Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012329.1 Kokia drynarioides strain JFW-HI SEQ_127331, 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: 151005
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1074 original size:74 final size:74
Alignment explanation
Indices: 948--1100 Score: 252
Period size: 74 Copynumber: 2.1 Consensus size: 74
938 GCGAAACAAT
* * *
948 AATTCTTGTACAAACCAATGAAGTAAGGTCATTTCCAATGGTCCACAAATTTAAATCTTTATAAT
1 AATTCTTATACAAACCAATGAAGTAAGGCCATTTCCAATGGTCCACAAATTTAAATCTTAATAAT
1013 ATTTAGAAC
66 ATTTAGAAC
* *
1022 AATTCTTATACAAACCAATGAAGTAAGGCCATTTTCAATGGTCCACAGATTTAAATCTTAATAAT
1 AATTCTTATACAAACCAATGAAGTAAGGCCATTTCCAATGGTCCACAAATTTAAATCTTAATAAT
1087 ATTTAGAAC
66 ATTTAGAAC
*
1096 CATTC
1 AATTC
1101 ATAAATATCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (74 bp):
AATTCTTATACAAACCAATGAAGTAAGGCCATTTCCAATGGTCCACAAATTTAAATCTTAATAAT
ATTTAGAAC
Found at i:3165 original size:219 final size:219
Alignment explanation
Indices: 2906--3325 Score: 822
Period size: 219 Copynumber: 1.9 Consensus size: 219
2896 TTTTGTACCA
2906 TGGGCCACAGCCGGATTCCAAAAAGAATTTCAAACATAGGCCCTTTTTGAGTTATGTTTAATAAT
1 TGGGCCACAGCCGGATTCCAAAAAGAATTTCAAACATAGGCCCTTTTTGAGTTATGTTTAATAAT
*
2971 ATTAATATATTTTTATTTTATATTTAATTTTAAAATATTTTTTAACTATTTAAATTAATTCAAGC
66 ATAAATATATTTTTATTTTATATTTAATTTTAAAATATTTTTTAACTATTTAAATTAATTCAAGC
3036 TGGAACGAAACAAAAAAGTCATTGTCCAAGCCTAGTTCAAGTTGGGTTGGGCCAGGACAGCTCTA
131 TGGAACGAAACAAAAAAGTCATTGTCCAAGCCTAGTTCAAGTTGGGTTGGGCCAGGACAGCTCTA
3101 GTGACAGCCTAGTTCAAGTTGGGT
196 GTGACAGCCTAGTTCAAGTTGGGT
3125 TGGGCCACAGCCGGATTCCAAAAAGAATTTCAAACATAGGCCCTTTTTGAGTTATGTTTAATAAT
1 TGGGCCACAGCCGGATTCCAAAAAGAATTTCAAACATAGGCCCTTTTTGAGTTATGTTTAATAAT
3190 ATAAATATATTTTTATTTTATATTTAATTTTAAAATATTTTTTAACTATTTAAATTAATTCAAGC
66 ATAAATATATTTTTATTTTATATTTAATTTTAAAATATTTTTTAACTATTTAAATTAATTCAAGC
3255 TGGAACGAAACAAAAAAGTCATTGTCCAAGCCTAGTTCAAGTTGGGTTGGGCCAGGACAGCTCTA
131 TGGAACGAAACAAAAAAGTCATTGTCCAAGCCTAGTTCAAGTTGGGTTGGGCCAGGACAGCTCTA
*
3320 TTGACA
196 GTGACA
3326 TCCTTCGGCT
Statistics
Matches: 199, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 199 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (219 bp):
TGGGCCACAGCCGGATTCCAAAAAGAATTTCAAACATAGGCCCTTTTTGAGTTATGTTTAATAAT
ATAAATATATTTTTATTTTATATTTAATTTTAAAATATTTTTTAACTATTTAAATTAATTCAAGC
TGGAACGAAACAAAAAAGTCATTGTCCAAGCCTAGTTCAAGTTGGGTTGGGCCAGGACAGCTCTA
GTGACAGCCTAGTTCAAGTTGGGT
Found at i:3216 original size:31 final size:29
Alignment explanation
Indices: 3176--3233 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
3166 CCTTTTTGAG
*
3176 TTATGTTTAATAATATAAATATATTTTTATT
1 TTATATTTAATAATA-AAATAT-TTTTTATT
**
3207 TTATATTTAATTTTAAAATATTTTTTA
1 TTATATTTAATAATAAAATATTTTTTA
3234 ACTATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 6 0.25
31 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (29 bp):
TTATATTTAATAATAAAATATTTTTTATT
Found at i:6614 original size:2 final size:2
Alignment explanation
Indices: 6564--6594 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6554 AAATTCGCTT
6564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6595 TGATAAGTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10516 original size:34 final size:34
Alignment explanation
Indices: 10473--10555 Score: 166
Period size: 34 Copynumber: 2.4 Consensus size: 34
10463 GAACCCAATT
10473 ATTTTCACTTTCTTTTCTTCTTTTTCTGAAAGGA
1 ATTTTCACTTTCTTTTCTTCTTTTTCTGAAAGGA
10507 ATTTTCACTTTCTTTTCTTCTTTTTCTGAAAGGA
1 ATTTTCACTTTCTTTTCTTCTTTTTCTGAAAGGA
10541 ATTTTCACTTTCTTT
1 ATTTTCACTTTCTTT
10556 AATAATAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.17, C:0.18, G:0.07, T:0.58
Consensus pattern (34 bp):
ATTTTCACTTTCTTTTCTTCTTTTTCTGAAAGGA
Found at i:31183 original size:52 final size:52
Alignment explanation
Indices: 31039--31216 Score: 229
