Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009121.1 Hibiscus syriacus cultivar Beakdansim tig00112611_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: 272059
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:208024 original size:4 final size:4
Alignment explanation
Indices: 208015--208045 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
208005 TAATACATCT
*
208015 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
208046 TATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:208024 original size:12 final size:12
Alignment explanation
Indices: 208007--208045 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
207997 AGAAAAATTA
208007 ATACATCTATAC
1 ATACATCTATAC
*
208019 ATACATATATAC
1 ATACATCTATAC
208031 ATACATAC-ATAC
1 ATACAT-CTATAC
208043 ATA
1 ATA
208046 TATATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.31
Consensus pattern (12 bp):
ATACATCTATAC
Found at i:208074 original size:25 final size:25
Alignment explanation
Indices: 208043--208150 Score: 73
Period size: 25 Copynumber: 4.4 Consensus size: 25
208033 ACATACATAC
* * *
208043 ATATATATATATATAATGATATAAG
1 ATATATATAAAAATAATAATATAAG
*
208068 ATATATATAAAAATAATAATATAAT
1 ATATATATAAAAATAATAATATAAG
* * *
208093 ATAAATAAAAAAAGGAAT-ATAGTAA-
1 ATATATATAAAAA-TAATAATA-TAAG
*
208118 ATAAATAAATAAAAAT-ATAAT-TAA-
1 AT--ATATATAAAAATAATAATATAAG
208142 ATATATATA
1 ATATATATA
208151 TATAAGGGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
22 6 0.09
24 5 0.08
25 39 0.59
26 8 0.12
27 8 0.12
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (25 bp):
ATATATATAAAAATAATAATATAAG
Found at i:208094 original size:23 final size:23
Alignment explanation
Indices: 208043--208138 Score: 70
Period size: 23 Copynumber: 4.1 Consensus size: 23
208033 ACATACATAC
* * *
208043 ATATATATATATATAATGATATAA
1 ATATATATAAAAATAATAATAT-A
208067 GATATATATAAAAATAATAATATA
1 -ATATATATAAAAATAATAATATA
* *
208091 ATATAAATAAAAA-AAGGAATATA
1 ATATATATAAAAATAA-TAATATA
* * *
208114 GTAAATA-AATAAATAAAAATATA
1 ATATATATAA-AAATAATAATATA
208137 AT
1 AT
208139 TAAATATATA
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 4 0.07
23 32 0.55
24 3 0.05
25 19 0.33
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (23 bp):
ATATATATAAAAATAATAATATA
Found at i:209664 original size:110 final size:110
Alignment explanation
Indices: 209467--209725 Score: 332
Period size: 110 Copynumber: 2.4 Consensus size: 110
209457 AGTATTGTTC
* * *
209467 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTC----TGAAACTGGGAAATTGTTTGTT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAATTGTTTGTT
* * * *
209528 GATAGCCAGCCGCCTCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
66 GACAACCAGCCGCCCCTTCGCTGTGAAGTTAAGCTTGTGTTGTCT
* * *
209573 CGAGTTCAATATTCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACT-GAAAAGTTGTTTGT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAA-TTGTTTGT
* *
209637 TGACAATCAGCCGCCCCTTCGTTGTGAAGTTAAGCTTGTGTTGTCT
65 TGACAACCAGCCGCCCCTTCGCTGTGAAGTTAAGCTTGTGTTGTCT
* *
209683 TGAGTCCAATATCCCTT-GCTGTGAAGTTGAAATTGGCTCTGAA
1 CGAGTCCAATAT-CCTTCGTTGTGAAGTTGAAATTGGCTCTGAA
209726 ACTGGGAAGC
Statistics
Matches: 130, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
106 34 0.26
109 4 0.03
110 89 0.68
111 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (110 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATGAAACTGGAAAATTGTTTGTT
GACAACCAGCCGCCCCTTCGCTGTGAAGTTAAGCTTGTGTTGTCT
Found at i:210610 original size:65 final size:67
Alignment explanation
Indices: 210458--210624 Score: 230
Period size: 65 Copynumber: 2.5 Consensus size: 67
210448 CATGAAAATG
* **
210458 GTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAAGAGAA
1 GTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAA
210523 ACT
65 ACT
* *
210526 GTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGA-TTT-TGTTTCAAGGGAAA
1 GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAA
210589 CT
66 CT
* * * *
210591 GTCTCAAGAGAGACGAAATTTGTTTCAAGAGAAA
1 GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
