Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000832.1 Hibiscus syriacus cultivar Beakdansim tig00001608_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: 141224
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2988 original size:22 final size:23
Alignment explanation
Indices: 2941--2988 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
2931 TGACCCAACT
2941 CCTGATCAGCACCGTTCTGTGACA
1 CCTGATCAGCACCGTTC-GTGACA
* *
2965 CCTGATCCGCACTGTTC-TGACA
1 CCTGATCAGCACCGTTCGTGACA
2987 CC
1 CC
2989 CTGAATATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
24 15 0.68
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.25
Consensus pattern (23 bp):
CCTGATCAGCACCGTTCGTGACA
Found at i:5031 original size:23 final size:23
Alignment explanation
Indices: 5005--5053 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
4995 TGGTGGTTAG
*
5005 TTTAATGG-ATGTTTGAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
5028 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
5051 TTT
1 TTT
5054 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:11799 original size:29 final size:30
Alignment explanation
Indices: 11738--11834 Score: 105
Period size: 29 Copynumber: 3.3 Consensus size: 30
11728 TAAAATTTAC
*
11738 AACTATAGT-ATTAAAATATAAAAAGTAATAA
1 AACT-TAGTGATTAAAATAT-AAAAGTATTAA
*
11769 AACTT-GT-AGTTAAAAAATAAAAGTATTAA
1 AACTTAGTGA-TTAAAATATAAAAGTATTAA
*
11798 AA-TTAGTGATTAAAATATAAAA-TATTTA
1 AACTTAGTGATTAAAATATAAAAGTATTAA
11826 AACTTAGTG
1 AACTTAGTG
11835 CTCTAATTTG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
28 9 0.16
29 35 0.60
30 10 0.17
31 4 0.07
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (30 bp):
AACTTAGTGATTAAAATATAAAAGTATTAA
Found at i:13018 original size:3 final size:3
Alignment explanation
Indices: 13012--13049 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
13002 TTTTTTTATT
*
13012 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA
13050 TGATGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:13314 original size:45 final size:45
Alignment explanation
Indices: 13216--13472 Score: 410
Period size: 45 Copynumber: 5.7 Consensus size: 45
13206 CACTATAGTT
*
13216 CTTACAGATGACCCGAAGGATTTT--AAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTGAAGGG
*
13260 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGAG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
** *
13305 CTTGTAGATGACCCGAAGGTTTTGAAAACAACATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
13350 CTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
13395 CTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
* *
13440 CTTACAGATGACCCGAAGGCTTTGAAAATATCA
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
13473 AAAAGCTCCC
Statistics
Matches: 196, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
43 4 0.02
44 19 0.10
45 173 0.88
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
Found at i:13449 original size:135 final size:134
Alignment explanation
Indices: 13216--13659 Score: 445
Period size: 135 Copynumber: 3.4 Consensus size: 134
13206 CACTATAGTT
* *
13216 CTTACAGATGACCCGAAGGATTTTAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGTT
1 CTTACAGATGACCCGAAGGATTTTAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
** *
13281 TTGAAAACATCATGCACTGAAGAGCTTGTAGATGACCCGAAGGTTTTGAAAACAACATGCACTGA
66 TTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACAACATGCACTGA
13346 AGGG
131 AGGG
*
13350 CTTACAGATGACCTGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 CTTACAGATGACCCGAAGGATTTT--AAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
* *
13414 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTG--AA-AATAT-CA--
64 TTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACAACATGCACT
**
13473 -AAAAG
129 GAAGGG
* * * ***** ** * * * *
13478 C-TCCCGA--A--GGCTTTTTTGAAAACATCCTGCACTGTAGGACTTACAGATGACCCGAAGGAT
1 CTTACAGATGACCCGAAGGATTTTAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG-T
* * *
13538 TTT--AAACATCATGCACTGAAG-GTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACT
65 TTTGAAAACATCATGCACTGAAGAG-CTTACAGATGACCCGAAGGCTTTGAAAACAACATGCACT
*
13600 GAAAGG
129 GAAGGG
* *
13606 CTTACAGATGACCCTAAGG-TTTTGAAAACATCATGCATTGAAGGGCTTACAGAT
1 CTTACAGATGACCCGAAGGATTTT--AAACATCATGCACTGAAGGGCTTACAGAT
13660 ATGGGAAAAA
Statistics
Matches: 249, Mismatches: 42, Indels: 38
0.76 0.13 0.12
Matches are distributed among these distances:
120 1 0.00
121 40 0.16
122 35 0.14
123 7 0.03
124 5 0.02
125 3 0.01
127 4 0.02
128 9 0.04
129 4 0.02
131 3 0.01
132 6 0.02
133 6 0.02
134 43 0.17
135 83 0.33
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (134 bp):
CTTACAGATGACCCGAAGGATTTTAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTT
TTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGCTTTGAAAACAACATGCACTGA
AGGG
Found at i:13585 original size:121 final size:121
Alignment explanation
Indices: 13369--13593 Score: 353
Period size: 121 Copynumber: 1.9 Consensus size: 121
13359 GACCTGAAGG
*
13369 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGTTTT-AAAACATCATGCACT