Period size: 52 Copynumber: 3.5 Consensus size: 52
31029 TTCACATTTA
* * **
31039 ATACTCACGACGACACATTA-TCATTGGACCTCATAATTTG-AAAAGGATTCAT
1 ATACTCACGATGACACA-TAGTCATCGGACCTCATAATCCGTAAAA-GATTCAT
* *
31091 ATACTCACGATGACAC--AGTCATCAGACCTCATAATCCGTAAAAAATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
* *
31141 ATACTCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
*
31193 ATACTCACGATGATACATAGTCAT
1 ATACTCACGATGACACATAGTCAT
31217 TAGACTTTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 8
0.85 0.08 0.06
Matches are distributed among these distances:
49 1 0.01
50 38 0.34
51 4 0.04
52 68 0.61
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
Found at i:38297 original size:24 final size:24
Alignment explanation
Indices: 38264--38314 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
38254 AGAAATAATC
* *
38264 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTCTGTTTAATTG
*
38288 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAATTG
38312 TTT
1 TTT
38315 AAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAATTG
Found at i:38323 original size:24 final size:24
Alignment explanation
Indices: 38272--38326 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
38262 TCTTTCAGTT
* *
38272 AAACTTTGTTTAATTGTTTCAATT
1 AAACTCTGTTTAATTGTTTCAATC
*
38296 AAACTCTGTTTATTTGTTT-AAGTC
1 AAACTCTGTTTAATTGTTTCAA-TC
38320 AAACTCT
1 AAACTCT
38327 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.29, C:0.13, G:0.09, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAATTGTTTCAATC
Found at i:42558 original size:29 final size:30
Alignment explanation
Indices: 42515--42573 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
42505 GAATTGGATC
* *
42515 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAGTTCATATATAAAATTGCACA
*
42545 AAATC-AAAGTTCATATATACAATTGCACA
1 AAATCAAAAGTTCATATATAAAATTGCACA
42574 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (30 bp):
AAATCAAAAGTTCATATATAAAATTGCACA
Found at i:49740 original size:14 final size:14
Alignment explanation
Indices: 49718--49751 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49708 GAATGTTCGG
49718 ATTTAAGATTCAAA
1 ATTTAAGATTCAAA
* *
49732 ATTTTAGATTTAAA
1 ATTTAAGATTCAAA
49746 ATTTAA
1 ATTTAA
49752 AGTTTGAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTTAAGATTCAAA
Found at i:54762 original size:20 final size:21
Alignment explanation
Indices: 54737--54778 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54727 AGTAAATTTG
*
54737 ATTTTTTAT-ATATTTTTTTA
1 ATTTTTTATAATAATTTTTTA
54757 ATTTTTTATAATAATTTTTTA
1 ATTTTTTATAATAATTTTTTA
54778 A
1 A
54779 CTTATAACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTTATAATAATTTTTTA
Found at i:54934 original size:16 final size:17
Alignment explanation
Indices: 54910--54953 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
54900 TCATAATTTA
54910 TTAAATAAAAATAAT-T
1 TTAAATAAAAATAATAT
* *
54926 TT-AATTAAAATATTAT
1 TTAAATAAAAATAATAT
54942 TTAAATAAAAAT
1 TTAAATAAAAAT
54954 TTTAAAATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 10 0.43
16 5 0.22
17 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATAAAAATAATAT
Found at i:54937 original size:15 final size:16
Alignment explanation
Indices: 54910--54951 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54900 TCATAATTTA
54910 TTAAATAAAAATAAT-T
1 TTAAAT-AAAATAATAT
* *
54926 TTAATTAAAATATTAT
1 TTAAATAAAATAATAT
54942 TTAAATAAAA
1 TTAAATAAAA
54952 ATTTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAAATAAAATAATAT
Found at i:55409 original size:16 final size:16
Alignment explanation
Indices: 55370--55410 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
55360 TCTATGATAA
55370 TTTTATAACAATTATC
1 TTTTATAACAATTATC
55386 TATTTATAACAATGTA-C
1 T-TTTATAACAAT-TATC
55403 TTTTATAA