210625 CTGTCTCAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
65 44 0.49
66 3 0.03
67 25 0.28
68 17 0.19
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (67 bp):
GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTGTTTCAAGAGAAA
CT
Found at i:210625 original size:36 final size:36
Alignment explanation
Indices: 210573--210691 Score: 166
Period size: 36 Copynumber: 3.3 Consensus size: 36
210563 ATTCAAAGAT
*
210573 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
210609 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
210645 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
210682 TTTGTTTCAA
1 TTTGTTTCAA
210692 ATAAAACATA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 42 0.58
37 30 0.42
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:210670 original size:37 final size:36
Alignment explanation
Indices: 210585--210676 Score: 130
Period size: 37 Copynumber: 2.5 Consensus size: 36
210575 TGTTTCAAGG
* * * *
210585 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
210621 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
210658 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
210677 TGAAATTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 23 0.46
37 27 0.54
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:212395 original size:69 final size:69
Alignment explanation
Indices: 212280--212417 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
212270 CTCTCTCTCT
* *
212280 TGATGCTCTATTATCTTCGAGTGGAGTGAATCAGTGATTCAGAAATGATTGTGCTTGATCAATCT
1 TGATGCTCTATGATCTTCGAGTGAAGTGAATCAGTGATTCAGAAATGATTGTGCTTGATCAATCT
212345 CATA
66 CATA
**
212349 TGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTC-GAAAATGATTGTGCTTGATCAATC
1 TGATGCTCTATGATCTTCGAGTGAAGTGAATCAGTGATTCAG-AAATGATTGTGCTTGATCAATC
212413 TCATA
65 TCATA
212418 GTTTGAATCT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.36
Consensus pattern (69 bp):
TGATGCTCTATGATCTTCGAGTGAAGTGAATCAGTGATTCAGAAATGATTGTGCTTGATCAATCT
CATA
Found at i:212517 original size:13 final size:13
Alignment explanation
Indices: 212488--212565 Score: 108
Period size: 13 Copynumber: 6.0 Consensus size: 13
212478 TTTTTCTTCA
212488 ATTTTC-CTTTGTT
1 ATTTTCTCTTT-TT
212501 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
212513 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
212526 ATTTTCTCTTTTT
1 ATTTTCTCTTTTT
212539 ATTTTCTCTTTGCTT
1 ATTTTCTCTTT--TT
212554 -TTTTCTCTTTTT
1 ATTTTCTCTTTTT
212566 TTCTCTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
12 9 0.15
13 40 0.66
14 10 0.16
15 2 0.03
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.76
Consensus pattern (13 bp):
ATTTTCTCTTTTT
Found at i:212530 original size:26 final size:26
Alignment explanation
Indices: 212488--212565 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 26
212478 TTTTTCTTCA
212488 ATTTTC-CTTTGTTTTTTCTCTTTTT
1 ATTTTCTCTTTGTTTTTTCTCTTTTT
212513 ATTTTCTCTTT-TTATTTTCTCTTTTT
1 ATTTTCTCTTTGTT-TTTTCTCTTTTT
212539 ATTTTCTCTTTGCTTTTTTCTCTTTTT
1 ATTTTCTCTTTG-TTTTTTCTCTTTTT
212566 TTCTCTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
25 8 0.16
26 27 0.55
27 12 0.24
28 2 0.04
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.76
Consensus pattern (26 bp):
ATTTTCTCTTTGTTTTTTCTCTTTTT
Found at i:212576 original size:26 final size:26
Alignment explanation
Indices: 212495--212577 Score: 107
Period size: 26 Copynumber: 3.2 Consensus size: 26
212485 TCAATTTTCC
212495 TTTGTTTTTTCTCTTTTTATTTTCTCT
1 TTTGTTTTTTCTCTTTTTATTTTCT-T
* *
212522 TTT-TATTTTCTCTTTTTATTTTCTC
1 TTTGTTTTTTCTCTTTTTATTTTCTT
*
212547 TTTGCTTTTTTCTCTTTTT-TTCTCTT
1 TTTG-TTTTTTCTCTTTTTATTTTCTT
212573 TTTGT
1 TTTGT
212578 ACTGATTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.08
26 29 0.59
27 16 0.33
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTGTTTTTTCTCTTTTTATTTTCTT
Found at i:215769 original size:18 final size:18
Alignment explanation
Indices: 215748--215782 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
215738 TATTAATGGA
215748 GTAAAA-AAATTTAAAAAG
