Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 99 of 226
Found at i:34009727 original size:31 final size:31
Alignment explanation
Indices: 34009689--34009750 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
34009679 ATTAATTTTT
* *
34009689 AACTATTC-AAAATTTTTCATTTAAGTCATTG
1 AACTATTCAAAAAATTTT-ATTTAAATCATTG
34009720 AACTATTCAAAAAATTTTATTTAAATCATTG
1 AACTATTCAAAAAATTTTATTTAAATCATTG
34009751 GGTTGTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTATTCAAAAAATTTTATTTAAATCATTG
Found at i:34011323 original size:33 final size:33
Alignment explanation
Indices: 34011280--34011346 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
34011270 ACTAATTCAC
*
34011280 TGTCATCCCTA-CGTCATAGCGAAACCAATACAA
1 TGTCACCCCTACCG-CATAGCGAAACCAATACAA
* *
34011313 TGTCACCCCTACCGCATAGCGAAACTAATTCAA
1 TGTCACCCCTACCGCATAGCGAAACCAATACAA
34011346 T
1 T
34011347 CTCATCTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.34, C:0.31, G:0.12, T:0.22
Consensus pattern (33 bp):
TGTCACCCCTACCGCATAGCGAAACCAATACAA
Found at i:34020017 original size:11 final size:11
Alignment explanation
Indices: 34020001--34020075 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
34019991 GATAATCACT
34020001 TTAATATTAAA
1 TTAATATTAAA
34020012 TTAATA--AAA
1 TTAATATTAAA
*
34020021 -TACTATTAAGA
1 TTAATATTAA-A
34020032 -TAATATTAAA
1 TTAATATTAAA
34020042 TTTAAT-TTAATA
1 -TTAATATTAA-A
34020054 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
34020067 ATAATATTA
1 TTAATATTA
34020076 TTTTTGAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 18
0.71 0.04 0.25
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 26 0.50
12 9 0.17
13 3 0.06
14 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:34020062 original size:36 final size:37
Alignment explanation
Indices: 34019985--34020075 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 37
34019975 TTTAATTCAA
*
34019985 TATTAAGATAATCACTTTAATATTAAATTAATAAAATAC
1 TATTAAGATAAT-A-TTAAATATTAAATTAATAAAATAC
* *
34020024 TATTAAGATAATATTAAAT-TTAATTTAATATTAA-AC
1 TATTAAGATAATATTAAATATTAAATTAATA-AAATAC
*
34020060 TATTAAAATAATATTA
1 TATTAAGATAATATTA
34020076 TTTTTGAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
36 27 0.57
37 7 0.15
38 1 0.02
39 12 0.26
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (37 bp):
TATTAAGATAATATTAAATATTAAATTAATAAAATAC
Found at i:34028351 original size:12 final size:12
Alignment explanation
Indices: 34028334--34028358 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34028324 AGCTAACTAT
34028334 AGTTGTACTTTG
1 AGTTGTACTTTG
34028346 AGTTGTACTTTG
1 AGTTGTACTTTG
34028358 A
1 A
34028359 CTTAGCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.24, T:0.48
Consensus pattern (12 bp):
AGTTGTACTTTG
Found at i:34060681 original size:43 final size:43
Alignment explanation
Indices: 34060620--34060913 Score: 272
Period size: 43 Copynumber: 6.8 Consensus size: 43
34060610 TAGGTTATAT
* *
34060620 TTCGGTTTATCTGATGATGAACTGTGTGTGCCAATATAGATGC
1 TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATGC
* * *
34060663 TTCGGTTTATCCGATGATGCACTATGTGTGCCAGTATATATGC
1 TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATGC
* * *
34060706 TTCGGTTTATTCGATGACGTAA-TGTGTGTGCCAGTATAGTTGC
1 TTCGGTTTATCCGATGATG-AACTGTGTGTGCCAGTATAGATGC
* * *
34060749 TTTGATTTATCAGATGATGCATAC--TGTGTGCCAGTATAGATGC
1 TTCGGTTTATCCGATGATG-A-ACTGTGTGTGCCAGTATAGATGC
* ** * ** *
34060792 TTCGATTTATCTAATGATGCACAATGTGTGCCAGTATAGATGT
1 TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATGC
* * * * *
34060835 TTTGGTTTATCCGCTGATGCATTGTGTGTTCCAGTATATG-TGC
1 TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTATA-GATGC
* * * * *
34060878 TTCAGTTCATCCGATGATGAATTGTATGCGCCAGTA
1 TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTA
34060914 AAATTGCTTC
Statistics
Matches: 204, Mismatches: 41, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
41 2 0.01
43 199 0.98
44 3 0.01
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (43 bp):
TTCGGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATGC
Found at i:34060758 original size:86 final size:86
Alignment explanation
Indices: 34060620--34060982 Score: 324
Period size: 86 Copynumber: 4.2 Consensus size: 86
34060610 TAGGTTATAT
* * *
34060620 TTCGGTTTATCTGATGATGAACTGTGTGTGCCAATATAGATGCTTCGGTTTATCCGATGATGCAC
1 TTCGGTTTATCTGATGATGAACTGTGTGTGCCAGTATAGATGCTTTGATTTATCCGATGATGCAC
34060685 TATGTGTGCCAGTATATATGC
66 TATGTGTGCCAGTATATATGC
* * *
34060706 TTCGGTTTAT-TCGATGACGTAA-TGTGTGTGCCAGTATAGTTGCTTTGATTTATCAGATGATGC
1 TTCGGTTTATCT-GATGATG-AACTGTGTGTGCCAGTATAGATGCTTTGATTTATCCGATGATGC
*
34060769 A-TACTGTGTGCCAGTATAGATGC
64 ACTA-TGTGTGCCAGTATATATGC
* * * ** * * * *
34060792 TTCGATTTATCTAATGATGCACAATGTGTGCCAGTATAGATGTTTTGGTTTATCCGCTGATGCAT
1 TTCGGTTTATCTGATGATGAACTGTGTGTGCCAGTATAGATGCTTTGATTTATCCGATGATGCAC
* * *
34060857 TGTGTGTTCCAGTATATGTGC
66 TATGTGTGCCAGTATATATGC
* * * * * * * * * *
34060878 TTCAGTTCATCCGATGATGAATTGTATGCGCCAGTA-AAATTGCTTCT-ATTAATCTGGTGATGC
1 TTCGGTTTATCTGATGATGAACTGTGTGTGCCAGTATAGA-TGCTT-TGATTTATCCGATGATGC
** * *
34060941 ACTACATGTGCCAGTATATTTCC
64 ACTATGTGTGCCAGTATATATGC
*
34060964 TTTC-GTTTATCCGATGATG
1 -TTCGGTTTATCTGATGATG
34060983 CACTACATGT
Statistics
Matches: 221, Mismatches: 47, Indels: 18
0.77 0.16 0.06
Matches are distributed among these distances:
85 6 0.03
86 207 0.94
87 8 0.04
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.39
Consensus pattern (86 bp):
TTCGGTTTATCTGATGATGAACTGTGTGTGCCAGTATAGATGCTTTGATTTATCCGATGATGCAC
TATGTGTGCCAGTATATATGC
Found at i:34060911 original size:129 final size:129
Alignment explanation
Indices: 34060632--34060980 Score: 346
Period size: 129 Copynumber: 2.7 Consensus size: 129
34060622 CGGTTTATCT
* * * *
34060632 GATGATGAACTGTGTGTGCCAATATAGATGCTTCGGTTTATCCGATGATGCACTATGTGTGCCAG
1 GATGATGAATTGTGTGTGCCAGTATAGATGCTTCGATTTATCTGATGATGCACTATGTGTGCCAG
* * * * *
34060697 TATATATGCTTCGGTTTATTCGATGACGTAATGTGTGTGCCAGTATAGTTGCTTTGATTTATCA
66 TATAGATGCTTCGGTTTATCCGATGACGCAATGTGTGTGCCAGTATAGTTGCTTAGATTCATCA
* ** * *
34060761 GATGATGCATACTGTGTGCCAGTATAGATGCTTCGATTTATCTAATGATGCACAATGTGTGCCAG
1 GATGATGAATTGTGTGTGCCAGTATAGATGCTTCGATTTATCTGATGATGCACTATGTGTGCCAG
* * * * * *
34060826 TATAGATGTTTTGGTTTATCCGCTGATGCATTGTGTGTTCCAGTATA-TGTGCTTCAG-TTCATC
66 TATAGATGCTTCGGTTTATCCGATGACGCAATGTGTGTGCCAGTATAGT-TGCTT-AGATTCATC
*
34060889 C
129 A
* * * * * * **
34060890 GATGATGAATTGTATGCGCCAGTA-AAATTGCTTCTATTAATCTGGTGATGCACTACATGTGCCA
1 GATGATGAATTGTGTGTGCCAGTATAGA-TGCTTCGATTTATCTGATGATGCACTATGTGTGCCA
** *
34060954 GTATATTTCCTTTC-GTTTATCCGATGA
65 GTATAGATGC-TTCGGTTTATCCGATGA
34060981 TGCACTACAT
Statistics
Matches: 176, Mismatches: 40, Indels: 8
0.79 0.18 0.04
Matches are distributed among these distances:
128 3 0.02
129 170 0.97
130 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (129 bp):
GATGATGAATTGTGTGTGCCAGTATAGATGCTTCGATTTATCTGATGATGCACTATGTGTGCCAG
TATAGATGCTTCGGTTTATCCGATGACGCAATGTGTGTGCCAGTATAGTTGCTTAGATTCATCA
Found at i:34060982 original size:43 final size:42
Alignment explanation
Indices: 34060624--34061050 Score: 255
Period size: 43 Copynumber: 10.0 Consensus size: 42
34060614 TTATATTTCG
* * * * **
34060624 GTTTATCTGATGATGAACTGTGTGTGCCAATATAGATGCTTC
1 GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
*
34060666 GGTTTATCCGATGATGCACTATGTGTGCCAGTATATATGCTTC
1 -GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
* * * * * * *
34060709 GGTTTATTCGATGACGTAATGTGTGTGCCAGTATAGTTGCTTT
1 -GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
* **
34060752 GATTTATCAGATGATGCA-TACTGTGTGCCAGTATAGATGCTTC
1 G-TTTATCCGATGATGCACTA-TGTGTGCCAGTATATTTGCTTC
** * ** * *
34060795 GATTTATCTAATGATGCACAATGTGTGCCAGTATAGATGTTTTG
1 G-TTTATCCGATGATGCACTATGTGTGCCAGTATATTTG-CTTC
* * * * *
34060839 GTTTATCCGCTGATGCATTGTGTGTTCCAGTATATGTGCTTC
1 GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
* * * * * * * *
34060881 AGTTCATCCGATGATGAATTGTATGCGCCAGTAAAATTGCTTC
1 -GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
* * ** *
34060924 -TATTAATCTGGTGATGCACTACATGTGCCAGTATATTTCCTTTC
1 GT-TT-ATCCGATGATGCACTATGTGTGCCAGTATATTTGC-TTC
