Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006278.1 Hibiscus syriacus cultivar Beakdansim tig00014976_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: 92874
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1269 original size:59 final size:60
Alignment explanation
Indices: 1101--1271 Score: 152
Period size: 59 Copynumber: 2.9 Consensus size: 60
1091 AATATGATAC
** * * *
1101 TACTTTGTTGAGTCTATCGACTATTAAAAGTTATAAAATAATCTCTCAAT-TATAGAGAGT
1 TACTTTGTTGAGTCCCTCGACTATT-AAAGTTATAAAATAATCACTGACTATATAGAGAGT
* * * * * ***
1161 TATTTTTGTTGAGT-CCTCAACTATAAAAGATACAAAATGGCCACTTGACTATA-AG-GAGT
1 TA-CTTTGTTGAGTCCCTCGACTATTAAAGTTATAAAATAATCAC-TGACTATATAGAGAGT
*
1220 TACTTTGTTGAGTCCCTCGACTATTAAATTTATAAAATAATCACATGACTAT
1 TACTTTGTTGAGTCCCTCGACTATTAAAGTTATAAAATAATCAC-TGACTAT
1272 TTATTATATT
Statistics
Matches: 84, Mismatches: 23, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
58 10 0.12
59 48 0.57
60 14 0.17
61 12 0.14
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (60 bp):
TACTTTGTTGAGTCCCTCGACTATTAAAGTTATAAAATAATCACTGACTATATAGAGAGT
Found at i:1814 original size:28 final size:29
Alignment explanation
Indices: 1750--1821 Score: 103
Period size: 28 Copynumber: 2.5 Consensus size: 29
1740 AACCTTGATT
1750 AAATATTTGATAATTTTAATTTCCCAAAA
1 AAATATTTGATAATTTTAATTTCCCAAAA
* *
1779 AAGTATTTGATAATTTT-ATTAT-TCAAAA
1 AAATATTTGATAATTTTAATT-TCCCAAAA
1807 AAATATTTGATAATT
1 AAATATTTGATAATT
1822 CTATATAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (29 bp):
AAATATTTGATAATTTTAATTTCCCAAAA
Found at i:3233 original size:39 final size:39
Alignment explanation
Indices: 3106--3233 Score: 98
Period size: 39 Copynumber: 3.2 Consensus size: 39
3096 ACGATGACTA
*
3106 GATGTCCTCAACATGACGGAACAACGTTGT-CCACAGATTT
1 GATGTCCTCAACATGACGGAACAA-GTT-TCCCACATATTT
* * * * * ** * * *
3146 GATGTCCTGAA-GTGAAGGATCAAATCTTCTAAAGATGACTA
1 GATGTCCTCAACATGACGGAACAAGT-TTC-CCACAT-ATTT
3187 GATGTCCTCAACATGACGGAACAAGTTTCCCACATATTT
1 GATGTCCTCAACATGACGGAACAAGTTTCCCACATATTT
3226 GATGTCCT
1 GATGTCCT
3234 GGAGTGAAGG
Statistics
Matches: 62, Mismatches: 21, Indels: 11
0.66 0.22 0.12
Matches are distributed among these distances:
38 2 0.03
39 20 0.32
40 15 0.24
41 15 0.24
42 10 0.16
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (39 bp):
GATGTCCTCAACATGACGGAACAAGTTTCCCACATATTT
Found at i:3249 original size:80 final size:81
Alignment explanation
Indices: 3098--3269 Score: 294
Period size: 80 Copynumber: 2.1 Consensus size: 81
3088 AGAGTGTGAC
3098 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
1 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
3163 GATCAAATCTTCTAAA
66 GATCAAATCTTCTAAA
* *
3179 GATGACTAGATGTCCTCAACATGACGGAACAA-GTT-TCCCACATATTTGATGTCCTGGAGTGAA
1 GATGACTAGATGTCCTCAACATGACGGAACAACGTTGT-CCACAGATTTGATGTCCTGAAGTGAA
3242 GGATCAAATCTTCTAAA
65 GGATCAAATCTTCTAAA
*
3259 GATGATTAGAT
1 GATGACTAGAT
3270 CTCTTCAATA
Statistics
Matches: 87, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
79 1 0.01
80 54 0.62
81 32 0.37
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (81 bp):
GATGACTAGATGTCCTCAACATGACGGAACAACGTTGTCCACAGATTTGATGTCCTGAAGTGAAG
GATCAAATCTTCTAAA
Found at i:7271 original size:19 final size:19
Alignment explanation
Indices: 7243--7279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
7233 CACTTATGTT
7243 ACATATCACA-TTCATATC
1 ACATATCACATTTCATATC
7261 ACATGATCACATTTCATAT
1 ACAT-ATCACATTTCATAT
7280 AACACTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 6 0.35
20 7 0.41
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (19 bp):
ACATATCACATTTCATATC
Found at i:7961 original size:21 final size:23
Alignment explanation
