Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005963.1 Hibiscus syriacus cultivar Beakdansim tig00014009_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: 72544
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:828 original size:74 final size:74
Alignment explanation
Indices: 700--1172 Score: 422
Period size: 74 Copynumber: 6.4 Consensus size: 74
690 ACATATCCGA
*
700 TAGGTAGTTTAATGTAATAGGTAGTGCCTA--TTTTTTTTACCGTTTACATTATTAACAACCTTC
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTACCGTTTACATTATTAACAACCTTC
763 AAAAACTGG
66 AAAAACTGG
* * **
772 TAGGTATTTTAATGT-ATAGGTAGCACCTATTTTTTTTTTTACATTTTACATTATTAACAACCTT
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTTTTACCGTTTACATTATTAACAACCTT
*
836 CAAAAAAATCGG
65 C-AAAAACT-GG
* * *
848 TATGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTTTACCGTTTACATTATTAGCAACCT
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTA--TTTTTTTTTTACCGTTTACATTATTAACAACCT
* *
913 T-AAAAAATCGT
64 TCAAAAACT-GG
* * * * * ** *
924 TAAGTATTTTAATGTAA-ATGTAGCGCTTA-TTTTATTTTACCGTTTACATTATTAGTAATCTTT
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTACCGTTTACATTATTAACAA-CCTT
* *
987 AAATAAAC-GA
65 CAA-AAACTGG
*
997 TAGGTAGTTTAA--T-ATAGGTAGTGCCTA--TTTTTTTTACCGTTTACATTATTAGTA-AACCT
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTACCGTTTACATTATTA--ACAACCT
1056 TCAAAAAATCT-G
64 TC-AAAAA-CTGG
* * * * *
1068 TA-GTAGTTTAATGTAATAGGTATCACATA-TTTTTTTTTACCGTTTACATTATTAGCAACTTTC
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTACCGTTTACATTATTAACAACCTTC
* *
1131 AAAAAAATTGA
66 --AAAAACTGG
* *
1142 TAGGTA-TTTAATATAATAGGTAGCGCTTATT
1 TAGGTAGTTTAATGTAATAGGTAGCGCCTATT
1173 ATATTTCTGG
Statistics
Matches: 334, Mismatches: 42, Indels: 47
0.79 0.10 0.11
Matches are distributed among these distances:
70 39 0.12
71 29 0.09
72 42 0.13
73 31 0.09
74 84 0.25
75 23 0.07
76 41 0.12
77 13 0.04
78 32 0.10
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (74 bp):
TAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTTTACCGTTTACATTATTAACAACCTTC
AAAAACTGG
Found at i:1721 original size:19 final size:20
Alignment explanation
Indices: 1677--1721 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
1667 ATATTTTAAC
1677 CAAAATATGAGATATTTTCCT
1 CAAAATATGAGATATTTT-CT
1698 C-AAATA-GAGATATATTT-T
1 CAAAATATGAGATAT-TTTCT
1716 CAAAAT
1 CAAAAT
1722 TTGTTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 8 0.36
21 1 0.05
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (20 bp):
CAAAATATGAGATATTTTCT
Found at i:12637 original size:23 final size:23
Alignment explanation
Indices: 12595--12656 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
12585 ATAGGGCAGA
*
12595 GGGAATCGATACCCCC-TTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
*
12617 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCTTTGAAG
12640 GGGAATCGATTCCCCCT
1 GGGAATCGATTCCCCCT
12657 AGGGTTCTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAATCGATTCCCCCTTTGAAG
Found at i:19651 original size:21 final size:21
Alignment explanation
Indices: 19625--19664 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19615 CCCCCTTTGA
*
19625 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
19646 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
19665 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:19707 original size:8 final size:8
Alignment explanation
Indices: 19694--19718 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19684 GGCAAGAACA
