGTTGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:66595 original size:31 final size:31
Alignment explanation
Indices: 66524--66601 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
66514 CTTTTAAAAC
**
66524 TTGCAATATAATCCCCCAACATTTAGTCCAT
1 TTGCAATATGGTCCCCCAACATTTAGTCCAT
* *
66555 TTGCAATATGGTCCCTCAACATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCAT
66586 TTGCAATATGGTCCCC
1 TTGCAATATGGTCCCC
66602 GACGTAACTG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCAT
Found at i:71828 original size:86 final size:88
Alignment explanation
Indices: 71679--71844 Score: 273
Period size: 86 Copynumber: 1.9 Consensus size: 88
71669 CATCATCTCT
71679 TCCTCAGTTTGTTTCTTTTTTCGAAATCAAAAAAAAAATCAAACTAAAGCTTTGATCTTCTCTTA
1 TCCTCAGTTTGTTTCTTTTTTCGAAAT-AAAAAAAAAATCAAACTAAAGCTTTGATCTTCTCTTA
71744 GTCCAATCTATATTCTTCTTTTCC
65 GTCCAATCTATATTCTTCTTTTCC
* ** *
71768 TCCTCAGTTTGTTTTTTTTTTCGAAAT-TGAAAAAACTCAAACTAAAG-TTTGATCTTCTCTTAG
1 TCCTCAGTTTGTTTCTTTTTTCGAAATAAAAAAAAAATCAAACTAAAGCTTTGATCTTCTCTTAG
71831 TCCAATCTATATTC
66 TCCAATCTATATTC
71845 CCCATTGACT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
86 30 0.41
87 17 0.23
89 26 0.36
ACGTcount: A:0.29, C:0.20, G:0.08, T:0.43
Consensus pattern (88 bp):
TCCTCAGTTTGTTTCTTTTTTCGAAATAAAAAAAAAATCAAACTAAAGCTTTGATCTTCTCTTAG
TCCAATCTATATTCTTCTTTTCC
Found at i:74330 original size:11 final size:12
Alignment explanation
Indices: 74301--74337 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
74291 ATTTATCATT
74301 TTAAAAACACAC
1 TTAAAAACACAC
74313 TTAAAAACACAC
1 TTAAAAACACAC
74325 TT-AAAACACAC
1 TTAAAAACACAC
74336 TT
1 TT
74338 CTCCCCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.54, C:0.24, G:0.00, T:0.22
Consensus pattern (12 bp):
TTAAAAACACAC
Found at i:74372 original size:41 final size:41
Alignment explanation
Indices: 74327--74410 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
74317 AAACACACTT
74327 AAAACACACTTCTCCCCCTTTTTGTTAAATCAAAAAGATTC
1 AAAACACACTTCTCCCCCTTTTTGTTAAATCAAAAAGATTC
74368 AAAACACACTTCTCCCCCTTTTTGTTAAATCAAAAAGATTC
1 AAAACACACTTCTCCCCCTTTTTGTTAAATCAAAAAGATTC
74409 AA
1 AA
74411 TAAACGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (41 bp):
AAAACACACTTCTCCCCCTTTTTGTTAAATCAAAAAGATTC
Found at i:76630 original size:41 final size:42
Alignment explanation
Indices: 76585--76663 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
76575 ACAGAACCCC
* *
76585 AGGGGGTATCGATTCCC-C-TGTGGGGGATCGGTTCCCTTCAA
1 AGGGGGAATCGATTCCCTCATG-GGGGGATCGATTCCCTTCAA
*
76626 AGGGGGAATCGGTTCCCTCATGGGGGGATCGATTCCCT
1 AGGGGGAATCGATTCCCTCATGGGGGGATCGATTCCCT
76664 CTGCACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 15 0.45
42 16 0.48
43 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.35, T:0.25
Consensus pattern (42 bp):
AGGGGGAATCGATTCCCTCATGGGGGGATCGATTCCCTTCAA
Found at i:76656 original size:20 final size:21
Alignment explanation
Indices: 76606--76664 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
76596 ATTCCCCTGT
76606 GGGGGATCGGTTCCCTTCAAAG
1 GGGGGATCGGTTCCC-TCAAAG
* *
76628 GGGGAATCGGTTCCCTC-ATG
1 GGGGGATCGGTTCCCTCAAAG
*
76648 GGGGGATCGATTCCCTC
1 GGGGGATCGGTTCCCTC
76665 TGCACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 14 0.42
ACGTcount: A:0.15, C:0.25, G:0.36, T:0.24
Consensus pattern (21 bp):
GGGGGATCGGTTCCCTCAAAG
Done.