Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005646.1 Hibiscus syriacus cultivar Beakdansim tig00013172_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: 80095
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:716 original size:12 final size:13
Alignment explanation
Indices: 687--734 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 13
677 AAAAAGAGAA
687 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
*
701 AAAGAGAAAATA-
1 AAAGAGAAAAAAC
713 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
726 AAAG-GAAAA
1 AAAGAGAAAA
735 TTGAAGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 16 0.52
13 4 0.13
14 11 0.35
ACGTcount: A:0.75, C:0.04, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:741 original size:24 final size:26
Alignment explanation
Indices: 686--735 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
676 CAAAAAGAGA
686 AAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAGAGAAAAAAGCAAAGAGAAAAT
712 AAAAGAGAAAAAA-CAAAG-GAAAAT
1 AAAAGAGAAAAAAGCAAAGAGAAAAT
736 TGAAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 13 0.54
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.04
Consensus pattern (26 bp):
AAAAGAGAAAAAAGCAAAGAGAAAAT
Found at i:1844 original size:32 final size:33
Alignment explanation
Indices: 1777--1865 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
1767 ATATTTGAAT
** * *
1777 ATTCAACATCAAATGCTAGGGTATTTTTTTGAG
1 ATTCAACATCAAATATTGGGGCATTTTTTTGAG
* *
1810 ATTTAACATCAAATTTTGGGGCATTTTTTT-AG
1 ATTCAACATCAAATATTGGGGCATTTTTTTGAG
*
1842 ATTCAACATCGAATATTGGGGCAT
1 ATTCAACATCAAATATTGGGGCAT
1866 CTTTGGGAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 23 0.48
33 25 0.52
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (33 bp):
ATTCAACATCAAATATTGGGGCATTTTTTTGAG
Found at i:3120 original size:36 final size:36
Alignment explanation
Indices: 3071--3146 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3061 AGACAGTTCC
3071 CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAA
1 CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAA
*
3107 CAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAA
1 CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAA
3143 CAAA
1 CAAA
3147 ATCTTTGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (36 bp):
CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAA
Found at i:3202 original size:36 final size:36
Alignment explanation
Indices: 3161--3248 Score: 142
Period size: 36 Copynumber: 2.4 Consensus size: 36
3151 TTGAATTTGT
3161 TTTCCCTTGAAACAAATTTTGTCTC-CTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTC-TTGAGACAG
* *
3197 TTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
3233 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
3249 ATCTTTGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
36 47 0.98
37 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:3247 original size:102 final size:102
Alignment explanation
Indices: 3071--3457 Score: 474
Period size: 102 Copynumber: 3.7 Consensus size: 102
3061 AGACAGTTCC
* *
3071 CAAATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCC
1 CAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCC
3136 CTTGAAACAAAATCTTTGAATTTGTTTTCCCTTGAAA
66 CTTGAAACAAAATCTTTGAATTTGTTTTCCCTTGAAA
* * *
3173 CAAATTTTGTCTCCTTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAGTTTCC
1 CAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCC
*
3238 CTTGAAACAAAATCTTTGAATGTGTTTT-CCTTGAAA
66 CTTGAAACAAAATCTTTGAATTTGTTTTCCCTTGAAA
* * * * * * * *
3274 CTAATTTCGTCTCCCTTAATACAGTTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTC
1 CAAATTTTGTCTCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCCCTTGAGACAGTTTC
* ** *
3339 TCTTGAAAC-AAAT-TTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
65 CCTTGAAACAAAATCTTTG--AAT-TT--G---TTTTCCCTTGAAA
* * *
3383 CAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAGAAATTTTGTCTCCCTTGAGACAGTTTCC
1 CAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCC
*
3448 CTTTAAACAA
66 CTTGAAACAA
3458 TTTTTTCTCT
Statistics
Matches: 243, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
100 4 0.02
101 38 0.16
102 125 0.51
103 1 0.00
105 1 0.00
108 38 0.16
109 36 0.15
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (102 bp):
CAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCCCTTGAGACAGTTTCC
CTTGAAACAAAATCTTTGAATTTGTTTTCCCTTGAAA
Found at i:3362 original size:21 final size:21
Alignment explanation
Indices: 3337--3401 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
3327 TGAGACAGTT
3337 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
3358 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
3375 -C-CTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
3394 TCTCTTGA
1 TCTCTTGA
3402 GACAGTTTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 7 0.21
16 1 0.03
17 3 0.09
18 4 0.12
19 3 0.09
20 1 0.03
21 15 0.44
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:3362 original size:36 final size:36
Alignment explanation
Indices: 3261--3493 Score: 306
Period size: 36 Copynumber: 6.5 Consensus size: 36
3251 CTTTGAATGT
* * * * * *
3261 GTTTTCCTTGAAACTAATTTCGTCTCCCTTAATACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
3297 GTTTCTCTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
*
3334 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
3370 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
3406 GTTTCTCTTGAAAGAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