*
13434 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
65 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * *
13491 TTTTGAAAACATCCTGCACTGTAGGACTTACAGATGACCCGAAGGATTTT-AAACATCATGCACT
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGG-TTTTAAAACATCATGCACT
* * *
13555 GAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCA
65 GAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
13594 TGCACTGAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
121 49 0.52
122 41 0.44
123 4 0.04
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (121 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCAAAGGTTTTAAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:13599 original size:45 final size:44
Alignment explanation
Indices: 13491--13659 Score: 234
Period size: 45 Copynumber: 3.8 Consensus size: 44
13481 CCGAAGGCTT
* *
13491 TTTTGAAAACATCCTGCACTGTAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGG
*
13536 ATTTT--AAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGG
1 -TTTTGAAAACATCATGCACTGAAGG-CTTACAGATGACCCGAAGG
*
13580 TTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCTAAGG
1 TTTTGAAAACATCATGCACTG-AAGGCTTACAGATGACCCGAAGG
*
13625 TTTTGAAAACATCATGCATTGAAGGGCTTACAGAT
1 TTTTGAAAACATCATGCACTGAA-GGCTTACAGAT
13660 ATGGGAAAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
43 4 0.04
44 37 0.33
45 63 0.56
46 8 0.07
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
TTTTGAAAACATCATGCACTGAAGGCTTACAGATGACCCGAAGG
Found at i:13599 original size:166 final size:166
Alignment explanation
Indices: 13324--13638 Score: 497
Period size: 166 Copynumber: 1.9 Consensus size: 166
13314 GACCCGAAGG
* *
13324 TTTTGAAAACAACATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACT
1 TTTTGAAAACAACATGCACTGAAGGACTTACAGATGACCCGAAGGTTTT-AAAACATCATGCACT
*
13389 GAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
65 GAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCC
*
13454 GAAGGCTTTGAAAATATCAAAAAGCTCCCGAAGGCTT
130 GAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * *
13491 TTTTGAAAACATCCTGCACTGTAGGACTTACAGATGACCCGAAGGATTTT-AAACATCATGCACT
1 TTTTGAAAACAACATGCACTGAAGGACTTACAGATGACCCGAAGG-TTTTAAAACATCATGCACT
* * *
13555 GAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCC
65 GAAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCC
* *
13620 TAAGGTTTTGAAAACATCA
130 GAAGGCTTTGAAAACATCA
13639 TGCATTGAAG
Statistics
Matches: 135, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
166 91 0.67
167 40 0.30
168 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (166 bp):
TTTTGAAAACAACATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTAAAACATCATGCACTG
AAGGGCTTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCG
AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:13650 original size:211 final size:211
Alignment explanation
Indices: 13279--13659 Score: 622
Period size: 211 Copynumber: 1.8 Consensus size: 211
13269 GACCCGAAGG
**
13279 TTTTGAAAACATCATGCACTGAAGAGCTTGTAGATGACCCGAAGGTTTTGAAAACAACATGCACT
1 TTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGTTTT-AAAACAACATGCACT
* *
13344 GAAGGGCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCC
65 GAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCC
13409 AAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAA
130 AAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAA
13474 AAAGCTCCCGAAGGCTT
195 AAAGCTCCCGAAGGCTT
* * *
13491 TTTTGAAAACATCCTGCACTGTAG-GACTTACAGATGACCCGAAGGATTTT-AAACATCATGCAC
1 TTTTGAAAACATCATGCACTGAAGAG-CTTACAGATGACCCGAAGG-TTTTAAAACAACATGCAC
* *
13554 TGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACC
64 TGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACC
* *
13619 CTAAGGTTTTGAAAACATCATGCATTGAAGGGCTTACAGAT
129 CAAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGAT
13660 ATGGGAAAAA
Statistics
Matches: 156, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
211 113 0.72
212 39 0.25
213 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (211 bp):
TTTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGTTTTAAAACAACATGCACTG
AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAAGGCTTACAGATGACCCA
AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAATATCAAA
AAGCTCCCGAAGGCTT
Found at i:14381 original size:22 final size:22
Alignment explanation
Indices: 14326--14382 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
14316 AATAAAGCTT
*
14326 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
14348 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
14370 TCATTTTTGAAGA
1 TCATCTTTGAAGA
14383 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:21131 original size:20 final size:20
Alignment explanation
Indices: 21108--21154 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
21098 TGCAAAAATG
21108 AAAATGTAAATACAAACGTA
1 AAAATGTAAATACAAACGTA
** *
21128 AAAATACAAATACAAATGTA
1 AAAATGTAAATACAAACGTA
*
21148 AATATGT
1 AAAATGT
21155 GAACGTAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.09, T:0.23