1 TTTTATAA
55411 TTATATAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 8 0.35
17 13 0.57
18 2 0.09
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.49
Consensus pattern (16 bp):
TTTTATAACAATTATC
Found at i:62596 original size:16 final size:16
Alignment explanation
Indices: 62575--62605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62565 GTTATCGAAT
*
62575 GAGTTGTATTTGAGCC
1 GAGTTGAATTTGAGCC
62591 GAGTTGAATTTGAGC
1 GAGTTGAATTTGAGC
62606 TTTACACTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (16 bp):
GAGTTGAATTTGAGCC
Found at i:62830 original size:17 final size:17
Alignment explanation
Indices: 62808--62881 Score: 94
Period size: 17 Copynumber: 4.4 Consensus size: 17
62798 AATTTTTAAA
62808 TAAATTTGAATTTATTT
1 TAAATTTGAATTTATTT
*
62825 TAAATTTTAATTTATTT
1 TAAATTTGAATTTATTT
* * * *
62842 TGAGTTTGAATTTACTC
1 TAAATTTGAATTTATTT
*
62859 TAAATTTAAATTTATTT
1 TAAATTTGAATTTATTT
62876 TAAATT
1 TAAATT
62882 AAAATTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
TAAATTTGAATTTATTT
Found at i:63569 original size:3 final size:3
Alignment explanation
Indices: 63555--63685 Score: 68
Period size: 3 Copynumber: 42.3 Consensus size: 3
63545 TCTTTGATAT
* * *
63555 TAA TAT TAA TAA TAA TAA CTAA TAA TAA TAA TAA GAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * **
63601 TAA -ATA TCGA CAA TAAA TGA CAT TAA TAA TAT TAA TAA TAA CT-G TCT
1 TAA TA-A T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
* *
63648 TAA TAA TAA TAA TAA TAA TTAG TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T
63686 TGAATAAAAA
Statistics
Matches: 94, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
2 2 0.02
3 82 0.87
4 10 0.11
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:74103 original size:77 final size:77
Alignment explanation
Indices: 74015--74162 Score: 251
Period size: 77 Copynumber: 1.9 Consensus size: 77
74005 TCCTTGGTAC
* * *
74015 CAAGACATCCTTCAATACGTTAAGGACCGTAAATACCCCGAAAGAGCTACTGAAAATGATAAAAG
1 CAAGACATCCTTCAATACGTGAAAGACCGTAAATACCCCGAAAGAGCTACTAAAAATGATAAAAG
74080 GACATTAAGTAT
66 GACATTAAGTAT
* *
74092 CAAGACATCCTTCAATACGTGAAAGACCGTAAATACCCCGAAGGAGTTACTAAAAATGATAAAAG
1 CAAGACATCCTTCAATACGTGAAAGACCGTAAATACCCCGAAAGAGCTACTAAAAATGATAAAAG
74157 GACATT
66 GACATT
74163 GAAAAGGCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (77 bp):
CAAGACATCCTTCAATACGTGAAAGACCGTAAATACCCCGAAAGAGCTACTAAAAATGATAAAAG
GACATTAAGTAT
Found at i:76283 original size:45 final size:44
Alignment explanation
Indices: 76199--76287 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 44
76189 TCAGAGACAT
76199 GAAGGGAAAGATCTAAGCCGCAACAGCGAATCCAATACCGCAAA
1 GAAGGGAAAGATCTAAGCCGCAACAGCGAATCCAATACCGCAAA
** * *
76243 GAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAA
1 GAAGGGAAAGATCTAAG-CCGCAACAGCGAATCCAATACCGCAAA
76288 AAAAAGGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 17 0.43
45 23 0.57
ACGTcount: A:0.40, C:0.24, G:0.26, T:0.10
Consensus pattern (44 bp):
GAAGGGAAAGATCTAAGCCGCAACAGCGAATCCAATACCGCAAA
Found at i:76443 original size:238 final size:235
Alignment explanation
Indices: 76013--76474 Score: 555
Period size: 238 Copynumber: 1.9 Consensus size: 235
76003 ACATGACGGC
* * *
76013 AAAGATCTAAGACCGCAATGGCGGATCCAGTATCACAAATAAGGGAAAGATTTAAGCTGCAACAG
1 AAAGATCTAAGACCGCAATGGCGGATCCAGTACCACAAAAAAAGGAAAGATTTAAGCTGCAACAG
* * *
76078 TGAACCTTGTACCTCAGAAGACAAAGGGAAAGATCTAAAACCGCAACGGTAAATCCAGTACTGCA
66 TGAACCTTGTACCTCAGAAGACAAAGGGAAAGATCTAAAACCGCAACGGCAAATCCAATACCGCA
*** * * *
76143 AAGATTTTAAGGGAAAGGTTCAAGTCGCAATGGTGAACCTAGTATCTCAGAGACATGAAGGGAAA
131 AAGATCAAAAGGGAAAGGTTCAAGTCACAATGGGGAACCTAGTACCTCAGAGACA-GAAGGGAAA
76208 GATCTAAGCCGCAAC-AGCGAATCCAATACCGCAAAGAAGGG
195 GATCTAAGCCGCAACGA-CGAATCCAATACCGCAAAGAAGGG
* *
76249 AAAGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAAAAAAGGAAAGGTTTAAG-T-CATA-