19694 CCCAAAAC
1 CCCAAAAC
19702 CCCAAAAC
1 CCCAAAAC
19710 CCCAAAAC
1 CCCAAAAC
19718 C
1 C
19719 TATTCTGCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (8 bp):
CCCAAAAC
Found at i:28243 original size:86 final size:86
Alignment explanation
Indices: 28136--28297 Score: 252
Period size: 86 Copynumber: 1.9 Consensus size: 86
28126 CAAGGGGAAA
* * * *
28136 AAAGTACCCACCTTCGTTAATTTAAATAGCGTCATTTACAATCGTTTGATGCAAACATGAAGGAT
1 AAAGTACACACCTTCATTAATTTAAATAGCGTCATTTACAATCGCTTGATGCAAACATAAAGGAT
28201 AGCCAGACATACTCGGGGGGG
66 AGCCAGACATACTCGGGGGGG
* *
28222 AAAGTACACACCTTTATTAATTTAAATAGCGTCATTTACAATCGCTTGATGCATACATAAAGGAT
1 AAAGTACACACCTTCATTAATTTAAATAGCGTCATTTACAATCGCTTGATGCAAACATAAAGGAT
* *
28287 AGTCGGACATA
66 AGCCAGACATA
28298 AAGAAGATAG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (86 bp):
AAAGTACACACCTTCATTAATTTAAATAGCGTCATTTACAATCGCTTGATGCAAACATAAAGGAT
AGCCAGACATACTCGGGGGGG
Found at i:33833 original size:3 final size:3
Alignment explanation
Indices: 33825--33864 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
33815 ATAAAACTAC
33825 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
33865 TTTTTCGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35516 original size:21 final size:19
Alignment explanation
Indices: 35488--35533 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
35478 TCATTGAATC
35488 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
35508 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
35527 ACTTAGT
1 A-TTAGT
35534 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:38808 original size:22 final size:19
Alignment explanation
Indices: 38783--38825 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 19
38773 GATGTATTGA
38783 ATGAGTATTAATGAGTTCAAGT
1 ATGAGTA-T-ATGAGTT-AAGT
38805 ATGAGTATATGAGTTAAGT
1 ATGAGTATATGAGTTAAGT
38824 AT
1 AT
38826 ATGTAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 1 0.05
22 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (19 bp):
ATGAGTATATGAGTTAAGT
Found at i:39020 original size:45 final size:46
Alignment explanation
Indices: 38924--39027 Score: 108
Period size: 45 Copynumber: 2.3 Consensus size: 46
38914 CCCTATGAAG
**
38924 GGGTATCAATACCCCCTCTTGAACGAAAAATTATAGAACGTCAGTA
1 GGGTATCAATACCCCCTCTTGAACGAAAAATTATAGAACGTCAACA
* *
38970 TGGTATCAATACCCCC-C-TGAA-GATAAAAATT-TCAGAATGTCAACA
1 GGGTATCAATACCCCCTCTTGAACG--AAAAATTAT-AGAACGTCAACA
*
39015 GGGTATCTATACC
1 GGGTATCAATACC
39028 ATAGACAGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
43 1 0.02
44 5 0.10
45 28 0.57
46 15 0.31
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (46 bp):
GGGTATCAATACCCCCTCTTGAACGAAAAATTATAGAACGTCAACA
Found at i:39077 original size:20 final size:20
Alignment explanation
Indices: 39012--39067 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
39002 CAGAATGTCA
39012 ACAGGGTATCTATACCATAG
1 ACAGGGTATCTATACCATAG
39032 ACAGGGTATCTATACCATAG
1 ACAGGGTATCTATACCATAG
39052 ACAGGGTATCTATACC
1 ACAGGGTATCTATACC
39068 TCAGTTAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (20 bp):
ACAGGGTATCTATACCATAG
Found at i:39885 original size:21 final size:21
Alignment explanation
Indices: 39859--39936 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
39849 GGGTTTCATA
39859 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
* *
39880 GGTCCTTCGGGATAATACAGC
1 GGTCCTTCGGGACAATACAGT
* *
39901 GGTCTTTCAGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
* * *
39922 AGTTCTTTGGGACAA