** ** * **
34060968 GTTTATCCGATGATGCACTACATGTATCAGTATATTTCCTAG
1 GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
* * * * *
34061010 GAATTATCCGGTGATGCACTAAGTGTGCCAGTGTAATTGCT
1 G-TTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCT
34061051 CCAACTTAAT
Statistics
Matches: 303, Mismatches: 71, Indels: 20
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.00
42 7 0.02
43 285 0.94
44 9 0.03
45 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
GTTTATCCGATGATGCACTATGTGTGCCAGTATATTTGCTTC
Found at i:34063651 original size:29 final size:29
Alignment explanation
Indices: 34063609--34063664 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
34063599 CACAGCCATG
*
34063609 TGGCCGTGGGGCAGAC-AGTGTGGGTCATA
1 TGGCCATGGGGCAGACTA-TGTGGGTCATA
*
34063638 TGGCCATGTGGCAGACTATGTGGGTCA
1 TGGCCATGGGGCAGACTATGTGGGTCA
34063665 CACAGCTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.18, C:0.18, G:0.41, T:0.23
Consensus pattern (29 bp):
TGGCCATGGGGCAGACTATGTGGGTCATA
Found at i:34065215 original size:14 final size:15
Alignment explanation
Indices: 34065172--34065215 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
34065162 TAAGTATGTA
**
34065172 TACTTTAGTTAAATT
1 TACTTTAGTTACTTT
34065187 TACTTTAGTTACTTT
1 TACTTTAGTTACTTT
34065202 TACTTTAG-TACTTT
1 TACTTTAGTTACTTT
34065216 AATGAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (15 bp):
TACTTTAGTTACTTT
Found at i:34067379 original size:40 final size:41
Alignment explanation
Indices: 34067323--34067549 Score: 260
Period size: 41 Copynumber: 5.5 Consensus size: 41
34067313 GTTACTGGCA
* *
34067323 TTTTTCCCATAAACGCCGCAAAAGTTCAAGCAACAGCGGCG
1 TTTTTCCCATAAACGCCGCAAAAGTTAAAGCAATAGCGGCG
* * * *
34067364 TTTTT-CCATAAACGCCGTAAAAGTTTAAAACGATAGTGGCG
1 TTTTTCCCATAAACGCCGCAAAAG-TTAAAGCAATAGCGGCG
** * * * * *
34067405 TTTTTTTCATAAACGCCGCTAAAGGTAAAGCAATGGCAGCA
1 TTTTTCCCATAAACGCCGCAAAAGTTAAAGCAATAGCGGCG
* *
34067446 TTTTT-GCATAAACGCCGCAAAAGGTTAAAACAATAGCGGCG
1 TTTTTCCCATAAACGCCGCAAAA-GTTAAAGCAATAGCGGCG
* *
34067487 TTTTTCCCATAAACGCCACTAAAGTTAAAGCAATAGCGGCG
1 TTTTTCCCATAAACGCCGCAAAAGTTAAAGCAATAGCGGCG
*
34067528 TTTTTCCCATAAATGCCGCAAA
1 TTTTTCCCATAAACGCCGCAAA
34067550 TATTTTTATT
Statistics
Matches: 152, Mismatches: 30, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
40 32 0.21
41 91 0.60
42 29 0.19
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (41 bp):
TTTTTCCCATAAACGCCGCAAAAGTTAAAGCAATAGCGGCG
Found at i:34067539 original size:123 final size:123
Alignment explanation
Indices: 34067320--34067546 Score: 307
Period size: 123 Copynumber: 1.8 Consensus size: 123
34067310 AGTGTTACTG
* * *
34067320 GCATTTTTCCCATAAACGCCGCAAAAGTTCAAGCAACAGCGGCGTTTTTCCATAAACGCCGTAAA
1 GCATTTTTCCCATAAACGCCGCAAAAGTTAAAACAACAGCGGCGTTTTTCCATAAACGCCCTAAA
* * **
34067385 AGTTTAAAACGATAGTGGCGTTTTTTTCATAAACGCCGCTAAAGGTAAAGCAATGGCA
66 AGTTTAAAACAATAGCGGCGTTTTTCCCATAAACGCCGCTAAAGGTAAAGCAATGGCA
* *
34067443 GCATTTTT-GCATAAACGCCGCAAAAGGTTAAAACAATAGCGGCGTTTTTCCCATAAACGCCACT
1 GCATTTTTCCCATAAACGCCGCAAAA-GTTAAAACAACAGCGGCGTTTTT-CCATAAACGCC-CT
* *
34067507 -AAAG-TTAAAGCAATAGCGGCGTTTTTCCCATAAATGCCGC
63 AAAAGTTTAAAACAATAGCGGCGTTTTTCCCATAAACGCCGC
34067547 AAATATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
122 16 0.18
123 58 0.64
124 15 0.17
125 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (123 bp):
GCATTTTTCCCATAAACGCCGCAAAAGTTAAAACAACAGCGGCGTTTTTCCATAAACGCCCTAAA
AGTTTAAAACAATAGCGGCGTTTTTCCCATAAACGCCGCTAAAGGTAAAGCAATGGCA
Found at i:34073211 original size:12 final size:12
Alignment explanation
Indices: 34073194--34073220 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
34073184 AACCAGTTTT
34073194 AAACTAGTATTA
1 AAACTAGTATTA
34073206 AAACTAGTATTA
1 AAACTAGTATTA
34073218 AAA
1 AAA
34073221 TCAAAAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (12 bp):
AAACTAGTATTA
Found at i:34073312 original size:29 final size:31
Alignment explanation
Indices: 34073273--34073340 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 31
34073263 ATTTCATAAT
*
34073273 AATTAGTTAATTAATTTTTTATTAATTAAATA
1 AATTA-TTAATTAATTTTTTATTAACTAAATA
34073305 AATTTAATTAATTAATTTTTTATTAACTAAATA
1 AA-TT-ATTAATTAATTTTTTATTAACTAAATA
34073338 AAT
1 AAT
34073341 AATCATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
32 3 0.09
33 29 0.88
34 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
AATTATTAATTAATTTTTTATTAACTAAATA
Found at i:34073381 original size:51 final size:51
Alignment explanation
Indices: 34073308--34073461 Score: 254
Period size: 51 Copynumber: 3.0 Consensus size: 51
34073298 TTAAATAAAT
* *
34073308 TTAATTAATTAATTTTTTATTAACTAAATAAATAATCATATTTCATAATAA
1 TTAATTAATTAATTTTCTATTAATTAAATAAATAATCATATTTCATAATAA
*
34073359 TTAATTAATTAATTTTCGATTAATTAAATAAATAATCATATTTCATAATAA
1 TTAATTAATTAATTTTCTATTAATTAAATAAATAATCATATTTCATAATAA
* * *
34073410 TTAATTAACTAATTTTCTATTATTTAATTAAATAATCATATTTCATAATAA
1 TTAATTAATTAATTTTCTATTAATTAAATAAATAATCATATTTCATAATAA
34073461 T
1 T
34073462 CATAAAAATC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 96 1.00
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.47
Consensus pattern (51 bp):
TTAATTAATTAATTTTCTATTAATTAAATAAATAATCATATTTCATAATAA
Found at i:34073382 original size:23 final size:22
Alignment explanation
Indices: 34073356--34073445 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 22
34073346 TATTTCATAA
34073356 TAATTAATTAATTAATTTTCGAT
1 TAATTAATTAATTAATTTTC-AT
* *
34073379 TAATTAAATAAATAATCATATTTCAT
1 TAATT-AATTAAT--TAAT-TTTCAT
*
34073405 AATAATTAATTAACTAATTTTCTAT
1 --TAATTAATTAATTAATTTTC-AT
* *
34073430 TATTTAATTAAATAAT
1 TAATTAATTAATTAAT
34073446 CATATTTCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
23 19 0.36
24 10 0.19
25 5 0.09
26 5 0.09
27 9 0.17
28 5 0.09
ACGTcount: A:0.46, C:0.06, G:0.01, T:0.48
Consensus pattern (22 bp):
TAATTAATTAATTAATTTTCAT
Found at i:34091866 original size:43 final size:43
Alignment explanation
Indices: 34091789--34091911 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 43
34091779 TGGTCTATAG
* ** * *
34091789 CGCCGCTAAAGAACATGATCTTTAGCAACACTTTTATTACAAA
1 CGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTATTAAAAA
* *
34091832 CGCTGCTATAGAACATGATCTTTAGCGGCGCTTTTACTAAAAA
1 CGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTATTAAAAA
* *
34091875 TGCCGCTATAGAACATGATTTTTAGCGGCGCTTTTAT
1 CGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTAT
34091912 AAGTAGTGTT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 69 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (43 bp):
CGCCGCTATAGAACATGATCTTTAGCGGCGCTTTTATTAAAAA
Found at i:34093715 original size:43 final size:43
Alignment explanation
Indices: 34093643--34093978 Score: 293
Period size: 43 Copynumber: 7.9 Consensus size: 43
34093633 ACAAGTTATA
* * * * *
34093643 CTTCGGTTTAT-CAATGAAGAACTGTGTGTGCCAATATAAATG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * * *
34093685 CTTCGGTTTATCCGATGTTGAACTGTGTGTG-CAGTGTATATG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * * *
34093727 CTTCAGCTTATCCAATGATGCACTGTGTGTGCCAGTATAGTTG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * * * *
34093770 TTTTAGTTTATCCGGTGATGTACTGTGTGTGTCAGTATAGATG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * * * *
34093813 CTTCAGATTATCTGATGAT-ACACTATGTGTACCAGTATAAATG
1 CTTCAGTTTATCCGATGATGA-ACTGTGTGTGCCAGTATAGATG
* * * * *
34093856 CTTCAGTTCATCCAATGATGCACTATGTGTGCGAGTATAGATG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * * * * *
34093899 CTTTAGTTTATCCGATGATGCACTTTGTGTGCCACTACATATG
1 CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
* * *
34093942 CTTC-GATTTATCTGATGATGAACTGTATTTGCCAGTA
1 CTTCAG-TTTATCCGATGATGAACTGTGTGTGCCAGTA
34093979 AAATTTCTTT
Statistics
Matches: 234, Mismatches: 55, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
42 46 0.20
43 188 0.80
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (43 bp):
CTTCAGTTTATCCGATGATGAACTGTGTGTGCCAGTATAGATG
Found at i:34093977 original size:129 final size:129
Alignment explanation
Indices: 34093663--34093982 Score: 380
Period size: 129 Copynumber: 2.5 Consensus size: 129
34093653 TCAATGAAGA
* * * * *