Consensus pattern (20 bp):
AAAATGTAAATACAAACGTA
Found at i:21408 original size:43 final size:43
Alignment explanation
Indices: 21324--21410 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
21314 CCGTGCATCA
* *
21324 AACAAAACTTTTACATGAAGGGGATAGCTTTCAGTCCTAACTTC
1 AACAAAACTTTTACAT-AAGGGGATAACTTTCACTCCTAACTTC
* * *
21368 AACAAAAC-TTTATATATAGGGGATAACTTTCCCTCTTAACTTC
1 AACAAAACTTTTACATA-AGGGGATAACTTTCACTCCTAACTTC
21411 TCTAAAGCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.03
43 28 0.76
44 8 0.22
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (43 bp):
AACAAAACTTTTACATAAGGGGATAACTTTCACTCCTAACTTC
Found at i:23793 original size:26 final size:26
Alignment explanation
Indices: 23757--23806 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
23747 TAAAATATAA
23757 AAAGTAATAAAACTAGTAATTAAATG
1 AAAGTAATAAAACTAGTAATTAAATG
* * *
23783 AAAGTATTAAAATTAGTGATTAAA
1 AAAGTAATAAAACTAGTAATTAAA
23807 ATGTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.02, G:0.12, T:0.30
Consensus pattern (26 bp):
AAAGTAATAAAACTAGTAATTAAATG
Found at i:24999 original size:2 final size:2
Alignment explanation
Indices: 24992--25020 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24982 AATATTAATA
24992 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
25021 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34117 original size:24 final size:24
Alignment explanation
Indices: 34090--34141 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
34080 CGTTCATTTA
* *
34090 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
34114 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
34138 CGTT
1 CGTT
34142 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:34128 original size:14 final size:14
Alignment explanation
Indices: 34111--34141 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34101 GTTCGGTTAT
*
34111 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
34125 GTTCGATTATGTTC
1 GTTCGATTATGTTC
34139 GTT
1 GTT
34142 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:34142 original size:24 final size:24
Alignment explanation
Indices: 34100--34161 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
34090 CGTTCGTGAA
*
34100 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
34124 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
34148 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
34162 TAATCCAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:34903 original size:10 final size:10
Alignment explanation
Indices: 34888--34946 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
34878 GGGTCTCCAA
34888 CGTTTATGTT
1 CGTTTATGTT
34898 CGTTTATGTT
1 CGTTTATGTT
34908 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
34919 ATGTTCGTGTT
1 -CGTTTATGTT
34930 CGTTTATGTT
1 CGTTTATGTT
34940 CGTTTAT
1 CGTTTAT
34947 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:34919 original size:16 final size:16
Alignment explanation
Indices: 34894--34950 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
34884 CCAACGTTTA
*
34894 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
34910 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
34926 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
34942 T-TT-ATTTAT
1 TGTTCATTTAT
34951 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:35033 original size:16 final size:16
Alignment explanation
Indices: 35012--35044 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35002 AAAAAAATTT
35012 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
35028 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
35044 T
1 T
35045 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:35097 original size:15 final size:15
Alignment explanation
Indices: 35077--35115 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
35067 TGAACATACC
35077 TCCGTTCGTGTGCGT
1 TCCGTTCGTGTGCGT
35092 TCCGTTCGTGTGCGT
1 TCCGTTCGTGTGCGT
*
35107 TCGGTTCGT
1 TCCGTTCGT
35116 TTACAGGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.33, T:0.41
Consensus pattern (15 bp):
TCCGTTCGTGTGCGT
Found at i:36051 original size:15 final size:15
Alignment explanation
Indices: 36033--36077 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
36023 GAATAAAGTG
*
36033 AAAAAAAATAAAATT
1 AAAAAAATTAAAATT
36048 AAAATAAATTAAAA-T
1 AAAA-AAATTAAAATT
36063 AAATAAAATTAAAAT
1 AAA-AAAATTAAAAT
36078 GAATAATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAAAATTAAAATT
Found at i:36066 original size:25 final size:26
Alignment explanation
Indices: 36024--36077 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
36014 TTTGGGCTAG
36024 AATAAAGTGAAAAAAAATAAAATTAA
1 AATAAAGTGAAAAAAAATAAAATTAA
* *
36050 AATAAA-TTAAAATAAATAAAATTAA
1 AATAAAGTGAAAAAAAATAAAATTAA
36075 AAT
1 AAT
36078 GAATAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (26 bp):
AATAAAGTGAAAAAAAATAAAATTAA
Found at i:36075 original size:10 final size:10
Alignment explanation
Indices: 36037--36071 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
36027 AAAGTGAAAA