3442 GTTTCCCTTTAAAC-AATTTTTTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
3477 GTTTCCCTTTAAACAAA
1 GTTTCCCTTGAAACAAA
3494 ATAATTAAAT
Statistics
Matches: 175, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
35 33 0.19
36 113 0.65
37 29 0.17
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:3436 original size:21 final size:21
Alignment explanation
Indices: 3373--3437 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 21
3363 TGAGACAGTT
*
3373 TCCCTTGAAACAAATTTTGTC
1 TCCCTTGAAAGAAATTTTGTC
* * *
3394 TCTCTTG--AGACA-GTT-TC
1 TCCCTTGAAAGAAATTTTGTC
3411 T--CTTGAAAGAAATTTTGTC
1 TCCCTTGAAAGAAATTTTGTC
3430 TCCCTTGA
1 TCCCTTGA
3438 GACAGTTTCC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 4 0.12
17 7 0.22
18 4 0.12
19 6 0.19
21 11 0.34
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.40
Consensus pattern (21 bp):
TCCCTTGAAAGAAATTTTGTC
Found at i:3833 original size:36 final size:36
Alignment explanation
Indices: 3789--3857 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
3779 TTTTGGAAGT
* *
3789 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTCTCCCTTGAAACAAA
*
3825 TTTTGTCTCTTTTGAGACAGTCTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAGTCTCCCTTGAAAC
3858 TTCAATCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTCTCCCTTGAAACAAA
Found at i:4701 original size:37 final size:37
Alignment explanation
Indices: 4660--4771 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
4650 AACATAGCGT
4660 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
4697 TAGAGTTTTACTAGGATTCAAACTCCTTAAAATATGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* **
4734 TAGAGTTCTACTATAATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
4771 T
1 T
4772 CCAGAAGCAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:5311 original size:29 final size:29
Alignment explanation
Indices: 5247--5305 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5237 TTCTACTGCA
5247 TATTATTTTGTGGAGTTACTTAGATGGTC
1 TATTATTTTGTGGAGTTACTTAGATGGTC
5276 TATTATTTTGTGGAGTTACTTAGATGGTC
1 TATTATTTTGTGGAGTTACTTAGATGGTC
5305 T
1 T
5306 TCTATTCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (29 bp):
TATTATTTTGTGGAGTTACTTAGATGGTC
Found at i:9893 original size:37 final size:38
Alignment explanation
Indices: 9838--9921 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
9828 TGGTAACCAA
9838 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
9875 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
9912 -GTTGAAAAAT
1 CTTTGAAAAAT
9922 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:14453 original size:21 final size:21
Alignment explanation
Indices: 14429--14494 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
14419 AACTTTGAAA
14429 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
14450 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
14464 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
14485 AAATGTTTTT
1 AAATGGTTTT
14495 TTGAAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 5 0.14
15 4 0.11
16 4 0.11
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:14520 original size:37 final size:37
Alignment explanation
Indices: 14422--14539 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 37
14412 GGTAACCAAC
*
14422 TTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTTC
1 TTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTTT
14459 TTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
* *
14494 TTTGAAAAATAGTTTTTCAAAGTTTGGTAGATG-TTT
1 TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
*
14530 GTTGAAAAAT
1 TTTGAAAAAT
14540 GATAATGGGA
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
35 29 0.39
36 21 0.28
37 24 0.32
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (37 bp):
TTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTT
Found at i:25591 original size:11 final size:11
Alignment explanation
Indices: 25575--25611 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
25565 TAAGATTATA
25575 TTTTATTCAAT
1 TTTTATTCAAT
25586 TTTTATT--AT
1 TTTTATTCAAT
25595 ATTTTATTCAAT
1 -TTTTATTCAAT
25607 TTTTA
1 TTTTA
25612 CTCCTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATTCAAT
Found at i:25595 original size:21 final size:21
Alignment explanation
Indices: 25569--25611 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25559 AAATGTTAAG
25569 ATTATATTTTATTCAATTTTT
1 ATTATATTTTATTCAATTTTT
25590 ATTATATTTTATTCAATTTTT
1 ATTATATTTTATTCAATTTTT
25611 A
1 A
25612 CTCCTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTATATTTTATTCAATTTTT
Found at i:26238 original size:2 final size:2
Alignment explanation
Indices: 26231--26262 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26221 ACCGGACATC
26231 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
26263 GAGTAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26639 original size:23 final size:23
Alignment explanation
Indices: 26609--26674 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
26599 CTGAATGATT
26609 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
26632 CAGTGCTGACTGATTCAGCAAAA
1 CAGTGCTGACTGATTCAGCAAAA
* *
26655 CAGTGTTGAATGATTCAGCA
1 CAGTGCTGACTGATTCAGCA
26675 CAGAAGTACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (23 bp):
CAGTGCTGACTGATTCAGCAAAA
Found at i:37545 original size:351 final size:353
Alignment explanation
Indices: 36893--37596 Score: 1304
Period size: 351 Copynumber: 2.0 Consensus size: 353
36883 ACAAAAGTAG
*
36893 TATCAAAATAAAAAATTAGGATAATATAAAATAAAACATAAAAAATGACTGGATTGAAATAATAA