1 GGTCCTTCGGGACAA
39937 ATTTCATATG
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGT
Found at i:48532 original size:21 final size:19
Alignment explanation
Indices: 48504--48549 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
48494 TCATTGAATC
48504 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
48524 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
48543 ACTTAGT
1 A-TTAGT
48550 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:48997 original size:131 final size:130
Alignment explanation
Indices: 48760--49121 Score: 510
Period size: 131 Copynumber: 2.8 Consensus size: 130
48750 TTGGTGGATG
* *
48760 ACACGGTTCCTACGTGATGAGGACGA-TAGGTTATTTAGGGGTGACACAGCTCCTACGTGATGAG
1 ACACGGTTCCTACGTGATGAGGACAACT-GGTTATCTAGGGGTGACACAGCTCCTACGTGAT-AG
* * * *
48824 GAGGTCTAGTCAGGGGATGACATGGTTCCTACATGATAAGGATGGCATGCCATCTTTAGGGATGA
64 GAGGTATGGTCAGGGGATGACATAGTTCCTACATGATAAGGATGGCATGCCATATTTAGGGATGA
48889 TA
129 TA
* *
48891 ACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAAGGGTGACACAACTCCTACGTGATAAGG
1 ACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACACAGCTCCTACGTGAT-AGG
* * *
48956 AGGTATGGTCAGGGGATGACATAGTTTCTACATGATGAGGATGGTATGCCATATTTAGGGATGAT
65 AGGTATGGTCAGGGGATGACATAGTTCCTACATGATAAGGATGGCATGCCATATTTAGGGATGAT
49021 A
130 A
* * * *
49022 ACACGGTTCCTACGTGATCATGAAAACTGGTTATCTAGGGGTGACACGGCTCCTACGTGATAGGA
1 ACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACACAGCTCCTACGTGATAGGA
* * * * *
49087 GGTATGGTCGGGGGATAACACAGTTCATACGTGAT
66 GGTATGGTCAGGGGATGACATAGTTCCTACATGAT
49122 GAAGACGACA
Statistics
Matches: 206, Mismatches: 24, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
130 33 0.16
131 172 0.83
132 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (130 bp):
ACACGGTTCCTACGTGATGAGGACAACTGGTTATCTAGGGGTGACACAGCTCCTACGTGATAGGA
GGTATGGTCAGGGGATGACATAGTTCCTACATGATAAGGATGGCATGCCATATTTAGGGATGATA
Found at i:49290 original size:31 final size:30
Alignment explanation
Indices: 49218--49290 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
49208 ACAAAATTTA
49218 TTTC-AAGAAAACGACTCAAAGATGGTTTTG
1 TTTCAAAGAAAACGACTCAAAGAT-GTTTTG
49248 TTTCAAGAGAAATA-GACTCAAAGAT-TTTGTG
1 TTTCAA-AGAAA-ACGACTCAAAGATGTTT-TG
49279 TTTCCAAAGAAA
1 TTT-CAAAGAAA
49291 CTGCCTCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
30 7 0.18
31 11 0.29
32 19 0.50
33 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (30 bp):
TTTCAAAGAAAACGACTCAAAGATGTTTTG
Found at i:49397 original size:36 final size:34
Alignment explanation
Indices: 49243--49405 Score: 104
Period size: 36 Copynumber: 4.7 Consensus size: 34
49233 TCAAAGATGG
*
49243 TTTTGTTTCAAGAGAAATAGACTCAAAGAT-T---
1 TTTTGTTTCAA-AGAAACAGACTCAAAGATGTAAA
* * * * *
49274 TTGTGTTTCCAAAGAAACTGCCTCAAGGGA-GACAAA
1 TTTTGTTT-CAAAGAAACAGACTCAA-AGATG-TAAA
* * ***
49310 ATTTGTTTCAATGAAAC-GATCTCAAAGATGTTTG
1 TTTTGTTTCAAAGAAACAGA-CTCAAAGATGTAAA
*
49344 TTTTGTTTCAAGGGAAACAGACTCAAAGATGGTAAA
1 TTTTGTTTCAA-AGAAACAGACTCAAAGAT-GTAAA
49380 TTTTGTTTCCAAAGAAACAGACTCAA
1 TTTTGTTT-CAAAGAAACAGACTCAA
49406 GGATTTTTCT
Statistics
Matches: 98, Mismatches: 21, Indels: 21
0.70 0.15 0.15
Matches are distributed among these distances:
31 18 0.18
32 5 0.05
34 13 0.13
35 28 0.29
36 31 0.32
37 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (34 bp):
TTTTGTTTCAAAGAAACAGACTCAAAGATGTAAA
Found at i:49459 original size:62 final size:62
Alignment explanation
Indices: 49381--49589 Score: 278
Period size: 62 Copynumber: 3.3 Consensus size: 62