36037 AAAATAAAATT
1 AAAAT-AAATT
36048 AAAATAAATT
1 AAAATAAATT
36058 AAAATAAA-T
1 AAAATAAATT
36067 AAAAT
1 AAAAT
36072 TAAAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.25
10 13 0.54
11 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATAAATT
Found at i:36082 original size:15 final size:15
Alignment explanation
Indices: 36049--36083 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36039 AATAAAATTA
36049 AAAT-AAATTAAAAT
1 AAATAAAATTAAAAT
36063 AAATAAAATTAAAAT
1 AAATAAAATTAAAAT
*
36078 GAATAA
1 AAATAA
36084 TTTGGAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATAAAATTAAAAT
Found at i:36693 original size:22 final size:22
Alignment explanation
Indices: 36650--36694 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
36640 TAACCTTGAA
* * *
36650 TTTCTTTTTTTTTTTGGGTGTT
1 TTTCTTGTTATTTTTGCGTGTT
*
36672 TTTCTTGTTATTTTTGCTTGTT
1 TTTCTTGTTATTTTTGCGTGTT
36694 T
1 T
36695 CTTAGGCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.02, C:0.07, G:0.16, T:0.76
Consensus pattern (22 bp):
TTTCTTGTTATTTTTGCGTGTT
Found at i:37193 original size:11 final size:11
Alignment explanation
Indices: 37179--37221 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 11
37169 GATGGATCTG
37179 AAATAAAAATA
1 AAATAAAAATA
37190 AAAT-AAAATA
1 AAATAAAAATA
37200 AAGATAAAAATGGA
1 AA-ATAAAAAT--A
37214 AAATAAAA
1 AAATAAAA
37222 TATTAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 6 0.21
12 5 0.18
13 6 0.21
14 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:37287 original size:21 final size:21
Alignment explanation
Indices: 37262--37314 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
37252 ATTATATAAT
37262 ATATATTATATTTCAAAAACA
1 ATATATTATATTTCAAAAACA
** * * **
37283 ATATAACATTTTTCAAAGATT
1 ATATATTATATTTCAAAAACA
37304 ATATATTATAT
1 ATATATTATAT
37315 ATGTTTTCAA
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATTATATTTCAAAAACA
Found at i:37321 original size:26 final size:26
Alignment explanation
Indices: 37292--37375 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
37282 AATATAACAT
37292 TTTTCAAAGATTATATATTATATATG
1 TTTTCAAAGATTATATATTATATATG
*
37318 TTTTCAAAGACCGTT-T-TAATA-ATATG
1 TTTTCAAAGA---TTATATATTATATATG
*
37344 TTTTC-AA-A-TACTATATTATATACG
1 TTTTCAAAGATTA-TATATTATATATG
37368 TTTTCAAA
1 TTTTCAAA
37376 AATTGTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
20 1 0.02
22 1 0.02
23 4 0.09
24 10 0.21
25 4 0.09
26 20 0.43
27 4 0.09
28 1 0.02
29 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (26 bp):
TTTTCAAAGATTATATATTATATATG
Found at i:37375 original size:24 final size:24
Alignment explanation
Indices: 37305--37375 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 24
37295 TCAAAGATTA
37305 TATATTATATATGTTTTCAAAGAC
1 TATATTATATATGTTTTCAAAGAC
** * *
37329 CGTTTTAATAATATGTTTTCAAATAC
1 TATATT-AT-ATATGTTTTCAAAGAC
*
37355 TATATTATATACGTTTTCAAA
1 TATATTATATATGTTTTCAAA
37376 AATTGTTTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 15 0.41
25 4 0.11
26 18 0.49
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (24 bp):
TATATTATATATGTTTTCAAAGAC
Found at i:37428 original size:38 final size:39
Alignment explanation
Indices: 37355--37492 Score: 181
Period size: 38 Copynumber: 3.5 Consensus size: 39
37345 TTTCAAATAC
* *
37355 TATATTATATACGTTTTCAAAAATTGTTTTCTAAAAAACTA
1 TATATTATAT--GTTTTCAAAAATCGTTTTTTAAAAAACTA
* * *
37396 TATTTTATATGTTTT-AAAAACCATTTTTTAAAAAACTA
1 TATATTATATGTTTTCAAAAATCGTTTTTTAAAAAACTA
*
37434 TATATTATATGTTTTCAAAAATCGCTTTTT-AAAAACTA
1 TATATTATATGTTTTCAAAAATCGTTTTTTAAAAAACTA
*
37472 TATATTAAATGTTTTCAAAAA
1 TATATTATATGTTTTCAAAAA
37493 AAAAAATTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
38 61 0.71
39 16 0.19
41 9 0.10
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (39 bp):
TATATTATATGTTTTCAAAAATCGTTTTTTAAAAAACTA
Found at i:37506 original size:38 final size:38
Alignment explanation
Indices: 37426--37512 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 38
37416 CCATTTTTTA
* ****** *
37426 AAAAACTATATATTATATGTTTTCAAAAATCGCTTTTT
1 AAAAACTATATATTAAATGTTTTCAAAAAAAAAAATTC
37464 AAAAACTATATATTAAATGTTTTCAAAAAAAAAAATTC
1 AAAAACTATATATTAAATGTTTTCAAAAAAAAAAATTC
37502 AAAAACTATAT
1 AAAAACTATAT
37513 TATATATCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (38 bp):
AAAAACTATATATTAAATGTTTTCAAAAAAAAAAATTC
Found at i:37537 original size:19 final size:21
Alignment explanation
Indices: 37499--37538 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
37489 AAAAAAAAAA
37499 TTCAAAAACTATATTATATATC
1 TTCAAAAAC-ATATTATATATC
37521 TTCAAAAAC-TA-TATATAT
1 TTCAAAAACATATTATATAT
37539 TGTATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
22 9 0.50
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (21 bp):
TTCAAAAACATATTATATATC
Found at i:39506 original size:37 final size:37
Alignment explanation
Indices: 39463--39554 Score: 157
Period size: 37 Copynumber: 2.5 Consensus size: 37
39453 ATTTTGCTTT
* *
39463 ACTACTCTTCCGTGAAGGCTTAAGATTGATTTCCTTC
1 ACTACTCTTCCGTGAAGGCTTAAGATCGATTTACTTC
39500 ACTACTCTTCCGTGAAGGCTTAAGATCGATTTACTTC