1 TATCAAAATAAAAAATTAGGATAATATAAAATAAAACATAAAAAATGACTGAATTGAAATAATAA
36958 TAAAACAGAGGTATAATTAAGAGGAAATCAGAGTACAAAACTAAAATAATGGATCTAAATGAAAT
66 TAAAACAGAGGTATAATTAAGAGGAAATCAGAGTACAAAACTAAAATAATGGATCTAAATGAAAT
* ***
37023 ATTAAAAAGAGGAGAGGACCAAAAACATAATTTAATTTTAATACTTGAAGGACTATGGGGAGAGT
131 ATTAAAAAGAAGAGAGGACCAAAAACATAATTTAACCGTAATACTTGAAGGACTATGGGGAGAGT
37088 TTACCCCAGAGTTCACCTTCCACCTGGGTTTGTTTCATTTCACGCAAAGAAAGCCAAAATAATGG
196 TTACCCCAGAGTTCACCTTCCACCTGGGTTTGTTTCATTTCACGCAAAGAAAGCCAAAATAATGG
37153 CTTTTACACTTACTTTGCCAGATGTGTCAAACGTGGGCCCTTGATGGGTATTTTAATGAAACTAT
261 CTTTTACACTTACTTTGCCAGATGTGTCAAACGTGGGCCCTTGATGGGTATTTTAATGAAACTAT
*
37218 AAAACTTAAATTATAATAATATAATTCA
326 AAAACTTAAACTATAATAATATAATTCA
37246 TATC-AAA-AAAAAATTAGGATAATATAAAATAAAACATAAAAAATGACTGAATTGAAATAATAA
1 TATCAAAATAAAAAATTAGGATAATATAAAATAAAACATAAAAAATGACTGAATTGAAATAATAA
*
37309 TAAAACAGAGGTATAATTAAGAGGAAATCAGAGTACAAAACTAAAATAATGGATCTAGATGAAAT
66 TAAAACAGAGGTATAATTAAGAGGAAATCAGAGTACAAAACTAAAATAATGGATCTAAATGAAAT
*
37374 ATTAAAAAGAAGAGAGGATCAAAAACATAATTTAACCGTAATACTTGAAGGACTATGGGGAGAGT
131 ATTAAAAAGAAGAGAGGACCAAAAACATAATTTAACCGTAATACTTGAAGGACTATGGGGAGAGT
* *
37439 TTACCCCAGAGTTCACCTTCCACGTGGGTTTGTTTCATTTCATGCAAAGAAAGCCAAAATAATGG
196 TTACCCCAGAGTTCACCTTCCACCTGGGTTTGTTTCATTTCACGCAAAGAAAGCCAAAATAATGG
37504 CTTTTACACTTACTTTGCCAGATGTGTCAAACGTGGGCCCTTGATGGGTATTTTAATGAAACTAT
261 CTTTTACACTTACTTTGCCAGATGTGTCAAACGTGGGCCCTTGATGGGTATTTTAATGAAACTAT
37569 AAAACTTAAACTATAATAATATAATTCA
326 AAAACTTAAACTATAATAATATAATTCA
37597 CTGTATTTTC
Statistics
Matches: 341, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
351 334 0.98
352 3 0.01
353 4 0.01
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (353 bp):
TATCAAAATAAAAAATTAGGATAATATAAAATAAAACATAAAAAATGACTGAATTGAAATAATAA
TAAAACAGAGGTATAATTAAGAGGAAATCAGAGTACAAAACTAAAATAATGGATCTAAATGAAAT
ATTAAAAAGAAGAGAGGACCAAAAACATAATTTAACCGTAATACTTGAAGGACTATGGGGAGAGT
TTACCCCAGAGTTCACCTTCCACCTGGGTTTGTTTCATTTCACGCAAAGAAAGCCAAAATAATGG
CTTTTACACTTACTTTGCCAGATGTGTCAAACGTGGGCCCTTGATGGGTATTTTAATGAAACTAT
AAAACTTAAACTATAATAATATAATTCA
Found at i:38258 original size:36 final size:36
Alignment explanation
Indices: 38131--38388 Score: 230
Period size: 36 Copynumber: 7.2 Consensus size: 36
38121 ATATATATAG
* *
38131 ATATATAT-ATATTATAG-TTTTAAAATATTTTTAAA
1 ATATATATAATA-TATAGTTTTTAAAGTATTTTGAAA
* *
38166 ACCTATATATAATATATAGTTTTGAAAGCATGTTTGAAA
1 A--TATATATAATATATAGTTTTTAAAGTAT-TTTGAAA
*
38205 ATATTTATATATTATATAGTTTTTAAAGTATTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAAGTATTTTGAAA
* *
38243 ATAAATATAATATATAGTTTTTACA-TATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTA-TTTTGAAA
* *
38279 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
* * * **
38315 ATAAATATACTATATAATTTTTAAAACATTTT----
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
* * *
38347 -T-TAAAAAATATATAGTTTTTAAA-CATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
38380 ATATATATA
1 ATATATATA
38389 GTTTTTAAAA
Statistics
Matches: 181, Mismatches: 27, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
29 6 0.03
30 17 0.09
31 1 0.01
34 1 0.01
35 7 0.04
36 82 0.45
37 16 0.09
38 21 0.12
39 30 0.17
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
Found at i:38308 original size:72 final size:74
Alignment explanation
Indices: 38132--38339 Score: 260
Period size: 72 Copynumber: 2.8 Consensus size: 74
38122 TATATATAGA
* * * *
38132 TATATATATATTATAG-TTTTAAAATATTTTTAAAACCTATATATAATATATAGTTTTGAAAGCA
1 TATATAT-TA-TATAGTTTTTAAAGTATTTTGAAAA--TAAATATAATATATAGTTTTTAAAGCA
38196 TGTTTGAAAATATT
62 TGTTTGAAAATA-T
* * *
38210 TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTACA-TATTTT
1 TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAAGCATGTT
38274 TGAAAATA-
66 TGAAAATAT
* * *
38282 TATGTATTATATAGTTTTTAAAGTATTTTGAAAATAAATATACTATATAATTTTTAAA
1 TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAA
38340 ACATTTTTTA
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
72 54 0.46
74 12 0.10
75 21 0.18
76 5 0.04
77 19 0.16
78 7 0.06
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (74 bp):
TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAAGCATGTT
TGAAAATAT
Found at i:38360 original size:30 final size:29
Alignment explanation
Indices: 38325--38398 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
38315 ATAAATATAC
* *
38325 TATATAATTTTTAAAACATTTTTTAAAAAA
1 TATATAGTTTTTAAAACA-TTTTGAAAAAA
*
38355 TATATAGTTTTT-AAACATTTTGAAAATA
1 TATATAGTTTTTAAAACATTTTGAAAAAA
38383 TATATAGTTTTTAAAA
1 TATATAGTTTTTAAAA
38399 AAATATTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 21 0.52
29 8 0.20
30 11 0.28
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (29 bp):
TATATAGTTTTTAAAACATTTTGAAAAAA
Found at i:38570 original size:36 final size:39
Alignment explanation
Indices: 38492--38585 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 39
38482 TTTTAAAAAC
* *
38492 TATATAATTTTGGAAATGTTTTTATAAAAAAACATATAA
1 TATATAATTTTGAAAATGATTTTATAAAAAAACATATAA
* * *
38531 TATATAATTTT-AAAAT-ATTTT-TAAAAATATATATTA
1 TATATAATTTTGAAAATGATTTTATAAAAAAACATATAA
* *
38567 TATAGATTTTTGGAAAATG
1 TATATAATTTT-GAAAATG
38586 TGTTTTTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
36 21 0.47
37 4 0.09
38 9 0.20
39 11 0.24
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (39 bp):
TATATAATTTTGAAAATGATTTTATAAAAAAACATATAA
Found at i:38609 original size:11 final size:11
Alignment explanation
Indices: 38588--38665 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