1 GTAAAAGAAA-TTAAAAAG
215766 GTAAAAGAAATTAAAAA
1 GTAAAAGAAATTAAAAA
215783 TGAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (18 bp):
GTAAAAGAAATTAAAAAG
Found at i:215922 original size:18 final size:18
Alignment explanation
Indices: 215895--215955 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 18
215885 TGATATTAAG
215895 AAAA-AAAATAATAGAAA
1 AAAATAAAATAATAGAAA
*
215912 AAAATAAAATAA-AG-TA
1 AAAATAAAATAATAGAAA
* *
215928 AAAATATAATATATATAAA
1 AAAATAAAATA-ATAGAAA
*
215947 TAAATAAAA
1 AAAATAAAA
215956 ACAAAAATAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 11 0.32
17 7 0.21
18 8 0.24
19 8 0.24
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
AAAATAAAATAATAGAAA
Found at i:216116 original size:25 final size:27
Alignment explanation
Indices: 216068--216118 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
216058 ATACATACAT
* *
216068 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
216095 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
216119 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:216121 original size:23 final size:23
Alignment explanation
Indices: 216068--216132 Score: 51
Period size: 25 Copynumber: 2.7 Consensus size: 23
216058 ATACATACAT
* *
216068 ATATATATATATATATAATGATATA
1 ATATATATA-ATA-AAAATAATATA
*
216093 AGATATATATAATAAAAATAATATA
1 ATATAT--ATAATAAAAATAATATA
*
216118 ATATAAATAA-AAAAA
1 ATATATATAATAAAAA
216133 GGAATGTAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.15
23 4 0.12
25 18 0.55
26 3 0.09
27 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATATATAATAAAAATAATATA
Found at i:216166 original size:21 final size:21
Alignment explanation
Indices: 216101--216166 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
216091 TAAGATATAT
*
216101 ATAATAAAAATAATATAATATAA
1 ATAA-AAAAAGAATATAAT-TAA
* *
216124 ATAAAAAAAGGAATGT-AGTAA
1 ATAAAAAAA-GAATATAATTAA
216145 ATAAATAAAA-AATATAATTAA
1 ATAAA-AAAAGAATATAATTAA
216166 A
1 A
216167 AATATATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 10 0.29
23 8 0.23
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (21 bp):
ATAAAAAAAGAATATAATTAA
Found at i:218872 original size:2 final size:2
Alignment explanation
Indices: 218865--218914 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
218855 TTAAAATGGA
* * * * *
218865 AT AT AT AT AA AT AT AT AC AT AT AC AT AT AT AT GT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218907 AT AT AT AT
1 AT AT AT AT
218915 TCTTGTTTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:220900 original size:20 final size:18
Alignment explanation
Indices: 220859--220922 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 18
220849 AAAATATTAA
220859 ATTTATTATT-A-TTATT
1 ATTTATTATTCATTTATT
220875 ATTTTATTATTCATTTGATT
1 A-TTTATTATTCATTT-ATT
* *
220895 CATTTAATATTTATTTATT
1 -ATTTATTATTCATTTATT
*
220914 ATTTTTTAT
1 ATTTATTAT
220923 CTAATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 9 0.23
18 8 0.21
19 5 0.13
20 15 0.38
21 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATTATTCATTTATT
Found at i:225396 original size:106 final size:106
Alignment explanation
Indices: 225210--225719 Score: 851
Period size: 106 Copynumber: 4.8 Consensus size: 106
225200 GACAAAGGGG
225210 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
*
225275 TCAACTTCACCGCGAAGGGGCGGCTGACTGTCAACAAACAA
66 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
225316 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
*
225381 TCAACTTCACAGCGAAGGGGCAGCTGACTGTCAACAAACAA
66 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
* * * * *
225422 CTTCCCAATTTAAGAGCCAATTTCAACTTCACAGCGAAAGATATTGGACTCTAGACAGCACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
*
225487 TCAACTTCATAGCGAAGGGGCGGCTGACTGTCAACAAACAA
66 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
*
225528 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAATACAACACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
*
225593 TCAACTTCACAGCGAAGGGGCGGCTGAATGTCAACAAACAA