Indices: 7937--7987 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
7927 GTTCCCCATA
7937 TATCGATAACCTCCA-CATA-GG
1 TATCGATAACCTCCACCATATGG
*
7958 TATCGAT-ACCTCTACCATATGG
1 TATCGATAACCTCCACCATATGG
7980 TATCGATA
1 TATCGATA
7988 CTATTCATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 11 0.42
22 9 0.35
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (23 bp):
TATCGATAACCTCCACCATATGG
Found at i:11512 original size:21 final size:22
Alignment explanation
Indices: 11472--11523 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
11462 TGTTCCCCAT
*
11472 GTATCGATACCCTCCACATA-A
1 GTATCGATACCCTACACATAGA
*
11493 GTATCGATACCTCTAC-CATAGG
1 GTATCGATACC-CTACACATAGA
11515 GTATCGATA
1 GTATCGATA
11524 ATTTTCATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
GTATCGATACCCTACACATAGA
Found at i:18654 original size:20 final size:22
Alignment explanation
Indices: 18626--18671 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
18616 TCGTTAAATA
*
18626 TTTATCTAAAACATT-AT-TTT
1 TTTAGCTAAAACATTAATGTTT
18646 TTTAGCTAAAACATTAATGTTT
1 TTTAGCTAAAACATTAATGTTT
18668 TTTA
1 TTTA
18672 ATATTTCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 2 0.09
22 7 0.30
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (22 bp):
TTTAGCTAAAACATTAATGTTT
Found at i:26740 original size:56 final size:55
Alignment explanation
Indices: 26668--26852 Score: 171
Period size: 56 Copynumber: 3.4 Consensus size: 55
26658 TGCTTGAATT
* * *
26668 AATGATTGAGCACCTCTATGTTTTAATCGACAAACTGATACCTTTGTACAGTTAAA
1 AATGATTGAGCACCTCTATGCTTTAATCGACAAACT-ATACCTCTGTGCAGTTAAA
* * * * * * ***
26724 AATGATTGAGCACCTCTGTGCTTTAGTCTAGAATCTATTACCTCAGTGC--TTTGT
1 AATGATTGAGCACCTCTATGCTTTAATCGACAAACTA-TACCTCTGTGCAGTTAAA
* * *
26778 AATGATTGAGCACCT-TTTGCTTCAATCGACAAACTAACACCTCTGTGCAGTTAAA
1 AATGATTGAGCACCTCTATGCTTTAATCGACAAACT-ATACCTCTGTGCAGTTAAA
26833 AATGACTT-AGCACCTCTATG
1 AATGA-TTGAGCACCTCTATG
26853 TAATTAAAAA
Statistics
Matches: 99, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
53 23 0.23
54 18 0.18
55 15 0.15
56 43 0.43
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.34
Consensus pattern (55 bp):
AATGATTGAGCACCTCTATGCTTTAATCGACAAACTATACCTCTGTGCAGTTAAA
Found at i:26969 original size:137 final size:136
Alignment explanation
Indices: 26719--26985 Score: 299
Period size: 137 Copynumber: 2.0 Consensus size: 136
26709 CTTTGTACAG
* * *
26719 TTAAAAATGATTGAGCACCTCTGTGCTTTAGTCTAGAATCTATTACCTCAGTGCTTTGTAATGAT
1 TTAAAAATGATTGAGCACCTCTGTGCTTTAGTCTAGAATCTATCACCTCAGTGCTTTGCAATAAT
* * *
26784 TGAGCACCTTTTGCTTCAATCGACAAACTAACACCTCTGTGCAGTTAAAAATGACTTAGCACCTC
66 TGAGCACCTTTTACTTCAAACGACAAACTAACACCTCTGTGCAGTTAAAAATGA-TTAACACCTC
26849 TATGTAA
130 TATGTAA
* * *
26856 TTAAAAATGACTT-AGCACCTCTGTG-TTTCATTTTAGAATCTGA-CACCTCTGTGCTTTGCAAT
1 TTAAAAATGA-TTGAGCACCTCTGTGCTTT-AGTCTAGAATCT-ATCACCTCAGTGCTTTGCAAT
* * ** * ** * *
26918 AATTGATCACCTTTATACTTCAAACTAGGATCTGGCACCTCTGTGC-TTTAAAACTGATTAACAC
63 AATTGAGCACCTTT-TACTTCAAACGACAAACTAACACCTCTGTGCAGTTAAAAATGATTAACAC
26982 CTCT
127 CTCT
26986 GTGCATTAAT
Statistics
Matches: 108, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
136 13 0.12
137 69 0.64
138 26 0.24
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (136 bp):
TTAAAAATGATTGAGCACCTCTGTGCTTTAGTCTAGAATCTATCACCTCAGTGCTTTGCAATAAT
TGAGCACCTTTTACTTCAAACGACAAACTAACACCTCTGTGCAGTTAAAAATGATTAACACCTCT
ATGTAA
Found at i:27099 original size:28 final size:27
Alignment explanation
Indices: 27042--27106 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
27032 GAGCACCTCA
*
27042 GTGCTACAATCGACAATTAAACAACTTT
1 GTGCT-CAATCGACAATTAAACAACGTT
** *
27070 GTGCTCAATTCGACAATTATGCACCGTT
1 GTGCTCAA-TCGACAATTAAACAACGTT
27098 GTGCATCAA
1 GTGC-TCAA