38578 GGAAAATGTG
38588 TTTTTAGTTTAT
1 TTTTTA-TTTAT
38600 TTTTTATTTAT
1 TTTTTATTTAT
**
38611 TTATTTACCT-T
1 TT-TTTATTTAT
*
38622 TTGTTATTTAT
1 TTTTTATTTAT
*
38633 TTATTATTTAT
1 TTTTTATTTAT
38644 TTTACTTATTT-T
1 TTT--TTATTTAT
38656 ATTTTTATTT
1 -TTTTTATTT
38666 TGTTGAAGGG
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.07
11 29 0.54
12 12 0.22
13 9 0.17
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:38611 original size:4 final size:4
Alignment explanation
Indices: 38590--38659 Score: 56
Period size: 4 Copynumber: 16.8 Consensus size: 4
38580 AAAATGTGTT
38590 TTTA GTTTA TTT- TTTA TTTA TTTA TTTA CCTTT- TGTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA --TTTA T-TTA TTTA TTTA
*
38636 -TTA TTTA TTTTA CTTA TTTTA TTT
1 TTTA TTTA -TTTA TTTA -TTTA TTT
38660 TTATTTTGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
3 7 0.13
4 33 0.60
5 12 0.22
6 3 0.05
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:38629 original size:29 final size:29
Alignment explanation
Indices: 38595--38665 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
38585 GTGTTTTTAG
38595 TTTATTTTTTATTTATTTA-TTTACCTT-T
1 TTTATTTTTTATTTATTTATTTTA-CTTAT
38623 TGTTATTTATTTA-TTATTTATTTTACTTAT
1 T-TTATTT-TTTATTTATTTATTTTACTTAT
38653 TTTA-TTTTTATTT
1 TTTATTTTTTATTT
38666 TGTTGAAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
27 4 0.11
28 5 0.13
29 19 0.50
30 10 0.26
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (29 bp):
TTTATTTTTTATTTATTTATTTTACTTAT
Found at i:39948 original size:2 final size:2
Alignment explanation
Indices: 39941--39993 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
39931 TATTTTTATT
39941 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39983 TA TA TA TA TA T
1 TA TA TA TA TA T
39994 TTGACTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41134 original size:17 final size:17
Alignment explanation
Indices: 41114--41146 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41104 CTCACTAACC
*
41114 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
41131 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
41147 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:41789 original size:18 final size:18
Alignment explanation
Indices: 41766--41807 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
41756 TAGACATTTC
41766 GCATTTCTTATTTTCTTT
1 GCATTTCTTATTTTCTTT
*
41784 GCATTTTGTTATTTTCTTT
1 GCA-TTTCTTATTTTCTTT
41803 GCATT
1 GCATT
41808 CACATTAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.12, C:0.14, G:0.10, T:0.64
Consensus pattern (18 bp):
GCATTTCTTATTTTCTTT
Found at i:45278 original size:84 final size:83
Alignment explanation
Indices: 45145--45975 Score: 922
Period size: 84 Copynumber: 10.1 Consensus size: 83
45135 AAGACCCCCA
* * * *
45145 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
45210 CTGCCAACCAAAGACCTTTG
65 CTGCC-ACCAAAGACCTTTG
* * *
45230 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATA
1 AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC
***
45295 TG---CCAAAGACCCCCG
66 TGCCACCAAAGACCTTTG
* * * *
45310 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
45375 CTGCCAACCAAAGACCTTTG
65 CTGCC-ACCAAAGACCTTTG
* * * *
45395 AGTTCGACTACGCTCAGCTCCAAAGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATA
1 AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC
***
45460 TG---CCAAAGACCCCCG
66 TGCCACCAAAGACCTTTG
* * * *
45475 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
45540 CTGCCAACCAAAGACCTTTG
65 CTGCC-ACCAAAGACCTTTG
* * * *
45560 AGTTCGACTACGCTCAGCTCCAAGGCACATCATTCGCAGCATAGCTTAAGTCGAGAAGGGCTATA
1 AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC
***
45625 TG---CCAAAGACCCCCG
66 TGCCACCAAAGACCTTTG
* * * *
45640 AGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTAT
1 AGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
45705 CTGCCAACCAAAGACCTTTG
65 CTGCC-ACCAAAGACCTTTG
* * * * * *
45725 AGTTTGACTACGCTCAGCTTCAAGGTACATCATTCGCAGCA-AAGCTTAAGTCAAGAAGGGCTAT
1 AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAA-CTTAAGTCGAGAAGGGCTAT
***
45789 CTGCCA--AAA-ACCCCCG
65 CTGCCACCAAAGACCTTTG
* * * * * * * *
45805 AGTTCAACTACGCTCAGCTCCAAGGCATATCATTTGTAGCACAACTTAAGTCTAGAAGGGTTGTC
1 AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC
* *
45870 TGCTAACAAAAGACCTTTG
66 TGC-CACCAAAGACCTTTG
* *
45889 AGTTCGACTACATTCAGCT-CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTAT
1 AGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTAT
*
45953 CTG---CTAAAGACCTTTG
65 CTGCCACCAAAGACCTTTG
45969 AGTTCGA
1 AGTTCGA
45976 TTATATTCAA
Statistics
Matches: 622, Mismatches: 102, Indels: 49
0.80 0.13 0.06
Matches are distributed among these distances:
80 156 0.25
81 136 0.22
83 9 0.01
84 228 0.37
85 93 0.15
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
AGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATC
TGCCACCAAAGACCTTTG
Found at i:45368 original size:165 final size:165
Alignment explanation
Indices: 45120--45978 Score: 1425
Period size: 165 Copynumber: 5.2 Consensus size: 165
45110 AGTTTAGCTT
*
45120 AAGGGCTATATGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
45185 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
66 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
45250 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
131 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
45285 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