49371 GATGGTAAAT
* *
49381 TTTGTTTCCAAAGAAACAGACTCAAGGATTTTTCTCAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCGAGAGACAAAA
*
49443 TTTGTTT-CAAATGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAA
1 TTTGTTTCCAAA-GAAACAAACTCAAAGA--TTTTTCTCAAAAGAAACTGTCTC--GAGAGAC-A
49507 AAA
60 AAA
* * * *
49510 TTTGTTTCCAGAGAAACATACTCAAAGATTTTTCTTAAAAGAAACTGTCTCGAGAGAAAAAA
1 TTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCGAGAGACAAAA
49572 TTTGTTT-CAAGAGAAACA
1 TTTGTTTCCAA-AGAAACA
49590 TCTCAAATGA
Statistics
Matches: 130, Mismatches: 9, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
61 6 0.05
62 39 0.30
63 6 0.05
64 22 0.17
65 21 0.16
66 7 0.05
67 26 0.20
68 3 0.02
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (62 bp):
TTTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTCAAAAGAAACTGTCTCGAGAGACAAAA
Found at i:49727 original size:33 final size:33
Alignment explanation
Indices: 49667--49747 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
49657 TTCACATCAA
** *
49667 GATGTTGAAT-CCCCAAAGATGCTCCAATATTC
1 GATGTTGAATGCTTCAAAGATGCCCCAATATTC
49699 GATGTTGAATGCTTCAAAGATGCCCCAATATTC
1 GATGTTGAATGCTTCAAAGATGCCCCAATATTC
*
49732 GATGTTGATTGCTTCA
1 GATGTTGAATGCTTCA
49748 GCACTAATTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 10 0.23
33 34 0.77
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (33 bp):
GATGTTGAATGCTTCAAAGATGCCCCAATATTC
Found at i:66927 original size:30 final size:30
Alignment explanation
Indices: 66839--66929 Score: 130
Period size: 30 Copynumber: 3.1 Consensus size: 30
66829 GAAGGACCTA
* * * *
66839 TCCAGATGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
66868 TCCAGAGGTCATACAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
66898 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
66928 TC
1 TC
66930 TATAAGGACC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
29 14 0.25
30 41 0.75
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:67940 original size:19 final size:19
Alignment explanation
Indices: 67916--67966 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
67906 TATTACTGGG
67916 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
67935 ATGCATCGATGCATGCCTT
1 ATGCATCGATGCATGCCTT
67954 ATGCATCGATGCA
1 ATGCATCGATGCA
67967 CTAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCATGCCTT
Found at i:68068 original size:64 final size:64
Alignment explanation
Indices: 67935--68091 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
67925 TGCATGCCTT
* * * * **
67935 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACATATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATAAG
*
67999 ATGCATCGATGCACTACATATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACATATGCATCGATGCACGAATTGCATTCGATGT-TTCATTATTAATAAG
68062 ACTGCATCGATGCACTACCA-ATGCATCGAT
1 A-TGCATCGATGCACTA-CATATGCATCGAT
68092 ACACCTTCAA
Statistics
Matches: 82, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
63 2 0.02
64 73 0.89
65 7 0.09
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACATATGCATCGATGCACGAATTGCATTCGATGTTTCATTATTAATAAG
Found at i:69511 original size:3 final size:3
Alignment explanation
Indices: 69503--69536 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
69493 GTAATAAATA
*
69503 AAC AAC AAC AAC AAC AAT AAC AAC AAC -AC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
69537 TAAAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.68, C:0.29, G:0.00, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:70568 original size:21 final size:22