1 AAAGATCTAAGACCGCAATGGCGGATCCAGTACCAC-AAAAAAAGGAAAGATTTAAGCTGCA-AC
* *
76311 A-TGGCAAACCTTGTACCTCAGAAG-CATGAAGGGAAAGATCTAAGACCGCAACGGCAGATCCAA
64 AGT-G--AACCTTGTACCTCAGAAGACA--AAGGGAAAGATCTAAAACCGCAACGGCAAATCCAA
* * *
76374 TACCGCAAAGATACAAAAGGGGAAGG-TCTAAGTCACAATGGCGGATCGT-GTACCTCAGAAGAC
124 TACCGCAAAGAT-CAAAAGGGAAAGGTTC-AAGTCACAATGG-GGAACCTAGTACCTCAG-AGAC
* *
76437 -GAAGGGAAAGATTTAAGCTGCAACGACGAATCCAATAC
185 AGAAGGGAAAGATCTAAGCCGCAACGACGAATCCAATAC
76475 TACGAAGACA
Statistics
Matches: 193, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
234 1 0.01
235 4 0.02
236 38 0.20
237 35 0.18
238 78 0.40
239 29 0.15
240 8 0.04
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (235 bp):
AAAGATCTAAGACCGCAATGGCGGATCCAGTACCACAAAAAAAGGAAAGATTTAAGCTGCAACAG
TGAACCTTGTACCTCAGAAGACAAAGGGAAAGATCTAAAACCGCAACGGCAAATCCAATACCGCA
AAGATCAAAAGGGAAAGGTTCAAGTCACAATGGGGAACCTAGTACCTCAGAGACAGAAGGGAAAG
ATCTAAGCCGCAACGACGAATCCAATACCGCAAAGAAGGG
Found at i:76504 original size:98 final size:100
Alignment explanation
Indices: 76243--76533 Score: 287
Period size: 98 Copynumber: 3.0 Consensus size: 100
76233 ATACCGCAAA
* * * * * *
76243 GAAGGGAAAGATCTAAGACCGCAATGGCGGATCCAGTACCGC-AA-AA-AAAA--GGAAAGGTTT
1 GAAGGGAAAGATCTAAGACCGCAACGACAGATCCAATACCACAAAGAACAAAAGGGGAAAGGTCT
* * *
76303 AAGTCATAATGGCAAACCTTGTACCTCAGAAGCAT
66 AAGTCACAATGGCGAACCTTGTACCTCAGAAGCAC
* *
76338 GAAGGGAAAGATCTAAGACCGCAACGGCAGATCCAATACCGCAAAGATACAAAAGGGG-AAGGTC
1 GAAGGGAAAGATCTAAGACCGCAACGACAGATCCAATACCACAAAGA-ACAAAAGGGGAAAGGTC
* * *
76402 TAAGTCACAATGGCGGATCGTGTACCTCAGAAG-AC
65 TAAGTCACAATGGCGAACCTTGTACCTCAGAAGCAC
* * * * *
76437 GAAGGGAAAGATTTAAG-CTGCAACGAC-GAATCCAATACTACGAAG-ACATGAAGGGGAAAGGT
1 GAAGGGAAAGATCTAAGACCGCAACGACAG-ATCCAATACCACAAAGAACA-AAAGGGGAAAGGT
** *
76499 CTAAGTTGCAATGGCGAACCTTATACCTCAGAAGC
64 CTAAGTCACAATGGCGAACCTTGTACCTCAGAAGC
76534 TGAAAAAGGG
Statistics
Matches: 163, Mismatches: 23, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
95 39 0.24
96 5 0.03
97 8 0.05
98 55 0.34
99 21 0.13
100 33 0.20
101 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.16
Consensus pattern (100 bp):
GAAGGGAAAGATCTAAGACCGCAACGACAGATCCAATACCACAAAGAACAAAAGGGGAAAGGTCT
AAGTCACAATGGCGAACCTTGTACCTCAGAAGCAC
Found at i:77041 original size:34 final size:34
Alignment explanation
Indices: 77002--77068 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
76992 TTTTTAAATA
* *
77002 AGTTTGAATTTATTTTAAATTCAAATTCATTTTG
1 AGTTTGAATTTACTCTAAATTCAAATTCATTTTG
* *
77036 AGTTTGAATTTACTCTAAATTTAAATTTATTTT
1 AGTTTGAATTTACTCTAAATTCAAATTCATTTT
77069 AAATTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.07, T:0.54
Consensus pattern (34 bp):
AGTTTGAATTTACTCTAAATTCAAATTCATTTTG
Found at i:77762 original size:3 final size:3
Alignment explanation
Indices: 77754--77877 Score: 65
Period size: 3 Copynumber: 40.3 Consensus size: 3
77744 ATATTACTAT
* *
77754 TAA TAA TAA TAA CTAA TAA TAA TAA TAA GAA TAT TAA TAA TAA -ATA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * * * * **
77800 TCGA CAA TAAA TGA CAT TAA TAA TAT TAA TAA TAA CT-G TCT TAA TAA
1 T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
77847 TAA TAA TAA TAA TTAG TAA TAA TAA -AA TAA T
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA T
77878 TGAATAAAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
2 4 0.04
3 76 0.84
4 10 0.11
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:78984 original size:29 final size:28
Alignment explanation
Indices: 78951--79045 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
78941 AGAGGTCCCT
78951 AAACTATTTAAAAATTATATTTTAACCTC
1 AAACT-TTTAAAAATTATATTTTAACCTC
** *
78980 AAACTTCTCCAAAATTATATTTTTAACCTTA
1 AAACTT-TTAAAAATTATA-TTTTAACC-TC
* * * *
79011 AAATTTTTGAAAATTACATTTTAACCCC
1 AAACTTTTAAAAATTATATTTTAACCTC