34093663 ACTGTGTGTGCCAATATAAATGCTTCGGTTTATCCGATGTTGAACTGTGTGTG-CAGTGTATATG
1 ACTGTGTGTGCCAATATAAATGCTTCGATTTATCTGATGATGAACTGTGTGTGCCAGTATAAATG
* * * * *
34093727 CTTCAGCTTATCCAATGATGCACTGTGTGTGCCAGTATAGTTGTTTTAGTTTATCCGGTGATGT
66 CTTCAGCTTATCCAATGATGCACTATGTGTGCCAGTATAGATGCTTTAGTTTATCCGATGATGC
* * * * *
34093791 ACTGTGTGTGTCAGTATAGATGCTTCAGA-TTATCTGATGAT-ACACTATGTGTACCAGTATAAA
1 ACTGTGTGTGCCAATATAAATGCTTC-GATTTATCTGATGATGA-ACTGTGTGTGCCAGTATAAA
*
34093854 TGCTTCAG-TTCATCCAATGATGCACTATGTGTGCGAGTATAGATGCTTTAGTTTATCCGATGAT
64 TGCTTCAGCTT-ATCCAATGATGCACTATGTGTGCCAGTATAGATGCTTTAGTTTATCCGATGAT
34093918 GC
128 GC
* * * * * *
34093920 ACTTTGTGTGCCACTACATATGCTTCGATTTATCTGATGATGAACTGTATTTGCCAGTA-AAAT
1 ACTGTGTGTGCCAATATAAATGCTTCGATTTATCTGATGATGAACTGTGTGTGCCAGTATAAAT
34093983 TTCTTTGATT
Statistics
Matches: 161, Mismatches: 25, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
127 1 0.01
128 49 0.30
129 110 0.68
130 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (129 bp):
ACTGTGTGTGCCAATATAAATGCTTCGATTTATCTGATGATGAACTGTGTGTGCCAGTATAAATG
CTTCAGCTTATCCAATGATGCACTATGTGTGCCAGTATAGATGCTTTAGTTTATCCGATGATGC
Found at i:34094056 original size:43 final size:43
Alignment explanation
Indices: 34093999--34094082 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
34093989 GATTAATATA
***
34093999 GTGATGCACTACATGTGTCAATATATTTCCTTCAGT-TTATCCG
1 GTGATGCACTACATGCACCAATATATTTCCTTC-GTATTATCCG
*
34094042 GTGATGCA-TAACATGCACCAGTATATTTCCTTCGTATTATC
1 GTGATGCACT-ACATGCACCAATATATTTCCTTCGTATTATC
34094083 TTATCATGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 3 0.09
43 32 0.91
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (43 bp):
GTGATGCACTACATGCACCAATATATTTCCTTCGTATTATCCG
Found at i:34096784 original size:38 final size:38
Alignment explanation
Indices: 34096677--34096784 Score: 153
Period size: 38 Copynumber: 2.8 Consensus size: 38
34096667 CATCAGCAGA
* * *
34096677 AAGCCTACTAGGCGCTAAGCCTGAATAACACAGGCACT
1 AAGCCTACTAGGCACTAAGCCTGAATAACACCGACACT
* * *
34096715 AAGTCTGCTAGGCACTAAGCCTAAATAACACCGACACT
1 AAGCCTACTAGGCACTAAGCCTGAATAACACCGACACT
*
34096753 GAGCCTACTAGGCACTAAGCCTGAATAACACC
1 AAGCCTACTAGGCACTAAGCCTGAATAACACC
34096785 CAATTTGAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.35, C:0.30, G:0.19, T:0.17
Consensus pattern (38 bp):
AAGCCTACTAGGCACTAAGCCTGAATAACACCGACACT
Found at i:34111071 original size:36 final size:36
Alignment explanation
Indices: 34111024--34111096 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
34111014 GTACCCATGA
34111024 TACTCGAAATCTATTAAATTCCTTAATTCCTAATAT
1 TACTCGAAATCTATTAAATTCCTTAATTCCTAATAT
34111060 TACTCGAAATCTATTAAATTCCTTAATTCCTAATAT
1 TACTCGAAATCTATTAAATTCCTTAATTCCTAATAT
34111096 T
1 T
34111097 TCATTTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (36 bp):
TACTCGAAATCTATTAAATTCCTTAATTCCTAATAT
Found at i:34115265 original size:11 final size:11
Alignment explanation
Indices: 34115249--34115301 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
34115239 CTATAAAGTT
34115249 TTTTCTAAATA
1 TTTTCTAAATA
34115260 TTTTCTAAATA
1 TTTTCTAAATA
34115271 TTTTCTACAAGCT-
1 TTTTCTA-AA--TA
34115284 TTTTCTAAATA
1 TTTTCTAAATA
34115295 TTTTCTA
1 TTTTCTA
34115302 CAAGCTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 25 0.66
12 4 0.11
13 7 0.18
14 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTTCTAAATA
Found at i:34115287 original size:24 final size:24
Alignment explanation
Indices: 34115260--34115308 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34115250 TTTCTAAATA
34115260 TTTTCTAAATATTTTCTACAAGCT
1 TTTTCTAAATATTTTCTACAAGCT
34115284 TTTTCTAAATATTTTCTACAAGCT
1 TTTTCTAAATATTTTCTACAAGCT
34115308 T
1 T
34115309 ATGTTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (24 bp):
TTTTCTAAATATTTTCTACAAGCT
Found at i:34115446 original size:22 final size:21
Alignment explanation
Indices: 34115414--34115457 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
34115404 GTTAGGGAAA
*
34115414 TAACAGTTCAAAATTTTTCTTT
1 TAACAGATC-AAATTTTTCTTT
*
34115436 TAACAGATCAATTTTTTCTTT
1 TAACAGATCAAATTTTTCTTT
34115457 T
1 T
34115458 CATTTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.52
Consensus pattern (21 bp):
TAACAGATCAAATTTTTCTTT
Found at i:34116090 original size:27 final size:28
Alignment explanation
Indices: 34116036--34116090 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
34116026 AGAAGAAAAG
* *
34116036 ACAAAGGAAGTTACTTGGGAAAAAACCA
1 ACAAAGGAAGCTACATGGGAAAAAACCA
*
34116064 ACAAAGGAAGCTACAT-GGAAGAAACCA
1 ACAAAGGAAGCTACATGGGAAAAAACCA
34116091 TAGTTGCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (28 bp):
ACAAAGGAAGCTACATGGGAAAAAACCA
Found at i:34116138 original size:37 final size:37
Alignment explanation
Indices: 34116097--34116191 Score: 111
Period size: 43 Copynumber: 2.4 Consensus size: 37
34116087 ACCATAGTTG
34116097 CATCTAGACAAAAAAGGAAGCAAAGTGGAAGCAACCA
1 CATCTAGACAAAAAAGGAAGCAAAGTGGAAGCAACCA
*
34116134 CATCTATGTCCAGACAAAAAAGGAAGCAACGTGGAAGCAACCA
1 CATC----T--AGACAAAAAAGGAAGCAAAGTGGAAGCAACCA
34116177 CATC-AGGACAAAAAA
1 CATCTA-GACAAAAAA
34116192 TATCATCAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
36 1 0.02
37 13 0.26
41 1 0.02
43 35 0.70
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.09
Consensus pattern (37 bp):
CATCTAGACAAAAAAGGAAGCAAAGTGGAAGCAACCA
Found at i:34122730 original size:51 final size:50
Alignment explanation
Indices: 34122637--34122770 Score: 146
Period size: 51 Copynumber: 2.6 Consensus size: 50
34122627 AGTTGCTAGG
***
34122637 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCATACCGGAT-AGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG-ATACCGGATGAAAAT-GA
* * * *
34122688 TCATGTGTGTAGTACTATGTGCAGGCTATTACATG-TATCGGATGAAAATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACT--ATGATACCGGATGAAAATGA
*
34122739 TCACATGTGTAGTACTATGTGCAGGCTACTAT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTAT
34122771 ATGAACCGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
49 2 0.03
51 63 0.90
52 2 0.03
53 3 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGATACCGGATGAAAATGA
Found at i:34126380 original size:20 final size:20
Alignment explanation
Indices: 34126355--34126392 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34126345 TGGGTTAGTG
*
34126355 ATTTAATATATATAATTATT
1 ATTTAACATATATAATTATT
34126375 ATTTAACATATATAATTA
1 ATTTAACATATATAATTA
34126393 ATATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTAACATATATAATTATT
Found at i:34128792 original size:13 final size:13
Alignment explanation
Indices: 34128774--34128799 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34128764 AAAAGAGAAA
34128774 TTTTATTTTTTAT
1 TTTTATTTTTTAT
34128787 TTTTATTTTTTAT
1 TTTTATTTTTTAT
34128800 GTCTGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:34129246 original size:20 final size:19
Alignment explanation
Indices: 34129216--34129268 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
34129206 AGTATTCTAG
34129216 AAATT-ATAAAAATTCAAA
1 AAATTAATAAAAATTCAAA
34129234 AAATTAA-ATAAAATTCAAA
1 AAATTAATA-AAAATTCAAA
*
34129253 AGATTAATAAACAATT
1 AAATTAATAAA-AATT
34129269 TCTAACTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.20
19 19 0.63
20 5 0.17
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATTAATAAAAATTCAAA
Found at i:34132126 original size:47 final size:47
Alignment explanation
Indices: 34132072--34132214 Score: 236
Period size: 47 Copynumber: 3.1 Consensus size: 47
34132062 ATCTTTTGGT
*
34132072 CATAATTTAAGAATATACAATTGAAATGACTAAGTCCCTATACATGC
1 CATAATTTAAGAATATACAATCGAAATGACTAAGTCCCTATACATGC
34132119 CATAATTTAAGAATATACAATCGAAATGACTAAGTCCCTATACATGC
1 CATAATTTAAGAATATACAATCGAAATGACTAAGTCCCTATACATGC
** *
34132166 CAT-AGCT-GGAATATACAATCGAAATGACTAAGTCCCTATACATGC
1 CATAATTTAAGAATATACAATCGAAATGACTAAGTCCCTATACATGC
34132211 CATA
1 CATA
34132215 GCTCGAAACA
Statistics
Matches: 91, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
45 40 0.44
46 2 0.02
47 49 0.54
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (47 bp):
CATAATTTAAGAATATACAATCGAAATGACTAAGTCCCTATACATGC
Found at i:34132193 original size:45 final size:46
Alignment explanation