27107 ACAGGCAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.77
29 4 0.13
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (27 bp):
GTGCTCAATCGACAATTAAACAACGTT
Found at i:32569 original size:189 final size:188
Alignment explanation
Indices: 32356--32745 Score: 699
Period size: 189 Copynumber: 2.1 Consensus size: 188
32346 ACACTTAAAA
*
32356 AACCCGACCCGACACGAACAAAATAAAGTTTCATCCGACCTGATCCAAATATATGAATTAGAAAT
1 AACCCGACCCGACACGAACAAAATAAAGTTTCATCCGACCAGATCCAAATATATGAATTAGAAAT
32421 CCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCC
66 CCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCC
32486 GACCCGACCTGAATTATATATATTTTCAGGTCGGTCCGGTTTTTTTCACCCTAAACCCG
131 GACCCGACCTGAATTATATATATTTTCAGGTCGGTCCGGTTTTTTT-ACCCTAAACCCG
* **
32545 AACCCGACCCGACTCGAACAAAATAAAGTTTCATCCGACCAGATCTGAATATATGAATTAGAAAT
1 AACCCGACCCGACACGAACAAAATAAAGTTTCATCCGACCAGATCCAAATATATGAATTAGAAAT
* *
32610 CCAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCT
66 CCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCC
* *
32675 GACCCGACCTGAATTATATATATTTTCGGGTCGGTCTGGTTTTTTTACCCTAAACCCG
131 GACCCGACCTGAATTATATATATTTTCAGGTCGGTCCGGTTTTTTTACCCTAAACCCG
32733 AACCCGACCCGAC
1 AACCCGACCCGAC
32746 CTGAATATAT
Statistics
Matches: 193, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
188 25 0.13
189 168 0.87
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (188 bp):
AACCCGACCCGACACGAACAAAATAAAGTTTCATCCGACCAGATCCAAATATATGAATTAGAAAT
CCAACCCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCC
GACCCGACCTGAATTATATATATTTTCAGGTCGGTCCGGTTTTTTTACCCTAAACCCG
Found at i:33887 original size:28 final size:27
Alignment explanation
Indices: 33839--33892 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
33829 AACCACTAAA
33839 ATAAATTTAATAATTAATTTATAATTAC
1 ATAAATTTAATAATTAATTTA-AATTAC
* *
33867 ATAAATTTTATATATT-TTTTAAATTA
1 ATAAATTTAATA-ATTAATTTAAATTA
33893 TAGTTAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.22
28 15 0.65
29 3 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATAAATTTAATAATTAATTTAAATTAC
Found at i:34006 original size:2 final size:2
Alignment explanation
Indices: 34001--34033 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
33991 TCATATATTC
34001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34034 ATCATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:37141 original size:20 final size:20
Alignment explanation
Indices: 37118--37156 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
37108 AAATATAAAC
*
37118 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
37138 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
37157 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:38050 original size:15 final size:16
Alignment explanation
Indices: 38025--38056 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
38015 GTTTAGTTGT
38025 TGTTATTTTTTTTCTC
1 TGTTATTTTTTTTCTC
38041 TGTT-TTTTTTTTCTC
1 TGTTATTTTTTTTCTC
38056 T
1 T
38057 CCAGTTCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.78
Consensus pattern (16 bp):
TGTTATTTTTTTTCTC
Found at i:38570 original size:3 final size:3
Alignment explanation
Indices: 38562--38664 Score: 188
Period size: 3 Copynumber: 34.3 Consensus size: 3
38552 TTAATATATT
* *
38562 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38610 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38658 TAA TAA T
1 TAA TAA T
38665 GATATGGGTA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39233 original size:113 final size:113
Alignment explanation
Indices: 38988--39771 Score: 1210
Period size: 113 Copynumber: 6.9 Consensus size: 113
38978 AGAATTATGC
* * * *
38988 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