79039 TAAACTT
1 -AAACTT
79046 CTCTAACATA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
28 1 0.02
29 28 0.54
30 17 0.33
31 6 0.12
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (28 bp):
AAACTTTTAAAAATTATATTTTAACCTC
Found at i:79006 original size:30 final size:29
Alignment explanation
Indices: 78961--79112 Score: 114
Period size: 30 Copynumber: 5.2 Consensus size: 29
78951 AAACTATTTA
*
78961 AAAATTATATTTTAACCTCAAACTTCTCC
1 AAAATTATATTTTAACCCCAAACTTCTCC
** * * **
78990 AAAATTATATTTTTAACCTTAAAATTTTTG
1 AAAATTATA-TTTTAACCCCAAACTTCTCC
* *
79020 AAAATTACATTTTAACCCCTAAACTTCTCT
1 AAAATTATATTTTAACCCC-AAACTTCTCC
* *
79050 AACA-TATATTTTTAACCCCGAACTT-TCC
1 AAAATTATA-TTTTAACCCCAAACTTCTCC
* *
79078 AAAAAATTACATTTTACCCCCAAACTT-T-C
1 --AAAATTATATTTTAACCCCAAACTTCTCC
79107 AAAATT
1 AAAATT
79113 TCATTTTTGA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.06
28 2 0.02
29 26 0.27
30 60 0.62
31 3 0.03
ACGTcount: A:0.39, C:0.22, G:0.01, T:0.38
Consensus pattern (29 bp):
AAAATTATATTTTAACCCCAAACTTCTCC
Found at i:79256 original size:58 final size:57
Alignment explanation
Indices: 79073--79464 Score: 366
Period size: 58 Copynumber: 6.7 Consensus size: 57
79063 AACCCCGAAC
* * * *
79073 TTTCCAAAAAATTA-CATTTTACCCCCAAACTTTCAAAATTTCATTTTTGACCTCGCTTTTT
1 TTTCC-AAAAATTATCATTTTACCCTCGAACTTCCAAAATTTCA-TTTTGACCTCG---ATT
* *
79134 TTTCCAAAAAATA-CATTTTACCC-CGAACTTTCCAAAATTCCATTTTGACCAT-GATTT
1 TTTCCAAAAATTATCATTTTACCCTCGAAC-TTCCAAAATTTCATTTTGACC-TCGA-TT
* * *
79191 TTTCCAAAAATTACCATTTTACTCTCGAACTTTCCAAAATTTCATTTTGGCCTCGATT
1 TTTCCAAAAATTATCATTTTACCCTCGAAC-TTCCAAAATTTCATTTTGACCTCGATT
* *
79249 TTTCCAAAAATTATCATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCTCGATTT
1 TTTCCAAAAATTATCATTTTACCCTCGAACTTCC-AAAATTTCATTTTGACCTCGA-TT
* * * ** * *
79308 TTTTC-AAAATTATCATTTTACCC-CAAAATTCCAAAAATTATGTTTTTGATCTTGATT
1 TTTCCAAAAATTATCATTTTACCCTCGAACTTCC-AAAATT-TCATTTTGACCTCGATT
* * * * *
79365 TCTCAAAAAATTACCATTTTACCCTC-AGACTTCCAAAAATTCCATTTTCAACCTCGATT
1 TTTCCAAAAATTATCATTTTACCCTCGA-ACTTCC-AAAATTTCATTTT-GACCTCGATT
* *
79424 TTTCCAAGAATTATCATTTTACCCTCGAACTTCTAAAATTT
1 TTTCCAAAAATTATCATTTTACCCTCGAACTTCCAAAATTT
79465 TTGTTTTTGA
Statistics
Matches: 277, Mismatches: 40, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
57 36 0.13
58 113 0.41
59 93 0.34
60 30 0.11
61 5 0.02
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (57 bp):
TTTCCAAAAATTATCATTTTACCCTCGAACTTCCAAAATTTCATTTTGACCTCGATT
Found at i:79316 original size:29 final size:30
Alignment explanation
Indices: 79132--79451 Score: 177
Period size: 30 Copynumber: 11.0 Consensus size: 30
79122 ACCTCGCTTT
* *
79132 TTTTTCCAAAAAATA-CATTTT-ACCCCGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
** *
79160 ACTTTCC-AAAATT-CCATTTTGACCAT-GA
1 TTTTTCCAAAAATTACCATTTTAACC-TCGA
79188 TTTTTTCCAAAAATTACCATTTT-ACTCTCGA
1 -TTTTTCCAAAAATTACCATTTTAAC-CTCGA
** * **
79219 ACTTTCC-AAAATT-TCATTTTGGCCTCGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
* *
79247 TTTTTCCAAAAATTATCATTTTACCCTCGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
**
79277 -ACTTCCAAAAATT-CCATTTTAACCTCGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
* * *
79305 TTTTTTTC-AAAATTATCATTTT-ACC-CCA
1 -TTTTTCCAAAAATTACCATTTTAACCTCGA
*** *** * * *
79333 AAATTCCAAAAATTATGTTTTTGATCTTGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
* * *
79363 TTTCTCAAAAAATTACCATTTTACCCTCAGA
1 TTTTTCCAAAAATTACCATTTTAACCTC-GA
*
79394 --CTTCCAAAAATT-CCATTTTCAACCTCGA
1 TTTTTCCAAAAATTACCATTTT-AACCTCGA
* * *
79422 TTTTTCCAAGAATTATCATTTTACCCTCGA
1 TTTTTCCAAAAATTACCATTTTAACCTCGA
79452 ACTTCTAAAA
Statistics
Matches: 218, Mismatches: 52, Indels: 42
0.70 0.17 0.13
Matches are distributed among these distances:
27 14 0.06
28 62 0.28
29 54 0.25
30 70 0.32
31 18 0.08