Indices: 34132079--34132217 Score: 226
Period size: 45 Copynumber: 3.0 Consensus size: 46
34132069 GGTCATAATT
* **
34132079 TAAGAATATACAATTGAAATGACTAAGTCCCTATACATGCCATAATT
1 TAAGAATATACAATCGAAATGACTAAGTCCCTATACATGCCAT-AGC
34132126 TAAGAATATACAATCGAAATGACTAAGTCCCTATACATGCCATAGC
1 TAAGAATATACAATCGAAATGACTAAGTCCCTATACATGCCATAGC
*
34132172 T-GGAATATACAATCGAAATGACTAAGTCCCTATACATGCCATAGC
1 TAAGAATATACAATCGAAATGACTAAGTCCCTATACATGCCATAGC
34132217 T
1 T
34132218 CGAAACATTT
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 44 0.50
46 2 0.02
47 42 0.48
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (46 bp):
TAAGAATATACAATCGAAATGACTAAGTCCCTATACATGCCATAGC
Found at i:34132800 original size:50 final size:50
Alignment explanation
Indices: 34132676--34132922 Score: 239
Period size: 50 Copynumber: 4.8 Consensus size: 50
34132666 AATAATAACA
* ** * * *
34132676 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * **
34132725 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
34132775 TGCCCATGCCATGTCCCAGACATGGTCTTAC-TGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATATCGG
* * * **
34132825 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATAATCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
34132881 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34132923 TTACCCAAAT
Statistics
Matches: 164, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 40 0.24
50 81 0.49
51 1 0.01
53 2 0.01
56 39 0.24
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:34134675 original size:27 final size:27
Alignment explanation
Indices: 34134618--34134685 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
34134608 GTTTTCCATG
* * * *
34134618 AAGGCGTTCATTTCGTATATTGCCACG
1 AAGGCATTCCTTTCGTATATTACCACA
*
34134645 AAGGCATTCCTTTCGTATATTACTACA
1 AAGGCATTCCTTTCGTATATTACCACA
*
34134672 AAGGCAATCCTTTC
1 AAGGCATTCCTTTC
34134686 ATAGCATGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (27 bp):
AAGGCATTCCTTTCGTATATTACCACA
Found at i:34140611 original size:20 final size:18
Alignment explanation
Indices: 34140582--34140618 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 18
34140572 CATTCATTAT
34140582 ATATTATTTTTAAATATGC
1 ATATTA-TTTTAAATATGC
34140601 ATATGTATTTTAAATATG
1 ATAT-TATTTTAAATATG
34140619 TGATTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (18 bp):
ATATTATTTTAAATATGC
Found at i:34142538 original size:22 final size:22
Alignment explanation
Indices: 34142503--34142547 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
34142493 GATGAATAAC
**
34142503 TAATTCTTTGTATACATACATT
1 TAATTCTTCATATACATACATT
* *
34142525 TAATTCTTCATATATATCCATT
1 TAATTCTTCATATACATACATT
34142547 T
1 T
34142548 CAATGGGGTA
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:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATTCTTCATATACATACATT
Found at i:34148549 original size:3 final size:3
Alignment explanation
Indices: 34148541--34148581 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
34148531 AGCCAACTAC
34148541 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
34148582 ATTTATTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34153476 original size:23 final size:24
Alignment explanation
Indices: 34153441--34153485 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
34153431 ATTAACTCAC
34153441 CTTTACTTATTTT-CTCATTTTAA
1 CTTTACTTATTTTACTCATTTTAA
* * *
34153464 CTTTTCTTTTTTTAGTCATTTT
1 CTTTACTTATTTTACTCATTTT
34153486 GGGTCTCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.16, C:0.16, G:0.02, T:0.67
Consensus pattern (24 bp):
CTTTACTTATTTTACTCATTTTAA
Found at i:34169849 original size:13 final size:13
Alignment explanation
Indices: 34169831--34169855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34169821 ATTACATCTT
34169831 GAATTTAAATTTA
1 GAATTTAAATTTA
34169844 GAATTTAAATTT
1 GAATTTAAATTT
34169856 TAACTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
GAATTTAAATTTA
Found at i:34174426 original size:21 final size:20
Alignment explanation
Indices: 34174402--34174440 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34174392 TTCTTTTATT
34174402 TATTTATAATTTGTTTATTAC
1 TATTTAT-ATTTGTTTATTAC
*
34174423 TATTTATGTTTGTTTATT
1 TATTTATATTTGTTTATT
34174441 TATTTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (20 bp):
TATTTATATTTGTTTATTAC
Found at i:34178120 original size:32 final size:33
Alignment explanation
Indices: 34178077--34178138 Score: 117
Period size: 32 Copynumber: 1.9 Consensus size: 33
34178067 AAGAAAATTA
34178077 AAAATTTTCTAAAATTTTAACACGATTGAAGCT
1 AAAATTTTCTAAAATTTTAACACGATTGAAGCT
34178110 AAAA-TTTCTAAAATTTTAACACGATTGAA
1 AAAATTTTCTAAAATTTTAACACGATTGAA
34178139 AATTAAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.35
Consensus pattern (33 bp):
AAAATTTTCTAAAATTTTAACACGATTGAAGCT
Found at i:34179834 original size:33 final size:33
Alignment explanation
Indices: 34179693--34179851 Score: 90
Period size: 33 Copynumber: 4.8 Consensus size: 33
34179683 GTGTTTATAT
* * *
34179693 ATAAGACCATGGCTGGGCTATGGAATTCTGATG
1 ATAAGACCATAGCTGGGCTATGGCATTCTGATA
* * * * *
34179726 ATAAGACCATAACTGGGTTATGGCACTATGGA-C
1 ATAAGACCATAGCTGGGCTATGGCATTCT-GATA
* * * * * *
34179759 GTAAGATCAT-GTTTGGACCATGGCAGTGT-TTATA
1 ATAAGACCATAG-CTGGGCTATGGCA-T-TCTGATA
*
34179793 TGTAAGACCATAGCTGGGCTATGGCATTCTGATA
1 -ATAAGACCATAGCTGGGCTATGGCATTCTGATA
* * *
34179827 ATAAGACCATAACTGAGTTATGGCA
1 ATAAGACCATAGCTGGGCTATGGCA
34179852 CTACGAATGT
Statistics
Matches: 92, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
33 63 0.68
34 8 0.09
35 20 0.22
36 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (33 bp):
ATAAGACCATAGCTGGGCTATGGCATTCTGATA
Found at i:34179852 original size:101 final size:101
Alignment explanation
Indices: 34179625--34179863 Score: 379
Period size: 101 Copynumber: 2.4 Consensus size: 101
34179615 GAATTGACGG
*
34179625 ATAAGACCATAACTGGGTTATGGCAATATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
* *
34179690 TATATAAGACCATGGCTGGGCTATGGAATTCTGATG
66 TATATAAGACCATAGCTGGGCTATGGAATTCTGATA
* * *
34179726 ATAAGACCATAACTGGGTTATGGCACTATGGACGTAAGATCATGTTTGGACCATGGCAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
* *
34179791 TATGTAAGACCATAGCTGGGCTATGGCATTCTGATA
66 TATATAAGACCATAGCTGGGCTATGGAATTCTGATA
* * *
34179827 ATAAGACCATAACTGAGTTATGGCACTACGAATGTAA
1 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
34179864 AGGATGAATT
Statistics
Matches: 126, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 126 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAGTGTTTA
TATATAAGACCATAGCTGGGCTATGGAATTCTGATA
Found at i:34180311 original size:154 final size:154
Alignment explanation
Indices: 34180031--34180496 Score: 878
Period size: 154 Copynumber: 3.0 Consensus size: 154
34180021 AAATAACATG
*
34180031 AGTTGTTTTTGGATGATATATGTATATGAAAAAACAGTAAGAGAATGATATGTGTCATGATATGT
1 AGTTGTTTTTGGATGATATATGTATATGAAGAAACAGTAAGAGAATGATATGTGTCATGATATGT
34180096 ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
66 ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
*
34180161 TAAGTGTGATATGTTGATAAAATA
131 CAAGTGTGATATGTTGATAAAATA
* * *
34180185 AGTTGTTTTTGGATGATATATGTATATGAAGAAACAATAAGAGAATGATATGTGTCATGATTTGC
1 AGTTGTTTTTGGATGATATATGTATATGAAGAAACAGTAAGAGAATGATATGTGTCATGATATGT
34180250 ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
66 ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
34180315 CAAGTGTGATATGTTGATAAAATA
131 CAAGTGTGATATGTTGATAAAATA
34180339 AGTTGTTTTTGGATGATATATGTATATGAAGAAACAGTAAGAGAATGATATGTGTCATGATATGT
1 AGTTGTTTTTGGATGATATATGTATATGAAGAAACAGTAAGAGAATGATATGTGTCATGATATGT
*
34180404 ATGTATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
66 ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
34180469 CAAGTGTGATATGTTGATAAAATA
131 CAAGTGTGATATGTTGATAAAATA
34180493 AGTT
1 AGTT
34180497 TATCAATGTT
Statistics
Matches: 303, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
154 303 1.00
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.37
Consensus pattern (154 bp):
AGTTGTTTTTGGATGATATATGTATATGAAGAAACAGTAAGAGAATGATATGTGTCATGATATGT
ATATATATCAATATCTTGATATGTTGATACATGGAAATTATGTAAGTTGTGATGAGTAATAAACT