1 ACTACTCTTCCGTGAAGGCTTAAGATCGATTTACTTC
*
39537 ACTACTCTTCTGTGAAGG
1 ACTACTCTTCCGTGAAGG
39555 TTTTAGATAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (37 bp):
ACTACTCTTCCGTGAAGGCTTAAGATCGATTTACTTC
Found at i:39913 original size:42 final size:41
Alignment explanation
Indices: 39840--39920 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
39830 AGGTTTTATG
*
39840 GATGGCCCGAAGGACTTATCATCTTGATCAAAAGACTTACA
1 GATGACCCGAAGGACTTATCATCTTGATCAAAAGACTTACA
* *
39881 GATGACCCGAAGGATTTAATCATCATT-CTCAAAAGACTTA
1 GATGACCCGAAGGACTT-ATCATC-TTGATCAAAAGACTTA
39921 TTGATGGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 15 0.43
42 18 0.51
43 2 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCTTGATCAAAAGACTTACA
Found at i:40155 original size:235 final size:237
Alignment explanation
Indices: 39653--40175 Score: 728
Period size: 235 Copynumber: 2.2 Consensus size: 237
39643 AGATGACGTA
* *
39653 AAGGATTTAATCATCATACTCAAAAGACTTACTGATGGCTCGAAGGTCTTACTAAGTAAGAAACT
1 AAGGATTTAATCATCATACTCAAAAGACTTACTGATGGCCCGAAGGTCTTAATAAGTAAGAAACT
*
39718 TTGGAAATCGCTTTATTACTTTTCAAAAATTTCATCTTTAAAAAACATTAAATGAGAAACTTTGA
66 TTGGAAATCGCTTTATTACTTTTCAAAAATTTCATCTTCAAAAAACATTAAATGAGAAACTTTGA
* * * * ** *
39783 AAATCACTTTCTCATTTTTCAAATTTATGTGAAAATATCCTACCCAAAGGTTTTATGGATGGCCC
131 AAATCACTTTCTCAATTTTCAAATTCATATGAAAACATCCTACCCAAAGGTCCTATGGATGACCC
*
39848 GAAGGACTTATCATCTTGATCAAAAGACTTACAGATGACCCG
196 GAAGGACTTATCATCTTCATCAAAAGACTTACAGATGACCCG
* * * *
39890 AAGGATTTAATCATCATTCTCAAAAGACTTATTGATGGCCCGGATGTCTTAATAAGTAAGAAACT
1 AAGGATTTAATCATCATACTCAAAAGACTTACTGATGGCCCGAAGGTCTTAATAAGTAAGAAACT
* * *
39955 TTGGAAATCGCTTTCTTACTTTTC-AAAATTTCATCTTCAAAAAACATTAAATGATAAACTTTTA
66 TTGGAAATCGCTTTATTACTTTTCAAAAATTTCATCTTCAAAAAACATTAAATGAGAAACTTTGA
* * *
40019 AAATCGCTTTCT-AATTTTCAAATTCATATGAAAACATCCTGCCCAAAGGTCCTATGGATGACCT
131 AAATCACTTTCTCAATTTTCAAATTCATATGAAAACATCCTACCCAAAGGTCCTATGGATGACCC
* * *** *
40083 G-AGAGACTTATTATCTTCCTTGGAAGGCTTACAGATGACCCG
196 GAAG-GACTTATCATCTTCATCAAAAGACTTACAGATGACCCG
* * * * *
40125 AATGATTTAATCATCATGCTCGACAGACTTACTGATGGCCCGAAGGACTTA
1 AAGGATTTAATCATCATACTCAAAAGACTTACTGATGGCCCGAAGGTCTTA
40176 TCATCTTCGA
Statistics
Matches: 250, Mismatches: 35, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
234 2 0.01
235 118 0.47
236 48 0.19
237 82 0.33
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (237 bp):
AAGGATTTAATCATCATACTCAAAAGACTTACTGATGGCCCGAAGGTCTTAATAAGTAAGAAACT
TTGGAAATCGCTTTATTACTTTTCAAAAATTTCATCTTCAAAAAACATTAAATGAGAAACTTTGA
AAATCACTTTCTCAATTTTCAAATTCATATGAAAACATCCTACCCAAAGGTCCTATGGATGACCC
GAAGGACTTATCATCTTCATCAAAAGACTTACAGATGACCCG
Found at i:44800 original size:75 final size:73
Alignment explanation
Indices: 44669--44894 Score: 257
Period size: 75 Copynumber: 3.1 Consensus size: 73
44659 ATTTGAATTA
* * *
44669 AATTCAAGTTTAGGATAATATTTTAAATATTATATTTTATCTTT--GTATTTTAGTTTAAATAGG
1 AATT-AAGTTTAGGATATTATTTT-TATATTTTATTTT-T-TTTAGGTATTTTAGTTTAAATAGG
*
44732 TTTTATTATTTT
62 TTTTAGTATTTT
44744 AATTAAGTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTT
1 AATTAAGTTTAGGATATTATTTTTATATTTTAT-TTT-TTTTAGGTATTTTAGTTTAAATAGGTT
44809 TTAGTATTTT
64 TTAGTATTTT
* * * *
44819 AATTAGGATTTAGAATATTA-TTTTAAATATTA--TTTTTTAGGTATTTTAGTTTAAATA-GTTT
1 AATTAAG-TTTAGGATATTATTTTTATATTTTATTTTTTTTAGGTATTTTAGTTTAAATAGGTTT
*
44880 TAAGTGTTTT
65 T-AGTATTTT
44890 AATTA
1 AATTA
44895 GGATTTAAGA
Statistics
Matches: 136, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
70 5 0.04
71 35 0.26
72 2 0.01
73 11 0.08
74 22 0.16
75 50 0.37
76 11 0.08
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (73 bp):
AATTAAGTTTAGGATATTATTTTTATATTTTATTTTTTTTAGGTATTTTAGTTTAAATAGGTTTT
AGTATTTT
Found at i:45260 original size:18 final size:18
Alignment explanation
Indices: 45237--45282 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
45227 AACTTTTGAA
45237 GAAGGATATTTGCTTATT
1 GAAGGATATTTGCTTATT
45255 GAAGGATATTTGCTTATT
1 GAAGGATATTTGCTTATT
* *
45273 AAAGTATATT
1 GAAGGATATT
45283 CGACTTCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (18 bp):
GAAGGATATTTGCTTATT
Found at i:50319 original size:32 final size:31
Alignment explanation
Indices: 50277--50338 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
50267 TTTAAATAAG
50277 TTTTAATATTTTA-ATTAAGTTTTAGGATATTA
1 TTTTAATATTTTATATT-AGTTTTAGG-TATTA
* *
50309 TTTTTATATTTTATATTTGTTTTAGGTATT
1 TTTTAATATTTTATATTAGTTTTAGGTATT
50339 TTAGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 4 0.15
32 20 0.74
33 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (31 bp):
TTTTAATATTTTATATTAGTTTTAGGTATTA
Found at i:50325 original size:76 final size:72
Alignment explanation
Indices: 50243--50447 Score: 234
Period size: 76 Copynumber: 2.8 Consensus size: 72
50233 ATTTTAAACA
* * *
50243 TTATATTTTATCTTTGTATTTTAGTTTAAATAAGTTTTAATATTTTAATTAAGTTTTAGGATATT
1 TTATATTTT-T-TTGGTATTTTAGTTTAAATAAGTTTTAATATTTTAATTAAGATTTAGAATATT
*
50308 ATTTTTATATT
64 A-TTTTACA-T
* * *
50319 TTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTATATTT-TTTT-GGTATTTTAGTTTAAATAAGTTTTAATATTTTAATTAAGATTTAGAATATT