39053 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
39100 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCCTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
39165 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
39213 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAATTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** *
39278 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
* *
39326 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * **
39391 TATGAACTTTCTCTGGAAAAGCTGATCCATTAAATGATGGATTCATAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
39439 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** *
39504 TATGAACTCGAACTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
*
39552 AAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
39617 TATGAACTTTCTCTGGAAAAGATGATCCATCAATTGACGAATTCATGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
* *
39665 AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
39730 TATGAACTTTTTCTGGAAAAGCTGATCCATCAAATGATGGAT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGAT
39772 CTGAATCTTT
Statistics
Matches: 606, Mismatches: 65, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
112 67 0.11
113 539 0.89
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
Found at i:40485 original size:84 final size:83
Alignment explanation
Indices: 40387--40901 Score: 942
Period size: 83 Copynumber: 6.2 Consensus size: 83
40377 TTCATCTTTT
* * *
40387 AATTCCAACGATTGGTTCTGTCC-AACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCT
1 AATT-CAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
40451 ATTGAGCAAATTCATCTTCCA
64 ATTG-GCAAATTCATCTTCCA
*
40472 AATTCACTGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
40537 TGAGCAAATTCATCTTCCA
66 TG-GCAAATTCATCTTCCA
40556 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
*
40621 TAGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
40639 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
40704 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
40722 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
40787 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
40805 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
40870 TGGCAAATTCATCTTCCA
66 TGGCAAATTCATCTTCCA
40888 AATTCAATGATTGG
1 AATTCAATGATTGG
40902 ACTAAGATAT
Statistics
Matches: 422, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
83 280 0.66
84 138 0.33
85 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
AATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
TGGCAAATTCATCTTCCA
Found at i:42044 original size:17 final size:17
Alignment explanation
Indices: 42022--42103 Score: 82
Period size: 17 Copynumber: 4.9 Consensus size: 17
42012 CTTGACCCCC
42022 TTTCTT-TTTTTCTTCTT
1 TTTCTTCTTTTTCTT-TT
*
42039 TTTCTTTTTTTTCTTTT
1 TTTCTTCTTTTTCTTTT
*
42056 TTT-TTCTTTTCTCCTTT
1 TTTCTTCTTTT-TCTTTT
*
42073 TTT-TTCTTCTT-TTTT
1 TTTCTTCTTTTTCTTTT
42088 TTTCTTTCTTTTTCTT
1 TTTC-TTCTTTTTCTT
42104 CAAGCATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
15 6 0.11
16 7 0.13
17 32 0.58
18 10 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTCTTCTTTTTCTTTT
Found at i:42050 original size:10 final size:10
Alignment explanation
Indices: 42026--42103 Score: 81
Period size: 10 Copynumber: 8.0 Consensus size: 10
42016 ACCCCCTTTC
42026 TTTTTTTC-T
1 TTTTTTTCTT
*
42035 TCTTTTTC-T
1 TTTTTTTCTT
42044 TTTTTTTCTT
1 TTTTTTTCTT
42054 TTTTTTTCTT
1 TTTTTTTCTT
**
42064 TTCTCCTT-TT
1 TT-TTTTTCTT
*
42074 TTTTCTTCTT
1 TTTTTTTCTT
42084 TTTTTTTCTT
1 TTTTTTTCTT
*
42094 TCTTTTTCTT
1 TTTTTTTCTT
42104 CAAGCATAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
9 19 0.32
10 37 0.63
11 3 0.05