CAAGTGTGATATGTTGATAAAATA
Found at i:34182272 original size:19 final size:19
Alignment explanation
Indices: 34182250--34182287 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34182240 TTAATTATAG
34182250 AAACAGAAATTAAGTAGAA
1 AAACAGAAATTAAGTAGAA
* *
34182269 AAACATAATTTAAGTAGAA
1 AAACAGAAATTAAGTAGAA
34182288 TTTAAATTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (19 bp):
AAACAGAAATTAAGTAGAA
Found at i:34182672 original size:20 final size:20
Alignment explanation
Indices: 34182647--34182686 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34182637 TCTTGACAAC
34182647 TATTTA-TCAAGATTCATTTT
1 TATTTATTC-AGATTCATTTT
*
34182667 TATTTATTCGGATTCATTTT
1 TATTTATTCAGATTCATTTT
34182687 GTATGCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.57
Consensus pattern (20 bp):
TATTTATTCAGATTCATTTT
Found at i:34182725 original size:18 final size:18
Alignment explanation
Indices: 34182702--34182748 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
34182692 CAAATTTTAA
34182702 TTATTTAAAAAAAAGATT
1 TTATTTAAAAAAAAGATT
*** *
34182720 TTATTTTTGAAAAATATT
1 TTATTTAAAAAAAAGATT
34182738 TT-TTTAAAAAA
1 TTATTTAAAAAA
34182749 TCTTTTGAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
TTATTTAAAAAAAAGATT
Found at i:34185879 original size:23 final size:23
Alignment explanation
Indices: 34185851--34185903 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
34185841 ATGATTTTTT
34185851 ATATTTAT-TTAGAGT-TTTAAAA
1 ATATTTATATTA-AGTATTTAAAA
*
34185873 ATAATTTATATTAATTATTTAAAA
1 AT-ATTTATATTAAGTATTTAAAA
34185897 ATATTTA
1 ATATTTA
34185904 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 13 0.48
24 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATATTTATATTAAGTATTTAAAA
Found at i:34188123 original size:30 final size:30
Alignment explanation
Indices: 34188052--34188124 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
34188042 GGGAATGTAA
* *
34188052 TGCTCACACAAGCTGACAATATTTCAGAGT
1 TGCTTACACAAGCTGACAATATTTCAGAAT
* * *
34188082 TGC-TCCACAAGCTGAC-ATTTTTACGGAAT
1 TGCTTACACAAGCTGACAATATTT-CAGAAT
34188111 TGCTTACACAAGCT
1 TGCTTACACAAGCT
34188125 AACGTCTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 5 0.14
29 18 0.51
30 12 0.34
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (30 bp):
TGCTTACACAAGCTGACAATATTTCAGAAT
Found at i:34193563 original size:22 final size:21
Alignment explanation
Indices: 34193515--34193573 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 21
34193505 CCATTATAAT
*
34193515 CATGTTACTAAAAACTATTTT
1 CATGTTACTAAAAACTATTTG
34193536 CA----ACTAAAAACTATTTG
1 CATGTTACTAAAAACTATTTG
34193553 CAATGTTACTAAAAACTATTT
1 C-ATGTTACTAAAAACTATTT
34193574 TTGTAATTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
17 15 0.47
18 1 0.03
21 2 0.06
22 14 0.44
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.37
Consensus pattern (21 bp):
CATGTTACTAAAAACTATTTG
Found at i:34201506 original size:21 final size:21
Alignment explanation
Indices: 34201480--34201536 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
34201470 TAACAGGTAA
34201480 AAATCATGCTTATCAAATAAC
1 AAATCATGCTTATCAAATAAC
* * *
34201501 AAATCATACTTATCACATTAC
1 AAATCATGCTTATCAAATAAC
*
34201522 AGATCATGCTTATCA
1 AAATCATGCTTATCA
34201537 TATTTCAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (21 bp):
AAATCATGCTTATCAAATAAC
Found at i:34201545 original size:21 final size:21
Alignment explanation
Indices: 34201482--34201545 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
34201472 ACAGGTAAAA
* *
34201482 ATCATGCTTATCAAATAACAA
1 ATCATGCTTATCAAATTACAG
* *
34201503 ATCATACTTATCACATTACAG
1 ATCATGCTTATCAAATTACAG
* *
34201524 ATCATGCTTATCATATTTCAG
1 ATCATGCTTATCAAATTACAG
34201545 A
1 A
34201546 ACATATTGAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.34
Consensus pattern (21 bp):
ATCATGCTTATCAAATTACAG
Found at i:34201770 original size:31 final size:31
Alignment explanation
Indices: 34201725--34201801 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
34201715 CCCACACGAT
* * * *
34201725 CGTGTGGACCACACAGCCTACTTGG-CCAGCC
1 CGTGTGG-CCACACAACCCAATTGGCCCAGAC
34201756 CGTGTGGCCTACACAACCCAATTGGCCCAGAC
1 CGTGTGGCC-ACACAACCCAATTGGCCCAGAC
34201788 CGTGTGGCTCACAC
1 CGTGTGGC-CACAC
34201802 GATGTAGCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
30 2 0.05
31 19 0.49
32 17 0.44
33 1 0.03
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.17
Consensus pattern (31 bp):
CGTGTGGCCACACAACCCAATTGGCCCAGAC
Found at i:34211318 original size:38 final size:38
Alignment explanation
Indices: 34211270--34211360 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 38
34211260 TAGATAAATG
* * *
34211270 CAGTTTGGGCCTGAGCCCGTTAC-AGTAACAGTCCAGTT
1 CAGTGTGGGCCTAAGCCC-TTACTAGAAACAGTCCAGTT
* * * *
34211308 CAGTGTGGGCCTAAGCCCTTTCTCGAAATAGTTCAGTT
1 CAGTGTGGGCCTAAGCCCTTACTAGAAACAGTCCAGTT
34211346 CAGTGTGGGCCTAAG
1 CAGTGTGGGCCTAAG
34211361 TCCAGTTCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 3 0.07
38 42 0.93
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.27
Consensus pattern (38 bp):
CAGTGTGGGCCTAAGCCCTTACTAGAAACAGTCCAGTT
Found at i:34211967 original size:27 final size:27
Alignment explanation
Indices: 34211937--34212190 Score: 230
Period size: 27 Copynumber: 9.5 Consensus size: 27
34211927 GGTATAAAAG
* *
34211937 TCATTTTACCATATAGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
34211964 TCATTTTACCCAATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
*
34211991 TCATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATGGGGGTATTTCGA
**
34212018 TCATTTTACTTTATGGGGGTATTTC-A
1 TCATTTTACCCTATGGGGGTATTTCGA
* ** *
34212044 GTCATTTTACCTTATAAGGGTACTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
* * *
34212072 TTATTTTACCCTAT--GAG-ATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGA
* * * *
34212096 TCATTTTACCCTCTAGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGA
* * *
34212123 TCATTTTACCCTATGAGCGTATTT-TA
1 TCATTTTACCCTATGGGGGTATTTCGA
** *
34212149 GTCATTTTACTTTATGGGGGTATTTCGG
1 -TCATTTTACCCTATGGGGGTATTTCGA
34212177 TCATTTTACCCTAT
1 TCATTTTACCCTAT
34212191 CTTTAGTAGT
Statistics
Matches: 182, Mismatches: 38, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
24 17 0.09
25 2 0.01
26 3 0.02
27 159 0.87
28 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:34211983 original size:54 final size:54
Alignment explanation
Indices: 34211935--34212190 Score: 277
Period size: 54 Copynumber: 4.8 Consensus size: 54
34211925 GGGGTATAAA
* *
34211935 AGTCATTTTACCATATAGGGGTATTTCGATCATTTTACCCAATGGGGGTATTTT
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT
* * * ** *
34211989 GGTCATTTTACCCTATGGGGGTATTTCAATCATTTTACTTTATGGGGGTATTTC
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT
* * * * *
34212043 AGTCATTTTACCTTATAAGGGTACTTCGATTATTTTACCCTAT--GAG-ATTTT
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT
* * * * *
34212094 -GATCATTTTACCCTCTAGGGGTATTTTGGTCATTTTACCCTATGAGCGTATTTT
1 AG-TCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT
** * *
34212148 AGTCATTTTACTTTATGGGGGTATTTCGGTCATTTTACCCTAT
1 AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTAT
34212191 CTTTAGTAGT
Statistics
Matches: 165, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
50 1 0.01
51 38 0.23
52 2 0.01
53 2 0.01
54 121 0.73
55 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (54 bp):
AGTCATTTTACCCTATAGGGGTATTTCGATCATTTTACCCTATGGGGGTATTTT
Found at i:34213649 original size:27 final size:27
Alignment explanation
Indices: 34213619--34213886 Score: 272
Period size: 27 Copynumber: 10.0 Consensus size: 27
34213609 TCATCTCCTA
**
34213619 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
34213646 GGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
34213673 GGGGTATTTCAGTCGTTTTAACCTATT
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
34213700 TGGGTATTTCGGTCATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * * *
34213727 ATGAGTATTTCGGTCAATTTACTCTATG
1 -GGGGTATTTCAGTCATTTTACCCTATG
* *
34213755 GTGGTATTTCAGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
34213782 AGGCTATTTCAGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