66 TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
* * * * * * *
225634 CTTCCCAATTTCATAGTCAATTTTAACTTCCCAGCGAAGGATATTGGACCCAAGACAATACAAGC
1 CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
225699 TCAACTTCAC-GACGAAGGGGC
66 TCAACTTCACAG-CGAAGGGGC
225720 CACCCGCGGT
Statistics
Matches: 378, Mismatches: 25, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
105 1 0.00
106 377 1.00
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (106 bp):
CTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGC
TCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAA
Found at i:226064 original size:36 final size:37
Alignment explanation
Indices: 226017--226121 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 37
226007 ATGCTCACCA
226017 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-TT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTT
*
226053 TTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTT
*
226090 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
226122 CCAATCTTCG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
36 33 0.51
37 32 0.49
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTT
Found at i:226212 original size:35 final size:35
Alignment explanation
Indices: 226131--226259 Score: 143
Period size: 35 Copynumber: 3.6 Consensus size: 35
226121 ACCAATCTTC
* *
226131 GAAATTGTTTCTCTTGAAAC-ACAAAAAAACCTTC
1 GAAATTGTTTCTCTTGAAACAAAAAAAAAACCTTT
* ** *
226165 GAGACAGCTTCTCTTGAAACAAAAAAAAAACCTTT
1 GAAATTGTTTCTCTTGAAACAAAAAAAAAACCTTT
226200 GAAATTGTTTCTCTTGAAACACAAAAAAGAAAAACCTTT
1 GAAATTGTTTCTCTTG-AA-AC-AAAAA-AAAAACCTTT
* *
226239 GAAAATGTTTCTCTTAAAACA
1 GAAATTGTTTCTCTTGAAACA
226260 CAAAGACCTT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
34 16 0.21
35 24 0.31
36 3 0.04
37 4 0.05
38 7 0.09
39 24 0.31
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (35 bp):
GAAATTGTTTCTCTTGAAACAAAAAAAAAACCTTT
Found at i:226248 original size:39 final size:38
Alignment explanation
Indices: 226131--226263 Score: 138
Period size: 39 Copynumber: 3.7 Consensus size: 38
226121 ACCAATCTTC
* *
226131 GAAATTGTTTCTCTTGAAACAC----AAAAAAACCTTC
1 GAAAATGTTTCTCTTGAAACACAAAAAAAAAAACCTTT
* *
226165 GAGACA-GCTTCTCTTG-AA-AC-AAAAAAAAAACCTTT
1 GA-AAATGTTTCTCTTGAAACACAAAAAAAAAAACCTTT
*
226200 GAAATTGTTTCTCTTGAAACACAAAAAAGAAAAACCTTT
1 GAAAATGTTTCTCTTGAAACACAAAAAA-AAAAACCTTT
*
226239 GAAAATGTTTCTCTTAAAACACAAA
1 GAAAATGTTTCTCTTGAAACACAAA
226264 GACCTTCGAG
Statistics
Matches: 81, Mismatches: 9, Indels: 13
0.79 0.09 0.13
Matches are distributed among these distances:
32 2 0.02
33 2 0.02
34 12 0.15
35 23 0.28
36 2 0.02
37 2 0.02
38 5 0.06
39 33 0.41
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (38 bp):
GAAAATGTTTCTCTTGAAACACAAAAAAAAAAACCTTT
Found at i:227797 original size:14 final size:14
Alignment explanation
Indices: 227774--227806 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
227764 TCATTTAATA
*
227774 TTTATTTATTATTT
1 TTTATCTATTATTT
227788 TTTATCTATTATTT
1 TTTATCTATTATTT
227802 TTTAT
1 TTTAT
227807 TTTTTAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATCTATTATTT
Found at i:227809 original size:7 final size:7
Alignment explanation
Indices: 227774--227812 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
227764 TCATTTAATA
227774 TTTATTT
1 TTTATTT
*
227781 ATTATTT
1 TTTATTT
*
227788 TTTATCT
1 TTTATTT
*
227795 ATTATTT
1 TTTATTT
227802 TTTATTT
1 TTTATTT
227809 TTTA
1 TTTA
227813 AGGGTATGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTATTT
Found at i:227871 original size:6 final size:6
Alignment explanation
Indices: 227860--227886 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
227850 GAACCGAATT
227860 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
227887 TTCCAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:229823 original size:3 final size:3
Alignment explanation
Indices: 229776--229808 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
229766 GTTTTTTTCG
229776 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