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTTTCCAAAAATTACCATTTTAACCTCGA
Found at i:79325 original size:116 final size:115
Alignment explanation
Indices: 79080--79464 Score: 412
Period size: 116 Copynumber: 3.3 Consensus size: 115
79070 AACTTTCCAA
* * *
79080 AAAATTA-CATTTTACCCCCAAACTTT-CAAAATTTCATTTTTGACCTCGCTTTTTTTTCCAAAA
1 AAAATTATCATTTTACCCTCGAACTTTCCAAAATTTCA-TTTTGACCTCG---ATTTTTCCAAAA
* *
79143 AATACATTTTACCC-CGAACTTTCC-AAAATTCCATTTTGACCAT-GATTTTTTCC
62 ATTACATTTTACCCTCGAAC-TTCCAAAAATTCCATTTTAACC-TCGATTTTTTCC
* * *
79196 AAAAATTACCATTTTACTCTCGAACTTTCCAAAATTTCATTTTGGCCTCGATTTTTCCAAAAATT
1 -AAAATTATCATTTTACCCTCGAACTTTCCAAAATTTCATTTTGACCTCGATTTTTCCAAAAATT
*
79261 ATCATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCTCGATTTTTTTC
65 A-CATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCTCGATTTTTTCC
** ** * * * *
79313 AAAATTATCATTTTACCC-C-AAAATTCCAAAAATTATGTTTTTGATCTTGATTTCTCAAAAAAT
1 AAAATTATCATTTTACCCTCGAACTTTCC-AAAATT-TCATTTTGACCTCGATTTTTCCAAAAAT
79376 TACCATTTTACCCTC-AGACTTCCAAAAATTCCATTTTCAACCTCGA-TTTTTCC
64 TA-CATTTTACCCTCGA-ACTTCCAAAAATTCCATTTT-AACCTCGATTTTTTCC
*
79429 AAGAATTATCATTTTACCCTCGAAC-TTCTAAAATTT
1 AA-AATTATCATTTTACCCTCGAACTTTCCAAAATTT
79465 TTGTTTTTGA
Statistics
Matches: 232, Mismatches: 23, Indels: 27
0.82 0.08 0.10
Matches are distributed among these distances:
114 6 0.03
115 22 0.09
116 95 0.41
117 67 0.29
118 30 0.13
119 12 0.05
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.40
Consensus pattern (115 bp):
AAAATTATCATTTTACCCTCGAACTTTCCAAAATTTCATTTTGACCTCGATTTTTCCAAAAATTA
CATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCTCGATTTTTTCC
Found at i:79517 original size:117 final size:113
Alignment explanation
Indices: 79080--79536 Score: 396
Period size: 116 Copynumber: 3.9 Consensus size: 113
79070 AACTTTCCAA
* * * ** *
79080 AAAATTA-CATTTTACCCCCAAACTTTCAAAATTTCATTTTTGACCTCGCTTTTTTTTCCAAAAA
1 AAAATTATCATTTTACCCTCGAACTTCCAAAATTTTGTTTTTGACCTCG----ATTTT-CAAAAA
* *
79144 ATA-CATTTTACCC-CGAACTTTCC-AAAATTCCATTTTGACCAT-GATTTTTTCC
61 TTACCATTTTACCCTCG-AC-TTCCAAAAATTCCATTTTAACC-TCGATTTTTTCC
* * ** *
79196 AAAAATTACCATTTTACTCTCGAACTTTCCAAAA-TTTCATTTTGGCCTCGATTTTTCCAAAAAT
1 -AAAATTATCATTTTACCCTCGAAC-TTCCAAAATTTTGTTTTTGACCTCGA-TTTT-CAAAAAT
* *
79260 TATCATTTTACCCTCGAACTTCCAAAAATTCCATTTTAACCTCGATTTTTTTC
62 TACCATTTTACCCTCG-ACTTCCAAAAATTCCATTTTAACCTCGATTTTTTCC
* * * * *
79313 AAAATTATCATTTTACCC-CAAAATTCCAAAAATTATGTTTTTGATCTTGATTTCTCAAAAAATT
1 AAAATTATCATTTTACCCTCGAACTTCC-AAAATTTTGTTTTTGACCTCGATTT-TC-AAAAATT
79377 ACCATTTTACCCTCAGACTTCCAAAAATTCCATTTTCAACCTCGA-TTTTTCC
63 ACCATTTTACCCTC-GACTTCCAAAAATTCCATTTT-AACCTCGATTTTTTCC
*
79429 AAGAATTATCATTTTACCCTCGAACTTCTAAAATTTTTGTTTTTGACCTCGAACTTTTC-AAAAT
1 AA-AATTATCATTTTACCCTCGAACTTCCAAAA-TTTTGTTTTTGACCTCG-A-TTTTCAAAAAT
* * *
79493 TACCATTTTGCCCAT-GAGTGTCC-AAAATTACCATTTTACCCTCG
62 TACCATTTTACCC-TCGACT-TCCAAAAATT-CCATTTTAACCTCG
79537 GGTATCCAAA
Statistics
Matches: 286, Mismatches: 33, Indels: 43
0.79 0.09 0.12
Matches are distributed among these distances:
114 4 0.01
115 24 0.08
116 106 0.37
117 93 0.33
118 46 0.16
119 10 0.03
120 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.40
Consensus pattern (113 bp):
AAAATTATCATTTTACCCTCGAACTTCCAAAATTTTGTTTTTGACCTCGATTTTCAAAAATTACC
ATTTTACCCTCGACTTCCAAAAATTCCATTTTAACCTCGATTTTTTCC
Found at i:79544 original size:28 final size:28
Alignment explanation
Indices: 79487--79547 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
79477 TCGAACTTTT
* *
79487 CAAAATTACCATTTTGCCCATGAGTGTC
1 CAAAATTACCATTTTACCCATGAGTATC
*
79515 CAAAATTACCATTTTACCC-TCGGGTATC
1 CAAAATTACCATTTTACCCAT-GAGTATC
79543 CAAAA
1 CAAAA
79548 ATCACATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 28 0.97
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.30