34213808 -GGG-ATTTCAATCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
34213833 GGGGTATTTCAGTCATTTTACCTTCTG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * *
34213860 AGGGTATTTCGGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
34213887 ACGGCATGTT
Statistics
Matches: 197, Mismatches: 40, Indels: 8
0.80 0.16 0.03
Matches are distributed among these distances:
24 19 0.10
25 2 0.01
26 3 0.02
27 151 0.77
28 22 0.11
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:34213754 original size:82 final size:80
Alignment explanation
Indices: 34213630--34213887 Score: 292
Period size: 82 Copynumber: 3.2 Consensus size: 80
34213620 GGGTATAACA
* * * *
34213630 GTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCAGTCGTTTTAAC
1 GTCATTTTATCCTAT-GAGGTATTTCGGTCATTTTACTCTATGGGGGTATTTCAGTCATTTTAAC
*
34213695 CTATTTGGGTATTTCG
65 CTATTAGGGTATTTCG
* * * *
34213711 GTCATTTTATCTTATGATGAGTATTTCGGTCAATTTACTCTATGGTGGTATTTCAGTCATTTTAC
1 GTCATTTTATCCTATGA-G-GTATTTCGGTCATTTTACTCTATGGGGGTATTTCAGTCATTTTAA
* * *
34213776 CCTATAAGGCTATTTCA
64 CCTATTAGGGTATTTCG
* **
34213793 GTCATTTTACCCTATG-GG-ATTTCAATCATTTTA-TCCTATGGGGGTATTTCAGTCATTTT-AC
1 GTCATTTTATCCTATGAGGTATTTCGGTCATTTTACT-CTATGGGGGTATTTCAGTCATTTTAAC
34213854 CT-TCTGAGGGTATTTCG
65 CTAT-T-AGGGTATTTCG
34213871 GTCATTTTATCCTATGA
1 GTCATTTTATCCTATGA
34213888 CGGCATGTTG
Statistics
Matches: 148, Mismatches: 23, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
76 1 0.01
77 4 0.03
78 59 0.40
79 1 0.01
80 2 0.01
81 14 0.09
82 67 0.45
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (80 bp):
GTCATTTTATCCTATGAGGTATTTCGGTCATTTTACTCTATGGGGGTATTTCAGTCATTTTAACC
TATTAGGGTATTTCG
Found at i:34216990 original size:27 final size:27
Alignment explanation
Indices: 34216949--34217018 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
34216939 CTAAGCCCTT
*
34216949 TCCTATGAGGGTATTTCGGTTATTTTA
1 TCCTATGAGGGTATTTCGGTCATTTTA
*
34216976 TCCTATGAGGTTATTTCGGTCATTTTA
1 TCCTATGAGGGTATTTCGGTCATTTTA
*
34217003 CCCTAT-AGGGGTATTT
1 TCCTATGA-GGGTATTT
34217019 TGATTATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (27 bp):
TCCTATGAGGGTATTTCGGTCATTTTA
Found at i:34217027 original size:27 final size:27
Alignment explanation
Indices: 34216950--34217027 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
34216940 TAAGCCCTTT
*
34216950 CCTATGAGGGTATTTCGGTTATTTTAT
1 CCTATGAGGGTATTTCGGTTATTTTAC
* *
34216977 CCTATGAGGTTATTTCGGTCATTTTAC
1 CCTATGAGGGTATTTCGGTTATTTTAC
* *
34217004 CCTAT-AGGGGTATTTTGATTATTT
1 CCTATGA-GGGTATTTCGGTTATTT
34217028 AGCCTATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
26 1 0.02
27 42 0.98
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (27 bp):
CCTATGAGGGTATTTCGGTTATTTTAC
Found at i:34220514 original size:20 final size:20
Alignment explanation
Indices: 34220491--34220543 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
34220481 AGGGTATCAA
34220491 AGTGCAGTCAGGGGCAC-CAT
1 AGTGCA-TCAGGGGCACGCAT
*
34220511 AGTGCATCCAAGGGCACGCAT
1 AGTGCAT-CAGGGGCACGCAT
34220532 -GTGCAATCAGGG
1 AGTGC-ATCAGGG
34220544 ACACTGAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 22 0.79
21 5 0.18
ACGTcount: A:0.26, C:0.25, G:0.34, T:0.15
Consensus pattern (20 bp):
AGTGCATCAGGGGCACGCAT
Found at i:34230123 original size:3 final size:3
Alignment explanation
Indices: 34230115--34230158 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
34230105 CATTTATAAC
34230115 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
34230159 CATCATAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:34231960 original size:3 final size:3
Alignment explanation
Indices: 34231952--34231985 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
34231942 CTCATTGCCA
34231952 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
34231986 TCTGTTCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:34236441 original size:18 final size:18
Alignment explanation
Indices: 34236418--34236457 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
34236408 TATAATTTTA
*
34236418 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
34236436 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
34236454 AAAA
1 AAAA
34236458 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:34240641 original size:27 final size:27
Alignment explanation
Indices: 34240611--34240708 Score: 128
Period size: 27 Copynumber: 3.6 Consensus size: 27
34240601 TAGAATGCGA
*
34240611 CACAAGGGCATTCCTTTT-ATAGATCAC
1 CACAAAGGC-TTCCTTTTCATAGATCAC
* *
34240638 CACAAAGACTTCTTTTTCATAGAT-AGC
1 CACAAAGGCTTCCTTTTCATAGATCA-C
*
34240665 CACAAAGGCTTCCTTTTCATAGATCGC
1 CACAAAGGCTTCCTTTTCATAGATCAC
34240692 CACAAAGGCTTCCTTTT
1 CACAAAGGCTTCCTTTT
34240709 TCTAGCGTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
26 8 0.13
27 54 0.87
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (27 bp):
CACAAAGGCTTCCTTTTCATAGATCAC
Found at i:34246247 original size:59 final size:63
Alignment explanation
Indices: 34246184--34246313 Score: 162
Period size: 59 Copynumber: 2.1 Consensus size: 63
34246174 TTGTTGGGTT
*
34246184 TTGAAATTATTATGTCTTGAA-TTTGTTAGATATTG-A-T-T-ATGTTTTAAGCTTGTTAGATA
1 TTGAAATTATTATGT-TTGAAGCTTGTTAGATATTGAATTATCATGTTTTAAGCTTGTTAGATA
* * * *
34246243 TTGAATTTATTATGTTTTAAGCTTGTTGGATATTGAATTTATCATGTTTTAAGCTTGTTGGATA
1 TTGAAATTATTATGTTTGAAGCTTGTTAGATATTGAA-TTATCATGTTTTAAGCTTGTTAGATA
34246307 TTGAAAT
1 TTGAAAT
34246314 GATTGACAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
58 4 0.07
59 26 0.44
60 1 0.02
62 1 0.02
63 1 0.02
64 26 0.44
ACGTcount: A:0.28, C:0.04, G:0.18, T:0.51
Consensus pattern (63 bp):
TTGAAATTATTATGTTTGAAGCTTGTTAGATATTGAATTATCATGTTTTAAGCTTGTTAGATA
Found at i:34246258 original size:32 final size:32
Alignment explanation
Indices: 34246219--34246311 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
34246209 TTAGATATTG
*
34246219 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
34246251 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
34246283 ATCATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
34246312 ATGATTGACA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:34247707 original size:19 final size:19
Alignment explanation
Indices: 34247662--34247699 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34247652 CATCCAAACA
34247662 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
34247681 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
34247700 TCCAAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:34247710 original size:14 final size:15
Alignment explanation
Indices: 34247691--34247726 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
34247681 CCAGAAAAGT
34247691 AAATCATTTTCCA-A
1 AAATCATTTTCCAGA
34247705 AAATCATTTTCCAGA
1 AAATCATTTTCCAGA
34247720 AAA-CATT
1 AAATCATT
34247727 GTACTAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATCATTTTCCAGA
Found at i:34255048 original size:3 final size:3
Alignment explanation
Indices: 34255040--34255095 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
34255030 ACCATAAAGA
34255040 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34255088 AAT AAT AA
1 AAT AAT AA
34255096 GATAACTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34255659 original size:22 final size:21
Alignment explanation
Indices: 34255634--34255688 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
34255624 TTGTTTTCAT
*
34255634 AAATTTAAATTCAAAACAATTC
1 AAATTTAAATTCAAAA-AATTA
*
34255656 AAATTTAAATTTTCAAAAATTTA
1 AAATTTAAA--TTCAAAAAATTA
34255679 AAATTTAAAT
1 AAATTTAAAT
34255689 CCATTTGTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
21 1 0.03
22 9 0.31
23 12 0.41
24 7 0.24
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATTTAAATTCAAAAAATTA
Found at i:34259740 original size:19 final size:19
Alignment explanation
Indices: 34259718--34259758 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
34259708 TTAGAAAATT
34259718 AAAAAAAATTCAAAATATA
1 AAAAAAAATTCAAAATATA
* * *
34259737 AAAATATATTTAAAATATA
1 AAAAAAAATTCAAAATATA
34259756 AAA
1 AAA
34259759 TATTTAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAAAATTCAAAATATA
Found at i:34259939 original size:30 final size:29