Alignment explanation
Indices: 70507--70615 Score: 75
Period size: 22 Copynumber: 4.9 Consensus size: 22
70497 GAAACTAAAA
70507 ATATATGAAAATA-AATAAATAGT
1 ATATAT-AAAATATAA-AAATAGT
*
70530 ATAAATAAAATAATAAAAATA-T
1 ATATATAAAAT-ATAAAAATAGT
70552 ATATATAAAATAT-AAAAT-GT
1 ATATATAAAATATAAAAATAGT
* * *
70572 ATGTATAATATA-ATAAAATACT
1 ATATATAAAATATA-AAAATAGT
*
70594 AAATAGTAATAATATAATAAAT
1 ATATA-TAA-AATATAA-AAAT
70616 GAAAAATAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
20 16 0.24
21 7 0.10
22 20 0.29
23 14 0.21
24 6 0.09
25 5 0.07
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (22 bp):
ATATATAAAATATAAAAATAGT
Found at i:70578 original size:22 final size:22
Alignment explanation
Indices: 70507--70589 Score: 82
Period size: 22 Copynumber: 3.8 Consensus size: 22
70497 GAAACTAAAA
*
70507 ATATATGAAAATAA-ATAAATAGT
1 ATATAT-AAAATAATAAAAATA-T
*
70530 ATAAATAAAATAATAAAAATAT
1 ATATATAAAATAATAAAAATAT
*
70552 ATATATAAAAT-AT-AAAATGT
1 ATATATAAAATAATAAAAATAT
* *
70572 ATGTATAATATAATAAAA
1 ATATATAAAATAATAAAA
70590 TACTAAATAG
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
20 15 0.29
21 4 0.08
22 21 0.41
23 11 0.22
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
ATATATAAAATAATAAAAATAT
Found at i:70586 original size:42 final size:45
Alignment explanation
Indices: 70507--70589 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 45
70497 GAAACTAAAA
70507 ATATATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATAT
1 ATATATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATAT
* ** *
70552 ATATAT-AAAATATA-AAAT-GTATGTATAATATAATAAAA
1 ATATATGAAAATAAATAAATAGTATAAATAAAATAATAAAA
70590 TACTAAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 17 0.50
43 4 0.12
44 7 0.21
45 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (45 bp):
ATATATGAAAATAAATAAATAGTATAAATAAAATAATAAAAATAT
Found at i:70754 original size:3 final size:3
Alignment explanation
Indices: 70746--70782 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
70736 AATATAGATA
70746 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT ATAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A
70783 GGAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:70809 original size:22 final size:24
Alignment explanation
Indices: 70768--70811 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
70758 AATAATAATA
*
70768 ATAATATATATAATAGGAAAAAAT
1 ATAATATACATAATAGGAAAAAAT
70792 ATAATATACATAA-A-GAAAAA
1 ATAATATACATAATAGGAAAAA
70812 TGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 1 0.05
24 12 0.63
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (24 bp):
ATAATATACATAATAGGAAAAAAT
Found at i:70832 original size:10 final size:9
Alignment explanation
Indices: 70819--70856 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
70809 AAATGAAAAA
70819 AAATTATAAT
1 AAATTA-AAT
70829 AAA-TAAAT
1 AAATTAAAT
70837 AAATTAAATT
1 AAATTAAA-T
70847 AAATTAAAT
1 AAATTAAAT
70856 A
1 A
70857 TATAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:70845 original size:23 final size:23
Alignment explanation
Indices: 70819--70863 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
70809 AAATGAAAAA
70819 AAATTATAA-TAAATAAATAAATT
1 AAATTA-AATTAAATAAATAAATT
*
70842 AAATTAAATTAAATATATAAAT
1 AAATTAAATTAAATAAATAAAT
70864 ATATACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATTAAATTAAATAAATAAATT
Found at i:71314 original size:37 final size:37