45350 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
66 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
*
45415 CAAAGCACATCATTTGCAGCATAGCTTAAGTCGAG
131 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
45450 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
45515 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
66 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
*
45580 CAAGGCACATCATTCGCAGCATAGCTTAAGTCGAG
131 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
45615 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* *
45680 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTTGACTACGCTCAGCTT
66 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
* * * *
45745 CAAGGTACATCATTCGCAGCAAAGCTTAAGTCAAG
131 CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * * * * * * * *
45780 AAGGGCTATCTGCCAAAAACCCCCGAGTTCAACTACGCTCAGC-TCCAAGGCATATCATTTGTAG
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
* * * * * **
45844 CACAACTTAAGTCTAGAAGGGTTGTCTGCTAACAAAAGACCTTTGAGTTCGACTACATTCAGCT-
66 CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
45908 CAACGGCACATCATTTGCAGCATAGCTTAAGTCGAG
131 CAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAG
* * ***
45944 AAGGGCTATCTGCTAAAGACCTTTGAGTTCGATTA
1 AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTA
45979 TATTCAACTT
Statistics
Matches: 656, Mismatches: 37, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
163 3 0.00
164 129 0.20
165 524 0.80
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
AAGGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAG
CATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTC
CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAG
Found at i:46716 original size:36 final size:36
Alignment explanation
Indices: 46587--46846 Score: 232
Period size: 36 Copynumber: 7.2 Consensus size: 36
46577 TTATATATAT
* *
46587 ATATATATATATATTATAG-TTTTAAAATATTTTTAAA
1 ATATATATA-ATA-TATAGTTTTTAAAGTATTTTGAAA
* *
46624 ACCTATATATAATATATAGTTTTGAAAGCATGTTTGAAA
1 A--TATATATAATATATAGTTTTTAAAGTAT-TTTGAAA
*
46663 ATATTTATATATTATATAGTTTTTAAAGTATTTTGAAA
1 ATA--TATATAATATATAGTTTTTAAAGTATTTTGAAA
* *
46701 ATAAATATAATATATAGTTTTTACA-TATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTA-TTTTGAAA
* *
46737 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
* * * **
46773 ATAAATATACTATATAATTTTTAAAACATTTT----
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
* * *
46805 -T-TAAAAAATATATAGTTTTTAAA-CATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
46838 ATATATATA
1 ATATATATA
46847 GTTTTTTAAA
Statistics
Matches: 182, Mismatches: 27, Indels: 30
0.76 0.11 0.13
Matches are distributed among these distances:
29 6 0.03
30 17 0.09
31 1 0.01
34 1 0.01
35 6 0.03
36 82 0.45
37 10 0.05
38 21 0.12
39 38 0.21
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAGTATTTTGAAA
Found at i:46766 original size:72 final size:73
Alignment explanation
Indices: 46587--46818 Score: 270
Period size: 72 Copynumber: 3.1 Consensus size: 73
46577 TTATATATAT
* * * *
46587 ATATATATATATATTATAG-TTTTAAAATATTTTTAAAACCTATATATAATATATAGTTTTGAAA
1 ATATATATAT-TA-TATAGTTTTTAAAGTATTTTGAAAA--TAAATATAATATATAGTTTTTAAA
46651 GCATGTTTGAAA
62 GCATGTTTGAAA
* *
46663 ATATTTATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTACA-T
1 ATA--TATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAAGC
*
46727 ATTTTTGAAA
64 ATGTTTGAAA
* * * *
46737 ATATATGTATTATATAGTTTTTAAAGTATTTTGAAAATAAATATACTATATAATTTTTAAAACAT
1 ATATATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAAGCAT
* *
46802 TTTTTAAA
66 GTTTGAAA
*
46810 AAATATATA
1 ATATATATA
46819 GTTTTTAAAC
Statistics
Matches: 137, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
72 54 0.39
73 16 0.12
74 12 0.09
75 21 0.15
76 8 0.06
77 19 0.14
78 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (73 bp):
ATATATATATTATATAGTTTTTAAAGTATTTTGAAAATAAATATAATATATAGTTTTTAAAGCAT
GTTTGAAA
Found at i:46833 original size:28 final size:30
Alignment explanation
Indices: 46783--46879 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 30
46773 ATAAATATAC
* *
46783 TATATAATTTTTAAAACATTTTTTAAAAAA
1 TATATAGTTTTTAAAACATTTTTGAAAAAA
*
46813 TATATAGTTTTT-AAACA-TTTTGAAAATA
1 TATATAGTTTTTAAAACATTTTTGAAAAAA
* *
46841 TATATAGTTTTTTAAAAAATATTTTGAAGAACA
1 TATATAG-TTTTTAAAACAT-TTTTGAA-AAAA
46874 TATATA
1 TATATA
46880 TATATTATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.28
29 10 0.18
30 15 0.26
32 7 0.12
33 9 0.16
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (30 bp):
TATATAGTTTTTAAAACATTTTTGAAAAAA
Found at i:46992 original size:37 final size:37
Alignment explanation
Indices: 46950--47047 Score: 108
Period size: 36 Copynumber: 2.6 Consensus size: 37
46940 TTTTAAAAAC
46950 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
1 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
* * * * *
46987 TATATAATTTT-AAAATATTTTTAAAAATATATATTA
1 TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
* *
47023 TATAGATTTTTGGAAAATGTGTTTT
1 TATATAATTTTGG-AAATGT-TTTT
47048 TAGTTTATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
36 29 0.59
37 11 0.22
38 5 0.10
39 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (37 bp):
TATATAATTTTGGAAATGTTTTTAAAAAAACATATAA
Found at i:47061 original size:12 final size:11
Alignment explanation
Indices: 47044--47118 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
47034 GGAAAATGTG
47044 TTTTTAGTTTAT
1 TTTTTA-TTTAT
47056 TTTTTATTTAT
1 TTTTTATTTAT
**
47067 TTATTTACCT-T
1 TT-TTTATTTAT
*