Alignment explanation
Indices: 34259898--34259977 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 29
34259888 TTTACAATTT
*
34259898 TATTTTATATATTTTTACAAATTATTAAATG
1 TATTTT-TATATTTTTACAAATT-TTAAATA
* *
34259929 T-TTTTCTATATTTATAATAAATTTTAAATA
1 TATTTT-TATATTT-TTACAAATTTTAAATA
34259959 TATTTTTATAATTTTTACA
1 TATTTTTAT-ATTTTTACA
34259978 TTTTTATAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
30 24 0.60
31 16 0.40
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (29 bp):
TATTTTTATATTTTTACAAATTTTAAATA
Found at i:34259959 original size:20 final size:20
Alignment explanation
Indices: 34259936--34259989 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
34259926 ATGTTTTTCT
34259936 ATATTTATAATAAATTTTAA
1 ATATTTATAATAAATTTTAA
* * * *
34259956 ATATATTTTTATAATTTTTAC
1 ATAT-TTATAATAAATTTTAA
*
34259977 ATTTTTATAATAA
1 ATATTTATAATAA
34259990 TGTTACTAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTTATAATAAATTTTAA
Found at i:34260087 original size:10 final size:10
Alignment explanation
Indices: 34260072--34260130 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
34260062 TTTTCTATAT
34260072 TATATATTTA
1 TATATATTTA
*
34260082 TATATATTTC
1 TATATATTTA
34260092 TGA-AT-TTT-
1 T-ATATATTTA
34260100 TATATATTTA
1 TATATATTTA
* *
34260110 TTTTATTTTTA
1 -TATATATTTA
34260121 TATATATTTA
1 TATATATTTA
34260131 ATAAAAGAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 6 0.15
10 20 0.51
11 9 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
TATATATTTA
Found at i:34264519 original size:18 final size:17
Alignment explanation
Indices: 34264486--34264532 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
34264476 ATAAAAATAA
34264486 AACGTTTGAAATTGAAT
1 AACGTTTGAAATTGAAT
34264503 AACGATTTGTAAA-TGAAT
1 AACG-TTTG-AAATTGAAT
*
34264521 AATGTTTTGAAA
1 AACG-TTTGAAA
34264533 ACGAACGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 16 0.62
19 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (17 bp):
AACGTTTGAAATTGAAT
Found at i:34264991 original size:15 final size:16
Alignment explanation
Indices: 34264966--34264995 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34264956 CATTTGAAAG
34264966 AATATATAATTAATTA
1 AATATATAATTAATTA
34264982 AATA-ATAATTAATT
1 AATATATAATTAATT
34264996 TTCATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATAATTAATTA
Found at i:34266052 original size:28 final size:29
Alignment explanation
Indices: 34266018--34266072 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
34266008 GCCCAATATG
34266018 CAATTATATACAC-AAACTTTAATTTTGT
1 CAATTATATACACAAAACTTTAATTTTGT
34266046 CAATTATATACACAAAACTTTAATTTT
1 CAATTATATACACAAAACTTTAATTTT
34266073 AATTCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.42
Consensus pattern (29 bp):
CAATTATATACACAAAACTTTAATTTTGT
Found at i:34275099 original size:2 final size:2
Alignment explanation
Indices: 34275092--34275121 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34275082 ATGATAAATA
34275092 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
34275122 GGAGTTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34275449 original size:25 final size:25
Alignment explanation
Indices: 34275403--34275450 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
34275393 TTTTTAAAAA
* *
34275403 TAATTTACATTTATTAATTGAATCT
1 TAATTTACATTTATAAAATGAATCT
34275428 TAATTT-CATTTATAAAAATGAAT
1 TAATTTACATTTAT-AAAATGAAT
34275451 TCGAGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (25 bp):
TAATTTACATTTATAAAATGAATCT
Found at i:34277169 original size:29 final size:28
Alignment explanation
Indices: 34277136--34277199 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
34277126 AAAATAATTC
* *
34277136 AATTTTTATATAATATTTTGATTTTTTAA
1 AATTTTTAAAT-ATATTTTAATTTTTTAA
* *
34277165 AATTTATAAATATTTTTTAATTTTTTAA
1 AATTTTTAAATATATTTTAATTTTTTAA
*
34277193 AAATTTT
1 AATTTTT
34277200 CAATTTTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
AATTTTTAAATATATTTTAATTTTTTAA
Found at i:34277191 original size:21 final size:21
Alignment explanation
Indices: 34277167--34277242 Score: 97
Period size: 22 Copynumber: 3.8 Consensus size: 21
34277157 TTTTTTAAAA
*
34277167 TTTATA-AATATTTTTTAATT
1 TTTATATAATATTTTTCAATT
*
34277187 TTT-TA-AA-AATTTTCAATT
1 TTTATATAATATTTTTCAATT
34277205 TTTATATAATAATTTTTCAATT
1 TTTATATAAT-ATTTTTCAATT
34277227 TTTATATAATATTTTT
1 TTTATATAATATTTTT
34277243 AAAAAAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.24
19 6 0.12
20 5 0.10
21 6 0.12
22 20 0.41
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATATAATATTTTTCAATT
Found at i:34277241 original size:20 final size:20
Alignment explanation
Indices: 34277133--34277241 Score: 87
Period size: 22 Copynumber: 5.1 Consensus size: 20
34277123 ATGAAAATAA
34277133 TTCAATTTTTATATAATATT
1 TTCAATTTTTATATAATATT
* *
34277153 TTGATTTTTTAAAATTTATAAATATTT
1 TTCAATTTTT---A--TAT-AATA-TT
* *
34277180 TTTAATTTTT-TA-AAAATT
1 TTCAATTTTTATATAATATT
34277198 TTCAATTTTTATATAATAATTT
1 TTCAATTTTTATATAAT-A-TT
34277220 TTCAATTTTTATATAATATT
1 TTCAATTTTTATATAATATT
34277240 TT
1 TT
34277242 TAAAAAAATT
Statistics
Matches: 71, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
18 11 0.15
19 5 0.07
20 14 0.20
21 4 0.06
22 19 0.27
23 1 0.01
25 3 0.04
26 4 0.06
27 10 0.14
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (20 bp):
TTCAATTTTTATATAATATT
Found at i:34278212 original size:14 final size:14
Alignment explanation
Indices: 34278184--34278223 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
34278174 GAATTATAAA
*
34278184 AAATA-AAAAATAT
1 AAATATAAATATAT
*
34278197 AAATATATATATAT
1 AAATATAAATATAT
34278211 AAATATAAATATA
1 AAATATAAATATA
34278224 CATATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:34278236 original size:20 final size:20
Alignment explanation
Indices: 34278191--34278228 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34278181 AAAAAATAAA
*
34278191 AAATATAAATATATATATAT
1 AAATATAAATATACATATAT
34278211 AAATATAAATATACATAT
1 AAATATAAATATACATAT
34278229 TTTAATATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATAAATATACATATAT
Found at i:34278696 original size:23 final size:21
Alignment explanation
Indices: 34278657--34278698 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
34278647 AAATCAACAA
*
34278657 TATACAAATCAATAAATAAAT
1 TATACAAATCAAAAAATAAAT
34278678 TATACACAATCAACAAAATAA
1 TATACA-AATCAA-AAAATAA
34278699 GAACAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (21 bp):
TATACAAATCAAAAAATAAAT
Found at i:34279164 original size:25 final size:25
Alignment explanation
Indices: 34279114--34279164 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
34279104 GATATTACAT
* * *
34279114 ATATTATATATGATTTCTTAACAGC
1 ATATTATATATAATTTCTAAAAAGC
34279139 ATATTATATATAATATT-TAAAAAGC
1 ATATTATATATAAT-TTCTAAAAAGC
34279164 A
1 A
34279165 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (25 bp):
ATATTATATATAATTTCTAAAAAGC
Found at i:34280999 original size:50 final size:50
Alignment explanation
Indices: 34280924--34281116 Score: 197
Period size: 50 Copynumber: 3.7 Consensus size: 50
34280914 TTTTCTGTAC
* * * **
34280924 TGCCAATGCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * *
34280974 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *
34281024 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
* *
34281080 TGCCAATACCATGCCCCAGACATGGTCTTACATGAGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGA
34281117 TCTCATTCCC
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
50 81 0.69
53 2 0.02
56 34 0.29
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:34283064 original size:19 final size:20
Alignment explanation
Indices: 34283018--34283070 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
34283008 TGTTACGGAA
34283018 AAAACTTATAAAATATTATTT
1 AAAA-TTATAAAATATTATTT
***
34283039 TTTATTATAAAATA-TATTT
1 AAAATTATAAAATATTATTT
34283058 AAAATTATAAAAT
1 AAAATTATAAAAT
34283071 TAATTTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.58
20 10 0.38
21 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAAAATATTATTT
Found at i:34289072 original size:30 final size:30