229809 CGTCATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:231428 original size:2 final size:2
Alignment explanation
Indices: 231421--231457 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
231411 GTTATTGTCA
231421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
231458 GGTGCATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:231920 original size:58 final size:55
Alignment explanation
Indices: 231808--231933 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 55
231798 TTCTACATTT
* *
231808 TATATTCGATTCATTATTTTAGTTTATTTTGTTGTATGTAAACATCAAAATTTTTATG
1 TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATC--AATTTTT-TG
* * * *
231866 TATATTCGATTTATTTTTTATCAATTTATTTTGTTGTATGAAAATATC-GTTTTTTG
1 TATATTCGATTCATTATTT-T-AATTTATTTTGTTGTATGAAAACATCAATTTTTTG
*
231922 TATATTCCATTC
1 TATATTCGATTC
231934 GTATCTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 12 0.21
57 5 0.09
58 17 0.29
59 1 0.02
60 23 0.40
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.56
Consensus pattern (55 bp):
TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATCAATTTTTTG
Found at i:237248 original size:4 final size:4
Alignment explanation
Indices: 237239--237300 Score: 58
Period size: 4 Copynumber: 15.2 Consensus size: 4
237229 TCACAAATCA
*
237239 ACAT ACAT ACAT -CAAT ACAA ACAT ATCAAT ACAT ACAT ACAT -CAAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT A-C-AT ACAT ACAT ACAT AC-AT
237285 ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT A
237301 AAATTTGCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 5 0.10
4 37 0.76
5 4 0.08
6 3 0.06
ACGTcount: A:0.53, C:0.23, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:237626 original size:35 final size:35
Alignment explanation
Indices: 237587--237690 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
237577 TGAGGGTGTT
* **
237587 TTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGC
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
237622 TTTCTAAAAACAAATTTTGTCTCGTTTGAGACAAA
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
237657 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 TT-TCTTAAAACAAATTTTGTCTCGCTTGAGACA
237691 TTTTTCCTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 32 0.54
36 27 0.46
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
Found at i:237776 original size:105 final size:105
Alignment explanation
Indices: 237657--237853 Score: 290
Period size: 105 Copynumber: 1.9 Consensus size: 105
237647 TTGAGACAAA
* *
237657 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACC-AATTTTGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CCAAATTTCGAATTT
237721 GATTCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTTGT
65 GATTCACATT-AAACAAAATTAATCTCACCTTAGATTGTTGT
* * *
237762 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
* * *
237827 TTTCACATTAAACAAAGTTGATCTCAC
66 ATTCACATTAAACAAAATTAATCTCAC
237854 TTGAGATCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.02
105 78 0.95
106 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (105 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACCTTAGATTGTTGT
Found at i:238238 original size:28 final size:28
Alignment explanation
Indices: 238175--238276 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 28
238165 TCTGGAGACA
* * *
238175 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
238203 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
238231 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
238261 ATTTCTTTTGAAAAAA
1 GTTTCTTTTGAAAAAA
238277 TTTATCTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 26 0.41
30 13 0.20
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:238331 original size:60 final size:63
Alignment explanation
Indices: 238232--238369 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
238222 CTTTGAGTTG
*
238232 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTG-AA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTT-TCTCTCTAAAGACA
238294 A
63 A
* * **
238295 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
*