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:42052 original size:26 final size:25
Alignment explanation
Indices: 42022--42100 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 25
42012 CTTGACCCCC
42022 TTTCTTTTTTTCTTCTTTTTCTTTTT
1 TTTCTTTTTTT-TTCTTTTTCTTTTT
42048 TTTCTTTTTTTTTCTTTTCTCCTTTTT
1 TTTCTTTTTTTTTCTTTT-T-CTTTTT
42075 TTTCTTCTTTTTTT-TTCTTTCTTTTT
1 TTTCTT-TTTTTTTCTT-TTTCTTTTT
42101 CTTCAAGCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
25 7 0.14
26 18 0.37
27 15 0.31
28 9 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTCTTTTTTTTTCTTTTTCTTTTT
Found at i:42073 original size:13 final size:12
Alignment explanation
Indices: 42057--42102 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
42047 TTTTCTTTTT
42057 TTTTCTTTTCTCC
1 TTTT-TTTTCTCC
*
42070 TTTTTTTTCTTC
1 TTTTTTTTCTCC
42082 TTTTTTTT-T-C
1 TTTTTTTTCTCC
42092 TTTCTTTTTCT
1 TTT-TTTTTCT
42103 TCAAGCATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.13
11 6 0.20
12 16 0.53
13 4 0.13
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCTCC
Found at i:52716 original size:23 final size:22
Alignment explanation
Indices: 52689--52737 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
52679 ACTTGCAAAT
52689 AAAATAA-AACATATAAATATTAG
1 AAAATAATAA-ATATAAAT-TTAG
*
52712 AAAATAATAAATATAAATTTTG
1 AAAATAATAAATATAAATTTAG
52734 AAAA
1 AAAA
52738 GAAAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 15 0.62
24 2 0.08
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATAATAAATATAAATTTAG
Found at i:53438 original size:13 final size:14
Alignment explanation
Indices: 53408--53468 Score: 63
Period size: 13 Copynumber: 4.4 Consensus size: 14
53398 TGAAAATATT
53408 TAAAATATAAAAAA
1 TAAAATATAAAAAA
*
53422 TAAAATA-AAACAA
1 TAAAATATAAAAAA
53435 TAAAATACTAAAACAA
1 TAAAATA-TAAAA-AA
* *
53451 T-ATATTTAAAAAA
1 TAAAATATAAAAAA
53464 TAAAA
1 TAAAA
53469 AAATGAAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 15 0.39
14 14 0.37
15 6 0.16
16 3 0.08
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAAATATAAAAAA
Found at i:53843 original size:157 final size:157
Alignment explanation
Indices: 53657--53969 Score: 522
Period size: 157 Copynumber: 2.0 Consensus size: 157
53647 TATTTATTAA
**
53657 AATTAAAGGATTAAATCTGTATTTATCCTAAATATATTATTTTAATATGAAGGACTAAAAT-AAA
1 AATTAAAGGATTAAATCTGTATTTATCCTAAATATATTATTTTAATAAAAAGGACTAAAATGAAA
* * *
53721 AAAATTAAAATTCGAAGACTGAATTAAAAATATTATAAATTAATTTAGTGACTAAAATATAAAA-
66 AAAATTAAAATTCAAAGACTGAATTAAAAATATTAT-AATTAAGTTAGTGACCAAAATATAAAAT
53785 TTACAAGTTAGGAGGACTGCGGACGGGG
130 TTACAAGTTAGGAGGACTGCGGACGGGG
53813 AATTAAAGGATTAAATCTGTCATTTATCCTAAATATATTATTTTAATAAAAAGGACTAAAATGAA
1 AATTAAAGGATTAAATCTGT-ATTTATCCTAAATATATTATTTTAATAAAAAGGACTAAAATGAA
* * *
53878 TAAAATTAAAATTCAAAGACTGAATTAAAATTATTATAATTAGGTTAGTGACCAAAATATAAAAT
65 AAAAATTAAAATTCAAAGACTGAATTAAAAATATTATAATTAAGTTAGTGACCAAAATATAAAAT
53943 TTACAAGTTAGGAGGACTGCGGACGGG
130 TTACAAGTTAGGAGGACTGCGGACGGG
53970 TTTAATTATT
Statistics
Matches: 146, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
156 20 0.14
157 63 0.43
158 63 0.43
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (157 bp):
AATTAAAGGATTAAATCTGTATTTATCCTAAATATATTATTTTAATAAAAAGGACTAAAATGAAA
AAAATTAAAATTCAAAGACTGAATTAAAAATATTATAATTAAGTTAGTGACCAAAATATAAAATT
TACAAGTTAGGAGGACTGCGGACGGGG
Found at i:54482 original size:17 final size:15
Alignment explanation
Indices: 54451--54481 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54441 GTTTAGTTGT
54451 TGTTATTTTTTTCTC
1 TGTTATTTTTTTCTC
54466 TGTTATTTTTTTCTC
1 TGTTATTTTTTTCTC
54481 T
1 T
54482 CCAGTCTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (15 bp):
TGTTATTTTTTTCTC