50384 ATTTTACAT
64 ATTTTACAT
* * * *
50393 AT-TATTTTTTAGGTATTTTAGTTTAAAT-AGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATATTTTTTTGGTATTTTAGTTTAAATAAGTTTTAA-TATTTTAATTAAGATTTA
50448 AGATGTTTTA
Statistics
Matches: 114, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
70 6 0.05
71 34 0.30
72 3 0.03
73 5 0.04
74 2 0.02
75 8 0.07
76 55 0.48
77 1 0.01
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.58
Consensus pattern (72 bp):
TTATATTTTTTTGGTATTTTAGTTTAAATAAGTTTTAATATTTTAATTAAGATTTAGAATATTAT
TTTACAT
Found at i:51047 original size:17 final size:17
Alignment explanation
Indices: 51022--51055 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51012 CTTTATCCCA
*
51022 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
51039 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
51056 CTTCTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:54919 original size:24 final size:25
Alignment explanation
Indices: 54861--54919 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
54851 AATGTCAAAT
54861 AATTTAAGAA-ATTAAAAATTTAGA
1 AATTTAAGAATATTAAAAATTTAGA
** *
54885 AGGTTATGAATA-T-AAAATTTAAGA
1 AATTTAAGAATATTAAAAATTT-AGA
54909 AATTTAAGAAT
1 AATTTAAGAAT
54920 TTAGAATGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 7 0.26
24 19 0.70
25 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (25 bp):
AATTTAAGAATATTAAAAATTTAGA
Found at i:54944 original size:40 final size:36
Alignment explanation
Indices: 54857--54957 Score: 87
Period size: 40 Copynumber: 2.6 Consensus size: 36
54847 TAATAATGTC
*
54857 AAATAATTTAAGAAATTAAAAATTTAGAAGGTTATG
1 AAATAATTTAAGAAATTAAAAATTTAGAAGGTAATG
* *
54893 AATATAAAATTTAAGAAATTTAAGAATTTAGAATGTCAAATTG
1 AA-AT--AATTTAAGAAA-TTAAAAATTTAGAAGGT--AA-TG
* *
54936 AAATAATTTGA-AAATTATAAAT
1 AAATAATTTAAGAAATTAAAAAT
54958 AATTATATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
36 2 0.04
37 2 0.04
38 6 0.12
39 14 0.27
40 21 0.40
42 3 0.06
43 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.11, T:0.35
Consensus pattern (36 bp):
AAATAATTTAAGAAATTAAAAATTTAGAAGGTAATG
Found at i:54983 original size:2 final size:2
Alignment explanation
Indices: 54978--55016 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
54968 AATAAAAACA
54978 AT 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 AT A
55017 ATAAATCTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58480 original size:8 final size:8
Alignment explanation
Indices: 58467--58491 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
58457 CGACGGAATA
58467 GGTTTTGG
1 GGTTTTGG
58475 GGTTTTGG
1 GGTTTTGG
58483 GGTTTTGG
1 GGTTTTGG
58491 G
1 G
58492 TGTTCTTGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (8 bp):
GGTTTTGG
Found at i:70448 original size:42 final size:43
Alignment explanation
Indices: 70378--70513 Score: 222
Period size: 42 Copynumber: 3.2 Consensus size: 43
70368 TAAAGGTCGT
*
70378 AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAATCTC
1 AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGAATCTC
*
70421 AATTATAAAGG-AAAAAGTGATATTAACAAAATTAGGAATCTC
1 AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGAATCTC
* *
70463 AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGTACCTC
1 AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGAATCTC
70506 -ATTATAAA
1 AATTATAAA
70514 CATAAAAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
42 48 0.55
43 39 0.45
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.24
Consensus pattern (43 bp):
AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGAATCTC
Found at i:70567 original size:85 final size:85
Alignment explanation
Indices: 70378--70555 Score: 218
Period size: 85 Copynumber: 2.1 Consensus size: 85
70368 TAAAGGTCGT
* * * * *
70378 AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAATCTCAATTATAAAGGAAAAAGTGATA
1 AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAACCTCAATTATAAAAGAAAAAATAAGA
70443 TTAACAAAATTAGGAATCTC
66 TTAACAAAATTAGGAATCTC
* * *
70463 AATTATAAAGGCAAAAAGTGATACTAACAAAATTAGGTACCTC-ATTATAAACATAAAAAATAAG
1 AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAACCTCAATTATAAA-AGAAAAAATAAG
* **
70527 ATTGAA-AAATTTAGGGCT-TC
65 ATT-AACAAAATTAGGAATCTC
70547 AATTATAAA
1 AATTATAAA
70556 AGGTTAAAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
84 19 0.24
85 59 0.74
86 2 0.03
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (85 bp):
AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAACCTCAATTATAAAAGAAAAAATAAGA
TTAACAAAATTAGGAATCTC
Found at i:70577 original size:42 final size:42
Alignment explanation
Indices: 70378--70737 Score: 250
Period size: 43 Copynumber: 8.4 Consensus size: 42
70368 TAAAGGTCGT
* * * * **
70378 AATTATAAAGGCAAAAAGTGAGACTAACAAAATTAGGAATCTC
1 AATTATAAAGGTAAAAAGTGTGATTAAAAAAATTAGG-GCCTC
* **
70421 AATTATAAAGG-AAAAAGTGAT-ATTAACAAAATTAGGAATCTC
1 AATTATAAAGGTAAAAAGTG-TGATTAAAAAAATTAGG-GCCTC
* * * *
70463 AATTATAAAGGCAAAAAGTGAT-ACTAACAAAATTAGGTACCTC
1 AATTATAAAGGTAAAAAGTG-TGATTAAAAAAATTAGG-GCCTC