Alignment explanation
Indices: 71273--71362 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 37
71263 GGATCATATC
71273 TTTAGGAGTTTAAATAATAG-AAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAA-AACTCTATCCTATT
* ** *
71310 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
71347 TTTAGGAGTTTGAAAT
1 TTTAGGAGTTT-AAAT
71363 CCTAGTAGGA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 41 0.89
38 5 0.11
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCCTATT
Found at i:71678 original size:36 final size:36
Alignment explanation
Indices: 71631--71705 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
71621 CTCGTTTAAA
71631 GACCTTGGATCGGAATCGAACTCAAAAATCTTCATT
1 GACCTTGGATCGGAATCGAACTCAAAAATCTTCATT
71667 GACCTTGGATCGGAATCGAACTCAAAAATCTTCATT
1 GACCTTGGATCGGAATCGAACTCAAAAATCTTCATT
71703 GAC
1 GAC
71706 AGATAGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (36 bp):
GACCTTGGATCGGAATCGAACTCAAAAATCTTCATT
Found at i:72473 original size:104 final size:106
Alignment explanation
Indices: 72144--72544 Score: 672
Period size: 106 Copynumber: 3.8 Consensus size: 106
72134 GCATTGTTCC
* *
72144 GAGTCTAATATCCTCCG-T-TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
72207 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
72248 GAGTCCAATATCCTTCGCCTGTGAAGTTG-AATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
*
72312 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
72354 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
72418 CCAGCGGT-CCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
72458 GAGTCCAATATCCTTCGTTGTGAAGTTGGAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
72522 CCA-CGGTCCCTTCGTCGTGAAGT
66 CCAGCGGTCCCTTCGTCGTGAAGT
Statistics
Matches: 281, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
103 6 0.02
104 120 0.43
105 26 0.09
106 121 0.43
107 8 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:72512 original size:210 final size:208
Alignment explanation
Indices: 72143--72544 Score: 684
Period size: 210 Copynumber: 1.9 Consensus size: 208
72133 AGCATTGTTC
*
72143 CGAGTCTAATATCCTCCGTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 CGAGTCCAATATCCTCCGTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
72208 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCCTGTGAA
66 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCCTGTGAA
*
72273 GTTGAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
131 GTTGAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAACCA-CGGTCCCTTCGTCGTGAAGTT
72338 GAACTTGCGTTGTCT
194 GAACTTGCGTTGTCT
* *
72353 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACA
1 CGAGTCCAATATCCTCCG-T-TGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
*
72417 ACCAGCGGT-CCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG-TTGTG
64 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCCTGTG
72480 AAGTTGGAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCACGGTCCCTTCGTCGTGAAGT
129 AAGTT-GAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCACGGTCCCTTCGTCGTGAAGT
Statistics
Matches: 183, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
208 20 0.11
209 22 0.12
210 89 0.49
211 16 0.09
212 36 0.20
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (208 bp):
CGAGTCCAATATCCTCCGTTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCCTGTGAA
GTTGAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAACCACGGTCCCTTCGTCGTGAAGTTGA
ACTTGCGTTGTCT
Done.