47078 TTGTTATTTAT
1 TTTTTATTTAT
*
47089 TTATTATTTAT
1 TTTTTATTTAT
47100 TTTACTTATTTTAT
1 TTT--TTA-TTTAT
47114 TTTTT
1 TTTTT
47119 TTTTGTTGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
10 4 0.08
11 23 0.45
12 13 0.25
13 3 0.06
14 8 0.16
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.75
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:47067 original size:4 final size:4
Alignment explanation
Indices: 47046--47115 Score: 56
Period size: 4 Copynumber: 16.8 Consensus size: 4
47036 AAAATGTGTT
47046 TTTA GTTTA TTT- TTTA TTTA TTTA TTTA CCTTT- TGTTA TTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA --TTTA T-TTA TTTA TTTA
*
47092 -TTA TTTA TTTTA CTTA TTTTA TTT
1 TTTA TTTA -TTTA TTTA -TTTA TTT
47116 TTTTTTTGTT
Statistics
Matches: 55, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
3 7 0.13
4 33 0.60
5 12 0.22
6 3 0.05
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:47085 original size:29 final size:28
Alignment explanation
Indices: 47051--47118 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
47041 GTGTTTTTAG
47051 TTTATTTTTTATTTATTTA-TTTACCTT-T
1 TTTATTTTTTA-TTATTTATTTTA-CTTAT
47079 TGTTATTTATTTATTATTTATTTTACTTAT
1 T-TTATTT-TTTATTATTTATTTTACTTAT
47109 TTTATTTTTT
1 TTTATTTTTT
47119 TTTTGTTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
28 4 0.11
29 22 0.61
30 10 0.28
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTATTTTTTATTATTTATTTTACTTAT
Found at i:48404 original size:2 final size:2
Alignment explanation
Indices: 48397--48467 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
48387 TATTTTTATT
48397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48439 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 T
48468 TTGACTTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49769 original size:2 final size:2
Alignment explanation
Indices: 49762--49798 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49752 TGTTGGCATT
49762 TA TA TA 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 TA TA TA T
49799 GGAAAATTAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53539 original size:21 final size:21
Alignment explanation
Indices: 53513--53555 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53503 TTTTCGGGCT
* *
53513 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
53534 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
53555 A
1 A
53556 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:53656 original size:68 final size:67
Alignment explanation
Indices: 53535--53686 Score: 198
Period size: 68 Copynumber: 2.3 Consensus size: 67
53525 ACCCATTCAA
* * *
53535 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGTTAGAGGGGAATCGGTACCCCCAG
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
*
53600 GG
66 AG
* * * *
53602 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTT-GGGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATG-TTAGAGGGGAATCGATACCCCC
53666 AGAG
64 AGAG
*
53670 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
53687 CATGAGAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
67 21 0.28
68 51 0.69
69 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
AG
Found at i:54089 original size:30 final size:31
Alignment explanation
Indices: 54047--54106 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
54037 AGAAAAAGTT
*
54047 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
* *
54078 ATATGC-CTATGTGTTAAAGTTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
54107 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:54400 original size:22 final size:22
Alignment explanation
Indices: 54326--54392 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
54316 TTATGGACAT
54326 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54348 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54370 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
54392 A
1 A
54393 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:60457 original size:21 final size:21
Alignment explanation
Indices: 60431--60473 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60421 TTTTCGGGCT
* *
60431 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
60452 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
60473 A
1 A
60474 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:60574 original size:68 final size:68
Alignment explanation
Indices: 60453--60605 Score: 202
Period size: 68 Copynumber: 2.2 Consensus size: 68
60443 ACCCATTCAA
* * *
60453 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGTTAGAGGGGAATCGGTACCCCCA-
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
60517 GGG
66 GGG
* * * *
60520 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTT-GGGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACG-AAATGAAATTCCAGAATG-TTAGAGGGGAATCGATACCCCC
60584 AGGGG
64 AGGGG
*
60589 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
60606 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
67 21 0.28
68 33 0.44
69 21 0.28
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGTTAGAGGGGAATCGATACCCCCAG
GGG
Found at i:60592 original size:22 final size:22
Alignment explanation
Indices: 60565--60606 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
60555 CAGATTGCTT
*
60565 GGGGGGAATCGATACCCCCAGG
1 GGGGGGAACCGATACCCCCAGG
*
60587 GGGGGGAACCGATTCCCCCA
1 GGGGGGAACCGATACCCCCA
60607 TGAGAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.38, T:0.10
Consensus pattern (22 bp):
GGGGGGAACCGATACCCCCAGG