Found at i:55573 original size:2 final size:2
Alignment explanation
Indices: 55566--55600 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
55556 TTTGAGTTTA
55566 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55601 TAAATAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55657 original size:28 final size:27
Alignment explanation
Indices: 55599--55679 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 27
55589 TAATATATAT
*
55599 ATTAAATAATTAAT--ATTTTTAATTA
1 ATTAATTAATTAATCAATTTTTAATTA
*
55624 ATTTAATTAATTAATCAATTTTGAATTGA
1 A-TTAATTAATTAATCAATTTTTAATT-A
*
55653 ATTAATT-GTTAATCAAATTTTTAATTA
1 ATTAATTAATTAATC-AATTTTTAATTA
55680 TTATCAATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 1 0.02
26 12 0.26
27 7 0.15
28 25 0.53
29 2 0.04
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (27 bp):
ATTAATTAATTAATCAATTTTTAATTA
Found at i:58024 original size:14 final size:14
Alignment explanation
Indices: 58005--58036 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
57995 CAAAATAAAA
58005 TAATAACATTTATT
1 TAATAACATTTATT
58019 TAATAACATTTATT
1 TAATAACATTTATT
58033 TAAT
1 TAAT
58037 GTTATACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATAACATTTATT
Found at i:59762 original size:3 final size:3
Alignment explanation
Indices: 59754--59788 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
59744 ATATGTAAGT
59754 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
59789 ATTAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:59775 original size:14 final size:14
Alignment explanation
Indices: 59756--59784 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
59746 ATGTAAGTTA
59756 ATAATAATAATAAT
1 ATAATAATAATAAT
59770 ATAATAATAATAAT
1 ATAATAATAATAAT
59784 A
1 A
59785 ATAAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:59794 original size:17 final size:17
Alignment explanation
Indices: 59754--59787 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
59744 ATATGTAAGT
59754 TAATAATAATAATAATA
1 TAATAATAATAATAATA
59771 TAATAATAATAATAATA
1 TAATAATAATAATAATA
59788 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAATAATAATA
Found at i:60126 original size:43 final size:40
Alignment explanation
Indices: 60089--60164 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
60079 CTGGTTATCT
* * *
60089 ATGGTTGACATGGCTCCTACGTGATGAAGAGATCTGGTCG
1 ATGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCG
* *
60129 GTGGATGACACGGCTCATACGTGATGAAGAGTTCTG
1 ATGGATGACACGGCTCATACGTGATGAAGAGATCTG
60165 ACCATCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (40 bp):
ATGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCG
Found at i:60222 original size:29 final size:30
Alignment explanation
Indices: 60189--60284 Score: 126
Period size: 29 Copynumber: 3.3 Consensus size: 30
60179 TAATGATTTC
60189 AAAAGAAA-ATGACTCAAAGATGATGTTTT
1 AAAAGAAACATGACTCAAAGATGATGTTTT
* *
60218 AAAAGAAACA-GATTCAAAGATGATGTTTC
1 AAAAGAAACATGACTCAAAGATGATGTTTT
*
60247 AAAAGAAACAT-ACTCAAAGATGATTTTGTT
1 AAAAGAAACATGACTCAAAGATGATGTT-TT
*
60277 AAGAGAAA
1 AAAAGAAA
60285 TTGTCTCAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 49 0.84
30 9 0.16
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.25
Consensus pattern (30 bp):
AAAAGAAACATGACTCAAAGATGATGTTTT
Found at i:60751 original size:36 final size:35
Alignment explanation
Indices: 60635--60754 Score: 101
Period size: 36 Copynumber: 3.5 Consensus size: 35
60625 AAGATAATTT
**
60635 TTTGTTTCATGAGAAA-AGGTCTCAAGGAAAATAAG
1 TTTGTTTCAAAAGAAACA-GTCTCAAGGAAAATAAG
* * *
60670 ATTTGTTTTAAGAGAAAC-GATCTC-A--AAAAT-TG
1 -TTTGTTTCAAAAGAAACAG-TCTCAAGGAAAATAAG
*
60702 -TTGTTTCATAAGAAACAGTCTCAAGGAAAATAAG
1 TTTGTTTCAAAAGAAACAGTCTCAAGGAAAATAAG