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCATGAGTATC
Found at i:92712 original size:15 final size:15
Alignment explanation
Indices: 92688--92718 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
92678 TCGTTCACAT
92688 GAAAAGAAAATAAAA
1 GAAAAGAAAATAAAA
*
92703 GAAAATAAAATAAAA
1 GAAAAGAAAATAAAA
92718 G
1 G
92719 GGTTTAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (15 bp):
GAAAAGAAAATAAAA
Found at i:101876 original size:2 final size:2
Alignment explanation
Indices: 101869--101896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
101859 TTTAGGGCTT
101869 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
101897 ATTCTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:113042 original size:22 final size:21
Alignment explanation
Indices: 113017--113069 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 21
113007 CAGTGATTAA
*
113017 AATATTTAAAATAAAAAAATT
1 AATATTTAAAAGAAAAAAATT
*
113038 GAATATTTAAACGAAAAAAATT
1 -AATATTTAAAAGAAAAAAATT
*
113060 AATAATTAAA
1 AATATTTAAA
113070 TAATCAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AATATTTAAAAGAAAAAAATT
Found at i:113056 original size:21 final size:21
Alignment explanation
Indices: 113029--113069 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
113019 TATTTAAAAT
*
113029 AAAAAAATTGAATATTTAAACG
1 AAAAAAATT-AATAATTAAACG
113051 AAAAAAATTAATAATTAAA
1 AAAAAAATTAATAATTAAA
113070 TAATCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAAAATTAATAATTAAACG
Found at i:114914 original size:19 final size:19
Alignment explanation
Indices: 114890--114926 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
114880 GATGAGCAAT
114890 ATAAATGCTAACAGGTAAA
1 ATAAATGCTAACAGGTAAA
114909 ATAAATGCTAACAGGTAA
1 ATAAATGCTAACAGGTAA
114927 GTATTGATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (19 bp):
ATAAATGCTAACAGGTAAA
Found at i:119741 original size:21 final size:19
Alignment explanation
Indices: 119707--119747 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
119697 GTTAAGTAAT
119707 AATATATGTTAAAAATTAA
1 AATATATGTTAAAAATTAA
119726 AATATAATGATTAAAAATTAA
1 AATAT-ATG-TTAAAAATTAA
119747 A
1 A
119748 TTTAAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AATATATGTTAAAAATTAA
Found at i:124950 original size:2 final size:2
Alignment explanation
Indices: 124945--124980 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
124935 AAAAATAATA
*
124945 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124981 TTTATCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127978 original size:21 final size:21
Alignment explanation
Indices: 127954--127998 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
127944 TAAACTCTCG
*
127954 ACCCTAAACCTTATACCTCAA
1 ACCCTAAACCTTAAACCTCAA
* *
127975 ACCCTAAACTTTAAATCTCAA
1 ACCCTAAACCTTAAACCTCAA
127996 ACC
1 ACC
127999 TTGAACCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCCTAAACCTTAAACCTCAA
Found at i:128162 original size:14 final size:14
Alignment explanation
Indices: 128105--128162 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
128095 GATCAAGGTT
*
128105 CAGGGTTCAGAGTC
1 CAGGGTTCAAAGTC
*
128119 CAGAGGTTCAAAGTT
1 CAG-GGTTCAAAGTC
* * *
128134 TAGGATTTAAAGTC
1 CAGGGTTCAAAGTC
*
128148 CAGGGTTCAATGTC
1 CAGGGTTCAAAGTC
128162 C
1 C
128163 TGGTTAAAAA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
14 22 0.67
15 11 0.33
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (14 bp):
CAGGGTTCAAAGTC
Found at i:128866 original size:15 final size:15
Alignment explanation
Indices: 128820--128870 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
128810 TACTTTTTTA
128820 CTGTTATTTTTGTTG
1 CTGTTATTTTTGTTG
* * * *
128835 GTTTTAATGTTGTTTG
1 CTGTTATTTTTG-TTG
128851 CTGTTATTTTTGTTG
1 CTGTTATTTTTGTTG
128866 CTGTT
1 CTGTT
128871 TTGATTGTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.08, C:0.06, G:0.22, T:0.65