Found at i:61006 original size:30 final size:31
Alignment explanation
Indices: 60964--61023 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
60954 AGAAAAAGTT
*
60964 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
* *
60995 ATATGC-CTATGTGTTAAAGTTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
61024 ACTATGTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:61317 original size:22 final size:22
Alignment explanation
Indices: 61243--61309 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
61233 TTATGGACAT
61243 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
61265 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
61287 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
61309 A
1 A
61310 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:68023 original size:16 final size:16
Alignment explanation
Indices: 67973--68016 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
67963 TTTAATTAAA
*
67973 AAAATATAAAAATATCT
1 AAAATATAAAAA-ATTT
67990 AAAATATAAAAAATTT
1 AAAATATAAAAAATTT
*
68006 AAAATTTAAAA
1 AAAATATAAAA
68017 TTTTTAAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATAAAAAATTT
Found at i:68487 original size:53 final size:54
Alignment explanation
Indices: 68375--68489 Score: 126
Period size: 53 Copynumber: 2.2 Consensus size: 54
68365 ACGTGTCTGT
* * ** * * *
68375 CTTAAAATTCGAATTTTTTTAGATTAATTGTTCATTTTATTAGAAGTGTTCATC
1 CTTAAAATTCAAATTTCTTTAGATTAATCATTCATTTTAATAAAAGTATTCATC
* * *
68429 C-TAAAATTCAAATTTCTTTATATTAATCATTTATTTTAATAAAAGTATTTA-C
1 CTTAAAATTCAAATTTCTTTAGATTAATCATTCATTTTAATAAAAGTATTCATC
68481 CTTAAAATT
1 CTTAAAATT
68490 TTATTTATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
52 2 0.04
53 47 0.94
54 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.49
Consensus pattern (54 bp):
CTTAAAATTCAAATTTCTTTAGATTAATCATTCATTTTAATAAAAGTATTCATC
Found at i:71736 original size:41 final size:41
Alignment explanation
Indices: 71691--71788 Score: 187
Period size: 41 Copynumber: 2.4 Consensus size: 41
71681 ATTCGCGTTG
*
71691 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
71732 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
71773 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
71789 TTTCCATTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:71741 original size:20 final size:20
Alignment explanation
Indices: 71716--71808 Score: 123
Period size: 20 Copynumber: 4.6 Consensus size: 20
71706 TAGTTGGAAA
71716 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
71736 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
71757 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
71777 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
71797 TCGCATTGCGAT
1 TCGCGTTGCGAT
71809 AGTCTACAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 46 0.75
21 15 0.25
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:71781 original size:61 final size:61
Alignment explanation
Indices: 71716--71835 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 61
71706 TAGTTGGAAA
*
71716 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCT-AAAAT-GTCGTTGCGATTTTCCATT
*
71777 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTACAATGTCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATGTCGTTGCGATTTTCCA
71836 AATTCGTTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
60 1 0.02
61 53 0.96
62 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (61 bp):
TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATGTCGTTGCGATTTTCCATT
Found at i:71844 original size:19 final size:19
Alignment explanation
Indices: 71760--71882 Score: 81
Period size: 20 Copynumber: 6.3 Consensus size: 19
71750 TTGAAAATCG
*
71760 CGTTGCGATTTTCC-ATTT
1 CGTTGCGATTTTCCAAATT
*
71778 CGCGTTGCGATTTTCC-ATTT
1 --CGTTGCGATTTTCCAAATT
** *
71798 CGCATTGCGATAGTCTACAATGT
1 CG--TTGCGATTTTCCA-AAT-T
71821 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** *
71840 CGTTGCGATAGT-CTAATGT
1 CGTTGCGATTTTCCAAAT-T
*
71859 TGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
71878 CGTTG
1 CGTTG
71883 TGATAGTTAA
Statistics
Matches: 81, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
18 6 0.07
19 26 0.32
20 34 0.42
21 10 0.12
22 2 0.02
23 3 0.04
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:71867 original size:38 final size:39
Alignment explanation
Indices: 71780--71893 Score: 153
Period size: 38 Copynumber: 2.9 Consensus size: 39
71770 TTCCATTTCG
*
71780 CGTTGCGATTTTCC-ATTTCGCATTGCGATAGTCTACAATGT
1 CGTTGCGATTTTCCAAATTCG--TTGCGATAGTCTA-AATGT
71821 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCT-AATGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTAAATGT
* *
71859 TGTTGCGATTTTCCAAATTCGTTGTGATAGT-TAAA
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTAAA
71894 AAAAAGATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
37 1 0.01
38 36 0.53
40 12 0.18
41 14 0.21
42 5 0.07
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (39 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTAAATGT
Found at i:72494 original size:6 final size:6
Alignment explanation
Indices: 72478--72522 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
72468 CATCCTCTCG
72478 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
72523 ATACATGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 34 0.87
ACGTcount: A:0.00, C:0.18, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:72640 original size:19 final size:19
Alignment explanation
Indices: 72616--72684 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