60736 CTTTGTTTCAAAAGAAACA
1 -TTTGTTTCAAAAGAAACA
60755 TATTGAAAGA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
30 17 0.25
31 2 0.03
32 1 0.01
33 10 0.15
34 1 0.01
35 2 0.03
36 34 0.51
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (35 bp):
TTTGTTTCAAAAGAAACAGTCTCAAGGAAAATAAG
Found at i:60986 original size:37 final size:37
Alignment explanation
Indices: 60920--61018 Score: 155
Period size: 37 Copynumber: 2.7 Consensus size: 37
60910 AAAAAATGTA
** *
60920 TCAAACGAGATGAAAA-TTGTTTTGAGAGAAATTATC
1 TCAAACGAGACAAAAATTTGTTTTAAGAGAAATTATC
*
60956 TCAAACGAGACAAAAATTTGTTTTAAGAGAAATTGTC
1 TCAAACGAGACAAAAATTTGTTTTAAGAGAAATTATC
60993 TCAAACGAGACAAAAATTTGTTTTAA
1 TCAAACGAGACAAAAATTTGTTTTAA
61019 AATTCTCAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 14 0.24
37 44 0.76
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (37 bp):
TCAAACGAGACAAAAATTTGTTTTAAGAGAAATTATC
Found at i:61132 original size:38 final size:37
Alignment explanation
Indices: 61072--61151 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
61062 TTGTTTTTCG
*
61072 AGAAATTGTCTCAAACGAGACAAAATTTATTTTTCAAA
1 AGAAATTGTCTCAAACGAGACAAAATTT-TGTTTCAAA
* * * * * *
61110 AGAAGTTGTCTCTAGCGCGACAATATTTTGTTTCAAG
1 AGAAATTGTCTCAAACGAGACAAAATTTTGTTTCAAA
61147 AGAAA
1 AGAAA
61152 CAACATCAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
37 11 0.32
38 23 0.68
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (37 bp):
AGAAATTGTCTCAAACGAGACAAAATTTTGTTTCAAA
Found at i:65575 original size:37 final size:38
Alignment explanation
Indices: 65520--65603 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
65510 TGGTAACCAA
65520 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
65557 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
65594 -GTTGAAAAAT
1 CTTTGAAAAAT
65604 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:66256 original size:2 final size:2
Alignment explanation
Indices: 66249--66313 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
66239 AGCTTTATTG
66249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66291 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
66314 TGGGTATACA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69129 original size:31 final size:30
Alignment explanation
Indices: 69094--69186 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
69084 TGATGAAAAA
*
69094 TAACACAAGCA-AATGAGAAAAAAT-AAGTTAG
1 TAACACAAACACAA-GAG-AAAAATGAA-TTAG
*
69125 TAACACAAACACCAGAGAAAAATGAATTAG
1 TAACACAAACACAAGAGAAAAATGAATTAG
* *
69155 TAACACAAACACCAGAGAAAAATGAGTTAG
1 TAACACAAACACAAGAGAAAAATGAATTAG
69185 TA
1 TA
69187 CAAATGATAA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
30 41 0.72
31 15 0.26
32 1 0.02
ACGTcount: A:0.56, C:0.14, G:0.15, T:0.15
Consensus pattern (30 bp):
TAACACAAACACAAGAGAAAAATGAATTAG
Found at i:69155 original size:30 final size:30
Alignment explanation
Indices: 69112--69186 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
69102 GCAAATGAGA
69112 AAAAAT-AAGTTAGTAACACAAACACCAGAG
1 AAAAATGAA-TTAGTAACACAAACACCAGAG
69142 AAAAATGAATTAGTAACACAAACACCAGAG
1 AAAAATGAATTAGTAACACAAACACCAGAG
*
69172 AAAAATGAGTTAGTA
1 AAAAATGAATTAGTA
69187 CAAATGATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
30 41 0.95
31 2 0.05
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.16
Consensus pattern (30 bp):
AAAAATGAATTAGTAACACAAACACCAGAG
Found at i:72707 original size:3 final size:3
Alignment explanation
Indices: 72699--72748 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
72689 ATATATAAGT
*
72699 TAA TAA TAA TAA TAA T-A TAAA TAA TAA TAA TAA T-A TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
72743 TAA TAA
1 TAA TAA