Consensus pattern (15 bp):
CTGTTATTTTTGTTG
Found at i:130662 original size:3 final size:3
Alignment explanation
Indices: 130656--130691 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
130646 GAACACCACC
*
130656 AAG AAG AAG AAG AAG AAG AAG AAG AAT AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
130692 GTGGCGGCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:134006 original size:124 final size:122
Alignment explanation
Indices: 133761--134006 Score: 456
Period size: 123 Copynumber: 2.0 Consensus size: 122
133751 TTTTTTTTTT
133761 TTTTTTTGCATTCTGGTTGAAAATGTGGATGAGAACCACGTGTTTCACATTCTGTGAATAAAAAT
1 TTTTTTTGCATTCTGGTTGAAAATGTGGATGAGAACCACGTGTTTCACATTCTGTGAATAAAAAT
*
133826 AAATGGGAAAATATTTTTTTATATGATGTATTATTAAATTGATTTTGATAATCAAAC
66 AAATGAGAAAATATTTTTTTATATGATGTATTATTAAATTGATTTTGATAATCAAAC
*
133883 NTTTTTTTGCATTCTGGTTGAAAATGTGGATGAGAACCACGTGTTTCACATTTTGTGAATAAAAA
1 -TTTTTTTGCATTCTGGTTGAAAATGTGGATGAGAACCACGTGTTTCACATTCTGTGAATAAAAA
133948 TAAATGAGAAAATATTTTTTTTATATGATGTATTATTAAATTGATTTTGATAATCAAAC
65 TAAATGAGAAAATA-TTTTTTTATATGATGTATTATTAAATTGATTTTGATAATCAAAC
134007 CGTATGTGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
123 76 0.63
124 44 0.37
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (122 bp):
TTTTTTTGCATTCTGGTTGAAAATGTGGATGAGAACCACGTGTTTCACATTCTGTGAATAAAAAT
AAATGAGAAAATATTTTTTTATATGATGTATTATTAAATTGATTTTGATAATCAAAC
Found at i:134582 original size:41 final size:41
Alignment explanation
Indices: 134525--134616 Score: 184
Period size: 41 Copynumber: 2.2 Consensus size: 41
134515 AAAAATGTGT
134525 GGTTGTTAGGATGCAAAGTGGATTATTTTGCACTTTGCAAA
1 GGTTGTTAGGATGCAAAGTGGATTATTTTGCACTTTGCAAA
134566 GGTTGTTAGGATGCAAAGTGGATTATTTTGCACTTTGCAAA
1 GGTTGTTAGGATGCAAAGTGGATTATTTTGCACTTTGCAAA
134607 GGTTGTTAGG
1 GGTTGTTAGG
134617 TGAGAACTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.25, C:0.09, G:0.29, T:0.37
Consensus pattern (41 bp):
GGTTGTTAGGATGCAAAGTGGATTATTTTGCACTTTGCAAA
Found at i:135427 original size:14 final size:15
Alignment explanation
Indices: 135396--135429 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
135386 TTAAAAGGTG
*
135396 GGAACATTAAATTCT
1 GGAAAATTAAATTCT
135411 GGAAAATTAAA-TCT
1 GGAAAATTAAATTCT
135425 GGAAA
1 GGAAA
135430 TTTGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (15 bp):
GGAAAATTAAATTCT
Found at i:149154 original size:27 final size:25
Alignment explanation
Indices: 149107--149156 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
149097 TATTGCTAAT
*
149107 TTATATGGTATGAAATTTTAATACA
1 TTATATGGTATGAAATATTAATACA
*
149132 TTATATTGTAATGTAAATATTAATA
1 TTATATGGT-ATG-AAATATTAATA
149157 AATATGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 3 0.14
27 10 0.48
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (25 bp):
TTATATGGTATGAAATATTAATACA
Found at i:149580 original size:23 final size:22
Alignment explanation
Indices: 149542--149595 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
149532 TCTTATCCAC
149542 AATAT-AT-ATTTATTTTGAGA
1 AATATAATAATTTATTTTGAGA
* *
149562 GAATATAATAATTTTTTTTGATA
1 -AATATAATAATTTATTTTGAGA
149585 AATTATAATAA
1 AA-TATAATAA
149596 CAGAAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 4 0.14
23 19 0.68
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
AATATAATAATTTATTTTGAGA
Found at i:150133 original size:28 final size:28
Alignment explanation
Indices: 150101--150156 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
150091 TTTTTCTCTC
* *
150101 TTTGTTGGTTTGAATCTTCTTGTTTTGA
1 TTTGTTGGTTTGAATCTTATCGTTTTGA
150129 TTTGTTGGTTTGAATCTTATCGTTTTGA
1 TTTGTTGGTTTGAATCTTATCGTTTTGA
150157 GTTGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.12, C:0.07, G:0.21, T:0.59
Consensus pattern (28 bp):
TTTGTTGGTTTGAATCTTATCGTTTTGA
Done.