238357 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
238370 TACCCACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 18 0.28
61 8 0.12
62 29 0.45
63 9 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:238509 original size:15 final size:15
Alignment explanation
Indices: 238486--238529 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
238476 TTTTGAGTCG
*
238486 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
238501 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
238516 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
238530 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:239010 original size:40 final size:40
Alignment explanation
Indices: 238952--239316 Score: 211
Period size: 40 Copynumber: 8.7 Consensus size: 40
238942 CCAGTCGTCC
* * *
238952 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
* * * * *
238992 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
239035 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
239081 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
239121 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * *
239163 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
239209 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
239249 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATCTCT
* * *
239291 TCATCACGTACGAGCAGTGTCGTCCC
1 TCATCACGTAGGAGCCGTGTCATCCC
239317 CAACAACCAA
Statistics
Matches: 250, Mismatches: 45, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 85 0.34
41 1 0.00
42 53 0.21
43 37 0.15
44 3 0.01
46 59 0.24
47 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
Found at i:239300 original size:128 final size:129
Alignment explanation
Indices: 238952--239284 Score: 589
Period size: 128 Copynumber: 2.6 Consensus size: 129
238942 CCAGTCGTCC
* * *
238952 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
*
239016 CATAGATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
239081 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
239145 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
239209 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
239274 ATAGATAACCA
66 ATAGATAACCA
239285 AACTCTTCAT
Statistics
Matches: 195, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
128 125 0.64
129 65 0.33
130 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:239511 original size:3 final size:3
Alignment explanation
Indices: 239467--239496 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
239457 GTTTTTTTCG
239467 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
239497 CGTCATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:241117 original size:2 final size:2
Alignment explanation
Indices: 241110--241222 Score: 226
Period size: 2 Copynumber: 56.5 Consensus size: 2
241100 GTTATTGTCA
241110 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
241152 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
241194 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 A
241223 GGTGCATGTT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 111 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246560 original size:23 final size:23
Alignment explanation
Indices: 246534--246579 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
246524 TGCAGTTGTG
*
246534 TTGTTATTTTGGTTGTGTAATCT
1 TTGTTATTTTGGTCGTGTAATCT
246557 TTGTTATTTTGGTCGTGTAATCT
1 TTGTTATTTTGGTCGTGTAATCT
246580 GAACTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.22, T:0.59
Consensus pattern (23 bp):
TTGTTATTTTGGTCGTGTAATCT
Found at i:252391 original size:42 final size:42
Alignment explanation
Indices: 252339--252471 Score: 248
Period size: 42 Copynumber: 3.2 Consensus size: 42
252329 GGCCCTATCC
* *
252339 GTAGTCCTTATAGGAGAGAGAAGCAAAGTGCTGAAAATGATG
1 GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
252381 GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
1 GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
252423 GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
1 GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