** * ** * * *
70506 -ATTATAAACATAAAAAATAAGATTGAAAAATTTAGGGCTTC
1 AATTATAAAGGTAAAAAGTGTGATTAAAAAAATTAGGGCCTC
* * * *
70547 AATTATAAAAGGTTAAAAGTGTGAATAAAAAACAATTAGGGGCTT
1 AATTAT-AAAGGTAAAAAGTGTG-ATTAAAAA-AATTAGGGCCTC
*
70592 AAGTTATAAAGGTAAGAAGT-TGTATT-AAAAAATTAGGGCCTC
1 AA-TTATAAAGGTAAAAAGTGTG-ATTAAAAAAATTAGGGCCTC
* * *
70634 AATTATAAAGGTAAAAATTGGGATTGAAAAAATTAGGAGCCTC
1 AATTATAAAGGTAAAAAGTGTGATTAAAAAAATTAGG-GCCTC
* * *
70677 GATTATAAAGGTAAAAAGTG-GTATTGAAAAAAATAAGAGCCAT-
1 AATTATAAAGGTAAAAAGTGTG-ATT-AAAAAAATTAGGGCC-TC
70720 AATTATAAAGGTAAAAAG
1 AATTATAAAGGTAAAAAG
70738 AAAGATAACA
Statistics
Matches: 259, Mismatches: 44, Indels: 28
0.78 0.13 0.08
Matches are distributed among these distances:
41 21 0.08
42 94 0.36
43 99 0.38
44 20 0.08
45 21 0.08
46 4 0.02
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (42 bp):
AATTATAAAGGTAAAAAGTGTGATTAAAAAAATTAGGGCCTC
Found at i:70682 original size:43 final size:43
Alignment explanation
Indices: 70333--70736 Score: 230
Period size: 43 Copynumber: 9.4 Consensus size: 43
70323 AATTAGAGGA
* * * *
70333 TCAATTATAAAGGT-AAAATATGATATTGAAAAAACTA-AAG-G
1 TCAATTATAAAGGTAAAAAT-TGGTATTGAAAAAATTAGGAGCC
* * * **
70374 TCGTAATTATAAAGGCAAAAAGTGAG-ACT-AACAAAATTAGGAATC
1 TC--AATTATAAAGGTAAAAATTG-GTATTGAA-AAAATTAGGAGCC
* * **
70419 TCAATTATAAAGG-AAAAAGTGATATT-AACAAAATTAGGAATC
1 TCAATTATAAAGGTAAAAATTGGTATTGAA-AAAATTAGGAGCC
* * * *
70461 TCAATTATAAAGGCAAAAAGTGATACT-AACAAAATTAGGTA-CC
1 TCAATTATAAAGGTAAAAATTGGTATTGAA-AAAATTAGG-AGCC
** ** * *
70504 TC-ATTATAAACATAAAAAATAAG-ATTGAAAAATTTAGG-GCT
1 TCAATTATAAAGGT-AAAAATTGGTATTGAAAAAATTAGGAGCC
* * * ** *
70545 TCAATTATAAAAGGTTAAAAGTGTGAATAAAAAACAATTAGG-GGC
1 TCAATTAT-AAAGGTAAAAATTG-GTATTGAAAA-AATTAGGAGCC
* *
70590 TTAAGTTATAAAGGTAAGAAGTT-GTATT-AAAAAATTAGG-GCC
1 TCAA-TTATAAAGGTAA-AAATTGGTATTGAAAAAATTAGGAGCC
*
70632 TCAATTATAAAGGTAAAAATTGGGATTGAAAAAATTAGGAGCC
1 TCAATTATAAAGGTAAAAATTGGTATTGAAAAAATTAGGAGCC
* * * *
70675 TCGATTATAAAGGTAAAAAGTGGTATTGAAAAAAATAAGAGCC
1 TCAATTATAAAGGTAAAAATTGGTATTGAAAAAATTAGGAGCC
70718 AT-AATTATAAAGGTAAAAA
1 -TCAATTATAAAGGTAAAAA
70737 GAAAGATAAC
Statistics
Matches: 290, Mismatches: 49, Indels: 46
0.75 0.13 0.12
Matches are distributed among these distances:
40 4 0.01
41 21 0.07
42 91 0.31
43 132 0.46
44 16 0.06
45 19 0.07
46 7 0.02
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (43 bp):
TCAATTATAAAGGTAAAAATTGGTATTGAAAAAATTAGGAGCC
Found at i:70751 original size:86 final size:84
Alignment explanation
Indices: 70336--70755 Score: 203
Period size: 85 Copynumber: 4.9 Consensus size: 84
70326 TAGAGGATCA
* * * **
70336 ATTATAAAGGTAAAATA-TGATATTGAAAAAACTAA-AG-GTCGTAATTATAAAGGCAAAAAGTG
1 ATTATAAAGGTAAAA-AGTGGTATT-AAAAAA-TAAGAGCCTC--AATTATAAAGGTAAAAAGAA
* * ** *
70398 AGACTAACAAAATTAGGAATCTCA
61 AGATTAAAAAAATTAGGAGCCTCG
* * ** * ** *
70422 ATTATAAAGG-AAAAAGTGATATTAACAAAATTAGGAATCTCAATTATAAAGGCAAAAAGTGATA
1 ATTATAAAGGTAAAAAGTGGTATTAA-AAAA-TAAGAGCCTCAATTATAAAGGTAAAAAGAAAGA
* *
70486 CTAACAAAATTAGGTA-CCTC-
64 TTAAAAAAATTAGG-AGCCTCG
** * * * * * * * ***
70506 ATTATAAACATAAAAAATAAG-ATTGAAAAATTTAGGGCTTCAATTATAAAAGGTTAAAAGTGTG
1 ATTATAAAGGTAAAAAGT-GGTATT-AAAAAATAAGAGCCTCAATTAT-AAAGGTAAAAAGAAAG
* * **
70570 AATAAAAAACAATTAGG-GGCTTA
63 -ATTAAAAA-AATTAGGAGCCTCG
* * * * ****
70593 AGTTATAAAGGTAAGAAGTTGTATTAAAAAATTAGGGCCTCAATTATAAAGGTAAAAATTGGGAT
1 A-TTATAAAGGTAAAAAGTGGTATTAAAAAATAAGAGCCTCAATTATAAAGGTAAAAAGAAAGAT
*
70658 TGAAAAAATTAGGAGCCTCG
65 TAAAAAAATTAGGAGCCTCG
70678 ATTATAAAGGTAAAAAGTGGTATTGAAAAAAATAAGAGCCAT-AATTATAAAGGTAAAAAGAAAG
1 ATTATAAAGGTAAAAAGTGGTATT--AAAAAATAAGAGCC-TCAATTATAAAGGTAAAAAGAAAG
70742 A-TAACAAAAATTAG
63 ATTAA-AAAAATTAG
70756 ATGTTTCAAT
Statistics
Matches: 263, Mismatches: 51, Indels: 40
0.74 0.14 0.11
Matches are distributed among these distances:
84 49 0.19
85 92 0.35
86 74 0.28
87 32 0.12
88 16 0.06
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (84 bp):
ATTATAAAGGTAAAAAGTGGTATTAAAAAATAAGAGCCTCAATTATAAAGGTAAAAAGAAAGATT
AAAAAAATTAGGAGCCTCG
Found at i:86519 original size:20 final size:19
Alignment explanation
Indices: 86475--86526 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
86465 TTAGTCAGGG
86475 AGTATCGATACCAATAGGT
1 AGTATCGATACCAATAGGT
86494 AGGTATCGATACCAA-AGGGT
1 A-GTATCGATACCAATA-GGT
*
86514 CAGTATCGGTACC
1 -AGTATCGATACC
86527 CACGAACATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (19 bp):
AGTATCGATACCAATAGGT
Found at i:90881 original size:11 final size:11
Alignment explanation
Indices: 90865--90889 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
90855 TTTATTTTCT
90865 TTCACTTGCAC
1 TTCACTTGCAC
90876 TTCACTTGCAC
1 TTCACTTGCAC
90887 TTC
1 TTC
90890 TTTTTGGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:97380 original size:2 final size:2
Alignment explanation
Indices: 97373--97427 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
97363 CACTATACAG
97373 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
97415 CT CG CT CT CT CT C
1 CT CT CT CT CT CT C
97428 GCTTTAAAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.02, T:0.47