72606 AAACGAATTT
72616 TCGCAACGAATTTAGAAAA
1 TCGCAACGAATTTAGAAAA
* **
72635 TCGCAACGATAACTGTAGACTA
1 TCGCAACG--AA-TTTAGAAAA
* *
72657 CCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTAGAAAA
72676 TCGCAACGA
1 TCGCAACGA
72685 CAACTGTAGA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 21 0.55
20 2 0.05
21 2 0.05
22 13 0.34
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (19 bp):
TCGCAACGAATTTAGAAAA
Found at i:72675 original size:41 final size:41
Alignment explanation
Indices: 72617--72704 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
72607 AACGAATTTT
*
72617 CGCAACGAATTTAGAAAATCGCAACGATAACTGTAGACTAC
1 CGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTAC
* *
72658 CGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTAT
1 CGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTAC
72699 CGCAAC
1 CGCAAC
72705 ACGATTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (41 bp):
CGCAACGAATTTAGAAAATCGCAACGACAACTGTAGACTAC
Found at i:72703 original size:22 final size:21
Alignment explanation
Indices: 72634--72704 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 21
72624 AATTTAGAAA
72634 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
* * * **
72656 ACCGCAACG-AA-TTTGGAAA
1 ATCGCAACGAAACTGTAGACT
72675 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGA-AACTGTAGACT
72697 ATCGCAAC
1 ATCGCAAC
72705 ACGATTTTCA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
19 12 0.33
20 2 0.06
21 2 0.06
22 20 0.56
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAGACT
Found at i:72801 original size:22 final size:22
Alignment explanation
Indices: 72771--72842 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
72761 AATTTGGAAA
*
72771 ATCGTAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
72793 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
72812 ATTGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
72834 ATCGCAACG
1 ATCGCAACG
72843 CGAACTGAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
19 12 0.33
20 2 0.06
21 2 0.06
22 20 0.56
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:72810 original size:41 final size:41
Alignment explanation
Indices: 72753--72842 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
72743 AACGCGATTT
*
72753 TCGCAACGAATTTGGAAAATCGTAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
*
72794 TCGCAACGAATTTGGAAAATTGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
72835 TCGCAACG
1 TCGCAACG
72843 CGAACTGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:72848 original size:22 final size:22
Alignment explanation
Indices: 72767--72885 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 22
72757 AACGAATTTG
*
72767 GAAAATCGTAACGAC-AACTGTA
1 GAAAATCGCAACG-CGAACTGTA
** * *
72789 GACTATCGCAA--CGAA-TTTG
1 GAAAATCGCAACGCGAACTGTA
*
72808 GAAAATTGCAACGAC-AACTGTA
1 GAAAATCGCAACG-CGAACTGTA
**
72830 GACTATCGCAACGCGAACTG-A
1 GAAAATCGCAACGCGAACTGTA
*
72851 -AAAATCGCAACGCGAAATG--
1 GAAAATCGCAACGCGAACTGTA
72870 GAAAATCGCAACGCGA
1 GAAAATCGCAACGCGA
72886 TTTTCAATTA
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
19 11 0.15
20 33 0.45
21 4 0.05
22 26 0.35
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.16
Consensus pattern (22 bp):
GAAAATCGCAACGCGAACTGTA
Found at i:72853 original size:41 final size:41
Alignment explanation
Indices: 72753--72862 Score: 150
Period size: 41 Copynumber: 2.7 Consensus size: 41
72743 AACGCGATTT
* *
72753 TCGCAACGAATTTGGAAAATCGTAACGACAACTGTAGACTA
1 TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
* *
72794 TCGCAACGAATTTGGAAAATTGCAACGACAACTGTAGACTA
1 TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
*
72835 TCGCAACGCGAA-CTGAAAAATCGCAACG
1 TCGCAA--CGAATCTGGAAAATCGCAACG
72863 CGAAATGGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 45 0.73
42 13 0.21
43 4 0.06
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
TCGCAACGAATCTGGAAAATCGCAACGACAACTGTAGACTA
Found at i:72859 original size:20 final size:20
Alignment explanation
Indices: 72834--72885 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
72824 ACTGTAGACT
*
72834 ATCGCAACGCGAACTGAAAA
1 ATCGCAACGCGAAATGAAAA
*
72854 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
72874 ATCGCAACGCGA
1 ATCGCAACGCGA
72886 TTTTCAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:76739 original size:14 final size:14
Alignment explanation
Indices: 76720--76754 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
76710 TAGAATGACG
76720 AAGAAGAAAAAGAA
1 AAGAAGAAAAAGAA
*
76734 AAGAAGAAAACGAA
1 AAGAAGAAAAAGAA
76748 AACGAAG
1 AA-GAAG
76755 CTTCTTTCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.71, C:0.06, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAGAA
Found at i:79155 original size:53 final size:55
Alignment explanation
Indices: 79029--79164 Score: 159
Period size: 53 Copynumber: 2.5 Consensus size: 55
79019 TCAATTCGAA
*
79029 CTTATTATATACACCTAATATAATATGAGAAAATTTGTTTTCAATTAAATTCTAAAC
1 CTTATTATATACACCT-A-ATAATATGAGAAAATTTATTTTCAATTAAATTCTAAAC
* * * * * *
79086 TTTATAATGTCCACCTAATAAT-T-AGAACATTTATTTTCAATTAAATTTTAAAC
1 CTTATTATATACACCTAATAATATGAGAAAATTTATTTTCAATTAAATTCTAAAC
* *
79139 CTTATTATATAGACCTAATAACATGA
1 CTTATTATATACACCTAATAATATGA
79165 TCAATTAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
53 43 0.67
54 2 0.03
55 6 0.09
56 1 0.02
57 12 0.19
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.40
Consensus pattern (55 bp):
CTTATTATATACACCTAATAATATGAGAAAATTTATTTTCAATTAAATTCTAAAC
Done.