252465 GTAGCCC
1 GTAGCCC
252472 CCATCACAGT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (42 bp):
GTAGCCCTTATAGGAGAGAGAAGCGAAGTGCTGAAAATGATG
Found at i:254584 original size:2 final size:2
Alignment explanation
Indices: 254577--254610 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
254567 TTTTCATGTG
*
254577 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
254611 CCAAACTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:257911 original size:17 final size:17
Alignment explanation
Indices: 257878--257912 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
257868 CATAAAGAAT
*
257878 ATATTATTATATATTTA
1 ATATTATTAAATATTTA
*
257895 ATATTATTAAATCTTTA
1 ATATTATTAAATATTTA
257912 A
1 A
257913 AAATTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTATTAAATATTTA
Found at i:261761 original size:60 final size:60
Alignment explanation
Indices: 261647--261777 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 60
261637 TTAGGGTAAA
* *
261647 TTACACAAATAATCTCTTGACTATAGGGTAATGCTTTGTTGAATCCCTCAACTATTAAAAG
1 TTACA-AAATGATCTCTTGACTATAGGGTAATGCTTTGTTGAATCCCCCAACTATTAAAAG
* * * ** * *
261708 TTATAAAATGATCTTTTGATTATAGGGTGTTGCTTTGTTGAGTCCCCCGACTATTAAAAG
1 TTACAAAATGATCTCTTGACTATAGGGTAATGCTTTGTTGAATCCCCCAACTATTAAAAG
261768 TTACAAAATG
1 TTACAAAATG
261778 GTCACCCAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 56 0.93
61 4 0.07
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (60 bp):
TTACAAAATGATCTCTTGACTATAGGGTAATGCTTTGTTGAATCCCCCAACTATTAAAAG
Found at i:262081 original size:60 final size:60
Alignment explanation
Indices: 262000--262115 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
261990 AGTTAAGTGG
* *
262000 TCATTTTGTAACTTTTCATAGTAGTGAGACTCAACAAAGCAACACCCTATAGTCGAATGA
1 TCATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGAATGA
* *
262060 TCATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCATCACCCTATAGTCGA
1 TCATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGA
262116 GGGACCATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (60 bp):
TCATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGAATGA
Found at i:262125 original size:60 final size:60
Alignment explanation
Indices: 262001--262134 Score: 189
Period size: 60 Copynumber: 2.2 Consensus size: 60
261991 GTTAAGTGGT
* * * *
262001 CATTTTGTAACTTTTCATAGTAGTGAGACTCAACAAAGCAACACCCTATAGTCGAATGAT
1 CATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGAAGGAC
* * *
262061 CATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGCATCACCCTATAGTCGAGGGAC
1 CATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGAAGGAC
262121 CA-TTTGTATACTTT
1 CATTTTGTA-ACTTT
262135 ACCCTGTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 6 0.09
60 60 0.91
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTAGAGAGACTCAACAAAGCAACACCCTATAGTCGAAGGAC
Found at i:262651 original size:3 final size:3
Alignment explanation
Indices: 262643--262677 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
262633 GTCATTAAAA
262643 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
262678 ATATGCATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:263970 original size:2 final size:2
Alignment explanation
Indices: 263963--263999 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
263953 TGATAAGAGT
*
263963 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
264000 TAATTTCGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:266106 original size:20 final size:21
Alignment explanation
Indices: 266081--266122 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
266071 ACAAGCTTGG
266081 TGCCATCTACAAC-AATTGTT
1 TGCCATCTACAACAAATTGTT
266101 TGCCATCTACAACAAATTGTT
1 TGCCATCTACAACAAATTGTT
266122 T
1 T
266123 AAACCTAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (21 bp):
TGCCATCTACAACAAATTGTT
Found at i:269857 original size:40 final size:37
Alignment explanation
Indices: 269813--270100 Score: 200
Period size: 37 Copynumber: 7.9 Consensus size: 37
269803 TTTTTGAAAC
269813 ATATAGTTTTTTAAAAAATCGATTTTTG-AAATATATATAA-