72749 ATTAAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:80203 original size:4 final size:4
Alignment explanation
Indices: 80194--80224 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
80184 TTCAACTATG
80194 TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TAT
80225 ACATGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:85685 original size:22 final size:19
Alignment explanation
Indices: 85660--85704 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
85650 TAAAATTTTG
85660 AGTAAAAAACGTATTTATGAAC
1 AGTAAAAAACG-A--TATGAAC
*
85682 AGTAAAATACGATATGAAC
1 AGTAAAAAACGATATGAAC
85701 AGTA
1 AGTA
85705 CCGTATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
21 1 0.05
22 10 0.45
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (19 bp):
AGTAAAAAACGATATGAAC
Found at i:86634 original size:18 final size:18
Alignment explanation
Indices: 86608--86642 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
86598 ATTGAATATT
*
86608 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
86626 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
86643 GTATATGTCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:86658 original size:22 final size:22
Alignment explanation
Indices: 86624--86670 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
86614 GAATGACCAC
* *
86624 TATGTCTCGAAGGACCACTGTA
1 TATGTCCCAAAGGACCACTGTA
*
86646 TATGTCCCAAAGGACCATTGTA
1 TATGTCCCAAAGGACCACTGTA
86668 TAT
1 TAT
86671 CCCTCGAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (22 bp):
TATGTCCCAAAGGACCACTGTA
Found at i:88369 original size:94 final size:95
Alignment explanation
Indices: 88148--88350 Score: 232
Period size: 95 Copynumber: 2.1 Consensus size: 95
88138 AGGTGTTACA
* * * ** *
88148 AGTATTGATACCATGGTAAGGGTATTGATACCAGG-TATCATCGAACCTAATTTTGGTATCGATA
1 AGTATCGATACTATGGTAAGGGTATCGATACTGGGCCA-CATCGAACCTAATTTTGGTATCGATA
* * *
88212 CCATATAGGGGTATTAGTACCATAGTATAGT
65 CCAGATAGGGGTATGAGTACCATAGTAGAGT
* * *
88243 AGTATTGATACTATGGTAAGGGTATCGATACTGGGCCACATCGAATCTAATTTTGTTATCGATAC
1 AGTATCGATACTATGGTAAGGGTATCGATACTGGGCCACATCGAACCTAATTTTGGTATCGATAC
** *
88308 TGGA-AGGGGTATCGA-TACCATAGTAGGGT
66 CAGATAGGGGTAT-GAGTACCATAGTAGAGT
88337 AGTATCGATACTAT
1 AGTATCGATACTAT
88351 TGTGGGAGTA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
94 33 0.36
95 58 0.63
96 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (95 bp):
AGTATCGATACTATGGTAAGGGTATCGATACTGGGCCACATCGAACCTAATTTTGGTATCGATAC
CAGATAGGGGTATGAGTACCATAGTAGAGT
Found at i:89179 original size:59 final size:59
Alignment explanation
Indices: 88690--89164 Score: 718
Period size: 59 Copynumber: 8.0 Consensus size: 59
88680 GATTACCAAA
* * **
88690 AGGGCACTACGTGTGCTAAAATGTCAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
88749 AAGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
88808 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAACTTT-CATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAA-TTTCCATAT
* *
88867 TGGGCACTTCGTGTGTTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
88926 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
88985 AGGGAACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATAAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * *
89044 AGGGGGGCACTTCGTATCCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTATAT
1 A---GGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * * *
89106 AGGGCGCTTCTTGTGCTAAAATGATAAGAAATTCATACTAATTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
89165 GGGAAATAAT
Statistics
Matches: 385, Mismatches: 26, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
58 3 0.01
59 328 0.85
60 3 0.01
62 51 0.13
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Done.