Consensus pattern (2 bp):
CT
Found at i:105471 original size:24 final size:24
Alignment explanation
Indices: 105444--105493 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
105434 ATAAAGAACC
105444 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
105468 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
105492 AA
1 AA
105494 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:106676 original size:15 final size:13
Alignment explanation
Indices: 106638--106681 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
106628 TTACTACACA
*
106638 TTTTTTT-CTCTT
1 TTTTTTTCCTTTT
106650 TTTTTTTCCTTTCT
1 TTTTTTTCCTTT-T
106664 TTTTTTTCACTTTT
1 TTTTTTTC-CTTTT
106678 TTTT
1 TTTT
106682 ACGCTGCTAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 7 0.25
13 3 0.11
14 14 0.50
15 4 0.14
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCCTTTT
Found at i:111067 original size:24 final size:24
Alignment explanation
Indices: 111040--111089 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
111030 ATAAAGAACC
111040 AAAATAAA-CTTAAACATACCATTA
1 AAAATAAAGCTTAAACAT-CCATTA
*
111064 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACATCCATTA
111088 AA
1 AA
111090 CCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAAGCTTAAACATCCATTA
Found at i:116125 original size:40 final size:40
Alignment explanation
Indices: 116071--116146 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
116061 AGGACAATGA
* *
116071 AAAAATACAGATCCAGTAAATCCTACTCAAAGCAAAGTAG
1 AAAAATAAAGATCCAGTAAATCCTACACAAAGCAAAGTAG
*
116111 AAAAATAAAGATCCAGTAGATCCTACACAAAGCAAA
1 AAAAATAAAGATCCAGTAAATCCTACACAAAGCAAA
116147 CCTCAACATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.16
Consensus pattern (40 bp):
AAAAATAAAGATCCAGTAAATCCTACACAAAGCAAAGTAG
Found at i:130865 original size:18 final size:18
Alignment explanation
Indices: 130842--130876 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
130832 AAGTTTATTT
*
130842 AGTATCGATACTCATGGG
1 AGTATCGATACCCATGGG
130860 AGTATCGATACCCATGG
1 AGTATCGATACCCATGG
130877 TAGAGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (18 bp):
AGTATCGATACCCATGGG
Found at i:132133 original size:74 final size:71
Alignment explanation
Indices: 132054--132276 Score: 254
Period size: 74 Copynumber: 3.1 Consensus size: 71
132044 TAAACTCAAG
*
132054 TTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGTTTTAGTATTT
1 TTTAGGATAATATTTTAAATATT-TATTTT-T-TTTGTATTTTAGTTTAAATAGTTTTAGTATTT
*
132119 TAATTAAGT
63 TAATTAAGA
*
132128 TTTAGGATATTATTTT--ATATTTATCTTTGTTTTAGGTATTTTAGTTTAAATAAGTTTTAGTAT
1 TTTAGGATAATATTTTAAATATTTAT-TTT-TTTT--GTATTTTAGTTTAAAT-AGTTTTAGTAT
*
132191 TTTAATTAGGA
61 TTTAATTAAGA
* * ** *
132202 TTAAGAATAATATTTTAAATA-TTATTTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTA
1 TTTAGGATAATATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAGTTTT-AGTATTTTA
*
132266 ATTAGGA
65 ATTAAGA
132273 TTTA
1 TTTA
132277 AGATGTTTTA
Statistics
Matches: 130, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
70 6 0.05
71 40 0.31
72 8 0.06
73 18 0.14
74 51 0.39
75 4 0.03
76 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (71 bp):
TTTAGGATAATATTTTAAATATTTATTTTTTTTGTATTTTAGTTTAAATAGTTTTAGTATTTTAA
TTAAGA
Found at i:132265 original size:71 final size:71
Alignment explanation
Indices: 132090--132279 Score: 249
Period size: 71 Copynumber: 2.6 Consensus size: 71
132080 TTTTATCTTT
* * * * * *
132090 GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTATATTTATCTT
1 GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTAAGAATAATATTTTAAATTTA--TT
132155 TGTTTTAG
64 TGTTTTAG
132163 GTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAGGATTAAGAATAATATTTTAAATATTA-T
1 GTATTTTAGTTTAAAT-AGTTTTAGTATTTTAATTAGGATTAAGAATAATATTTTAAAT-TTATT
132227 T-TTTTAG
64 TGTTTTAG
*
132234 GTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGA
1 GTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGA-TTAAGA
132280 TGTTTTACAT
Statistics
Matches: 106, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
70 6 0.06
71 37 0.35
72 8 0.08
73 16 0.15
74 36 0.34
75 3 0.03
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (71 bp):
GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTAAGAATAATATTTTAAATTTATTTG
TTTTAG
Found at i:132743 original size:15 final size:14
Alignment explanation
Indices: 132715--132742 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
132705 TCGAAGAAAG
132715 CAGTGCAGAAAAAA
1 CAGTGCAGAAAAAA
132729 CAGTGCAGAAAAAA
1 CAGTGCAGAAAAAA
132743 ATAGATTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.21, T:0.07
Consensus pattern (14 bp):
CAGTGCAGAAAAAA
Found at i:135266 original size:20 final size:19
Alignment explanation
Indices: 135223--135269 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
135213 ATATTTATTA
*
135223 ATTTATTATTTCCCTTTTT
1 ATTTATTATTTCCATTTTT
135242 ATTTATTATTATCCA-TTTT
1 ATTTATTATT-TCCATTTTT
135261 ATTTTATTA
1 A-TTTATTA
135270 AATCTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTATTATTTCCATTTTT
Done.