1 ATATAGTTTTTT--AAAA-C-A-TTTTGAAAATATATATAAT
*
269853 ATATAGTTTTTTCAAACATTTTGAAAAATATATATAAT
1 ATATAGTTTTTTAAAACATTTTG-AAAATATATATAAT
*
269891 ATATAG-TTTTTGAAACATTTTG-AAATAT-TATATAT
1 ATATAGTTTTTTAAAACATTTTGAAAATATATATA-AT
* *
269926 AATATAGATTTTGAAAACATTTTGAAAACT-TATATAAT
1 -ATATAGTTTTTTAAAACATTTTGAAAA-TATATATAAT
* * *
269964 ATATAG-TTTTGAAAATATTTTTGAAAACATA-AT-A-
1 ATATAGTTTTTTAAAACA-TTTTGAAAATATATATAAT
* *
269998 ATATA--TTTTGAAAACATTTTTGAAAA-CTATAT-A-
1 ATATAGTTTTTTAAAACA-TTTTGAAAATATATATAAT
* *
270031 ATATAG-TTTTGAAAACATTTTTAAAA-ATATAT-AT
1 ATATAGTTTTTTAAAACATTTTGAAAATATATATAAT
* **
270065 ATATA-TTTTTCAAAATGTTTTCGAAAATATAATATA
1 ATATAGTTTTTTAAAACATTTT-GAAAATAT-ATATA
270101 TTTTTATTAA
Statistics
Matches: 215, Mismatches: 14, Indels: 40
0.80 0.05 0.15
Matches are distributed among these distances:
32 2 0.01
33 42 0.20
34 37 0.17
35 18 0.08
36 21 0.10
37 63 0.29
38 15 0.07
39 5 0.02
40 12 0.06
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTTTAAAACATTTTGAAAATATATATAAT
Found at i:269901 original size:37 final size:37
Alignment explanation
Indices: 269841--270070 Score: 236
Period size: 37 Copynumber: 6.5 Consensus size: 37
269831 TCGATTTTTG
**
269841 AAATATATATAA-ATATAGTTTTTTCAAACATTTTGAA
1 AAATATATATAATATATAG-TTTTGAAAACATTTTGAA
269878 AAATATATATAATATATAGTTTTTG-AAACATTTTGAA
1 AAATATATATAATATATAG-TTTTGAAAACATTTTGAA
* *
269915 ATATTATATATAATATAGA-TTTTGAAAACATTTTGAA
1 A-AATATATATAATATATAGTTTTGAAAACATTTTGAA
* *
269952 AACT-TATATAATATATAGTTTTGAAAATATTTTTG-A
1 AAATATATATAATATATAGTTTTGAAAACA-TTTTGAA
*
269988 AAACATA-AT-A-ATATA-TTTTGAAAACATTTTTG-A
1 AAATATATATAATATATAGTTTTGAAAACA-TTTTGAA
* *
270021 AAA-CTATAT-A-ATATAGTTTTGAAAACATTTTTAA
1 AAATATATATAATATATAGTTTTGAAAACATTTTGAA
270055 AAATATATAT-ATATAT
1 AAATATATATAATATAT
270071 TTTTCAAAAT
Statistics
Matches: 170, Mismatches: 12, Indels: 23
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.01
33 32 0.19
34 20 0.12
35 19 0.11
36 26 0.15
37 45 0.26
38 26 0.15
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
AAATATATATAATATATAGTTTTGAAAACATTTTGAA
Found at i:270127 original size:12 final size:11
Alignment explanation
Indices: 270097--270169 Score: 55
Period size: 12 Copynumber: 6.5 Consensus size: 11
270087 GAAAATATAA
270097 TATATTTTTAT
1 TATATTTTTAT
*
270108 TA-ATTTTTGGT
1 TATATTTTT-AT
270119 TATATTTTTAT
1 TATATTTTTAT
270130 T-T-TTATTTAT
1 TATATT-TTTAT
270140 TATATGTTTTA-
1 TATAT-TTTTAT
*
270151 TATTATATTATAT
1 TA-TAT-TTTTAT
270164 TATATT
1 TATATT
270170 AATTTTATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
9 2 0.04
10 13 0.26
11 11 0.22
12 21 0.42
13 3 0.06
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.68
Consensus pattern (11 bp):
TATATTTTTAT
Found at i:270154 original size:24 final size:23
Alignment explanation
Indices: 270123--270168 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
270113 TTTGGTTATA
*
270123 TTTTTATTTTTATT-TATTATATG
1 TTTTTA-TTATATTATATTATATG
270146 TTTTATATTATATTATATTATAT
1 TTTT-TATTATATTATATTATAT
270169 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTTATTATATTATATTATATG
Found at i:270161 original size:19 final size:17
Alignment explanation
Indices: 270129--270163 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
270119 TATATTTTTA
270129 TTTTTATTTATTATATG
1 TTTTTATTTATTATATG
270146 TTTTATATTATATTATAT
1 TTTT-TATT-TATTATAT
270164 TATATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTATTTATTATATG
Found at i:271643 original size:31 final size:31
Alignment explanation
Indices: 271581--271667 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
271571 GAAGGACCTA
* *
271581 TCCATAT-TTCCGAAGAACATAGGT-AACTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
*
271610 TCCCTATGTCCCGAAGGACATAGGTAAACTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTG
** *
271641 TCCATATGTCTAGAAAGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
271668 CCCTTGACTC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 6 0.12
30 15 0.31
31 28 0.57
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAACTG
Done.