Alignment explanation
Indices: 34289028--34289334 Score: 380
Period size: 30 Copynumber: 10.2 Consensus size: 30
34289018 TGAATTCAAA
* * *
34289028 TGTATATGGTTATACATTGTCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* * *
34289058 CGTATGTAGATATACATTGCCAAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* *
34289088 TATATATAGATGTACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* *
34289118 CGTATTTAGATATACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* *
34289148 TGTATTTGGATATACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* * *
34289178 TGTATATGGTTATACATTGTCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
** *
34289208 TGTACGTGGATATACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
*
34289238 TGTATATAGATGTACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* * * * *
34289268 CGTATTTGGATATACATTACCAAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
* *
34289298 TGTATATAGGTGTACATTGCCGAATTGATT
1 TGTATATAGATATACATTGCCGAATTGATT
34289328 TGTATAT
1 TGTATAT
34289335 GTATATATAT
Statistics
Matches: 236, Mismatches: 41, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 236 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (30 bp):
TGTATATAGATATACATTGCCGAATTGATT
Found at i:34295968 original size:30 final size:30
Alignment explanation
Indices: 34295922--34296232 Score: 399
Period size: 30 Copynumber: 10.4 Consensus size: 30
34295912 ATTCAAAGGC
* * *
34295922 ATATGGTTATAAATTGCCGAATTGATTCGT
1 ATATGGATATACATTGCCGAATTGATTTGT
*
34295952 ATGTGGATATACATTGCCGAATTGATTTGT
1 ATATGGATATACATTGCCGAATTGATTTGT
* * *
34295982 ATATAGATGTACATTGCCGAATTGATTCGT
1 ATATGGATATACATTGCCGAATTGATTTGT
*
34296012 ATTTGGATATACATTGCCGAATTGATTTGT
1 ATATGGATATACATTGCCGAATTGATTTGT
* **
34296042 ATTTGGATATACATTGCTTAATTGATTTGT
1 ATATGGATATACATTGCCGAATTGATTTGT
* **
34296072 ATATGGTTATACATTGCCGAATTGATTCAT
1 ATATGGATATACATTGCCGAATTGATTTGT
*
34296102 ATGTGGATATACATTGCCGAATTGATTTGT
1 ATATGGATATACATTGCCGAATTGATTTGT
* * *
34296132 ATATAGATGTACATTGCCGAATTGATTCGT
1 ATATGGATATACATTGCCGAATTGATTTGT
* * *
34296162 ATTTGGATATACATTTCCAAATTGATTTGT
1 ATATGGATATACATTGCCGAATTGATTTGT
*
34296192 ATATAGG-TGTACATTGCCGAATTGATTTGT
1 ATAT-GGATATACATTGCCGAATTGATTTGT
*
34296222 ATATGTATATA
1 ATATGGATATA
34296233 TATGTATTGC
Statistics
Matches: 239, Mismatches: 40, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
29 1 0.00
30 236 0.99
31 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (30 bp):
ATATGGATATACATTGCCGAATTGATTTGT
Found at i:34300448 original size:17 final size:17
Alignment explanation
Indices: 34300428--34300464 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
34300418 TTCGTTTCAC
* *
34300428 TTTCTTTTTCATTCTTT
1 TTTCTTCTTCACTCTTT
34300445 TTTCTTCTTCACTCTTT
1 TTTCTTCTTCACTCTTT
34300462 TTT
1 TTT
34300465 TCTCTCGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTCTTCACTCTTT
Found at i:34302795 original size:35 final size:35
Alignment explanation
Indices: 34302749--34302817 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
34302739 TCCTCCTATA
*
34302749 CCTCATTTTTCTTTCTTT-TTTCTTTTT-TTATTTTC
1 CCTCATCTTTCTTT-TTTCTTT-TTTTTCTTATTTTC
34302784 CCTCATCTTTCTTTTTTCTTTTTTTTCTTATTTT
1 CCTCATCTTTCTTTTTTCTTTTTTTTCTTATTTT
34302818 TCTTTTCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 8 0.26
35 23 0.74
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (35 bp):
CCTCATCTTTCTTTTTTCTTTTTTTTCTTATTTTC
Found at i:34302993 original size:105 final size:107
Alignment explanation
Indices: 34302873--34303070 Score: 296
Period size: 105 Copynumber: 1.9 Consensus size: 107
34302863 TCCATAGAAC
*
34302873 CCTCTCAAATTTTCTCTCATTTGT-TTACCATCCAATCACCATCAAAA-T-TTC-TTCTTTCTTC
1 CCTCTCAAATTTTCTCTCATTT-TCTTACCATCCAATCACCACCAAAATTCTTCTTTCTTTCTTC
34302934 TATCAAATTATACACTAAATCTTTCTTCTTTCTTTCGTCAAAAA
65 TATCAAATTATACACT-AATCTTTCTTCTTTCTTTCGTCAAAAA
* *
34302978 CCTCTTAAATTTTCTCTCATTTTCTTGCCATCCAATCACCACCAAAATTTCTTCTTTCTTTCTTC
1 CCTCTCAAATTTTCTCTCATTTTCTTACCATCCAATCACCACCAAAA-TTCTTCTTTCTTTCTTC
* *
34303043 TGTCAAATTATACACTTATCTTTCTTCT
65 TATCAAATTATACACTAATCTTTCTTCT
34303071 GTCAAAAACT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
104 1 0.01
105 42 0.51
107 1 0.01
108 14 0.17
109 25 0.30
ACGTcount: A:0.25, C:0.28, G:0.02, T:0.45
Consensus pattern (107 bp):
CCTCTCAAATTTTCTCTCATTTTCTTACCATCCAATCACCACCAAAATTCTTCTTTCTTTCTTCT
ATCAAATTATACACTAATCTTTCTTCTTTCTTTCGTCAAAAA
Found at i:34313210 original size:2 final size:2
Alignment explanation
Indices: 34313203--34313236 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34313193 TTCATTTGTA
34313203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34313237 TTGTAGGAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34318500 original size:23 final size:23
Alignment explanation
Indices: 34318451--34318501 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
34318441 AACATTAATA
34318451 AACTTATTTTATTAACATATCAC
1 AACTTATTTTATTAACATATCAC
34318474 -ACTTGATTTTATT-AC-TCATCAC
1 AACTT-ATTTTATTAACAT-ATCAC
34318496 AACTTA
1 AACTTA
34318502 CATAATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 12 0.48
23 12 0.48
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (23 bp):
AACTTATTTTATTAACATATCAC
Found at i:34318797 original size:33 final size:32
Alignment explanation
Indices: 34318752--34318914 Score: 105
Period size: 33 Copynumber: 5.0 Consensus size: 32
34318742 ACATTCGCAG
* * *
34318752 TGCCATAACCCAGTTATGGTCTTATCATCAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAAAA
* *
34318785 TGCCATAGCCCAGCTATGATCTTACAT-AACAC
1 TGCCATAGCCCAGCTATGGTCTTACATCAA-AA
* * * * * * *
34318817 TGTCATGGTCCAAAC-ATGGTCTTACGTTCATAG
1 TGCCATAG-CCCAGCTATGGTCTTAC-ATCAAAA
* * * *
34318850 TGTCATAACCCAGTTATGGTCTGATCATCAAAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATCAAAA
* *
34318883 TGCCATAGCCCAACTATGGTCTTACATAAAAA
1 TGCCATAGCCCAGCTATGGTCTTACATCAAAA
34318915 CATTGCCATG
Statistics
Matches: 96, Mismatches: 28, Indels: 13
0.70 0.20 0.09
Matches are distributed among these distances:
31 1 0.01
32 29 0.30
33 64 0.67
34 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (32 bp):
TGCCATAGCCCAGCTATGGTCTTACATCAAAA
Found at i:34325457 original size:45 final size:45
Alignment explanation
Indices: 34325400--34325488 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
34325390 ATTTTTACAC
*
34325400 ATATCAAACACTTAAATGTATGTGATTTAAACTCTTTTATTCTAT
1 ATATCAAACACTTAAATGTACGTGATTTAAACTCTTTTATTCTAT
*
34325445 ATATCAAGCACTTAAATGTACGTGATTTAAACTCTTTTATTCTA
1 ATATCAAACACTTAAATGTACGTGATTTAAACTCTTTTATTCTA
34325489 CTAATATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.43
Consensus pattern (45 bp):
ATATCAAACACTTAAATGTACGTGATTTAAACTCTTTTATTCTAT
Found at i:34331050 original size:41 final size:41
Alignment explanation
Indices: 34331005--34331149 Score: 211
Period size: 41 Copynumber: 3.5 Consensus size: 41
34330995 GACTTTAAGT
*
34331005 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
34331046 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
34331087 CTAGCAGGCTAAGCGCCGGTGAAT-GGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTG-ATCTGAATCAGGTTATAAAC
* *
34331128 CTAGCAGGCTAAATGCCAGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
34331150 ATATGTTAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
40 1 0.01
41 92 0.97
42 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:34331064 original size:82 final size:82
Alignment explanation
Indices: 34330960--34331150 Score: 210
Period size: 82 Copynumber: 2.3 Consensus size: 82
34330950 TTTAGGTTTA
** * *
34330960 AAACCTAGCAGGCTTAAG-GCCGGTGAAAT-AATTCAGACTT-TAAGTCTAGCAGGCTAAGTGCT
1 AAACCTAGCAGGC-TAAGTGCCGGTGAAATGAA-TCAG-CTTATAAACCTAGCAGGCTAAGCGCC
* *
34331022 GGTG-ATCTGAATCAGGTTAT
63 GGTGAAT-GGAATCAGGCTAT
** *
34331042 AAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGT
1 AAACCTAGCAGGCTAAGTGCCGGTGAAATGAATCAGCTTATAAACCTAGCAGGCTAAGCGCCGGT
34331107 GAATGGAATCAGGCTAT
66 GAATGGAATCAGGCTAT
* * *
34331124 AAGCCTAGCAGGCTAAATGCCAGTGAA
1 AAACCTAGCAGGCTAAGTGCCGGTGAA
34331151 TATGTTAAAT
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
81 6 0.07
82 82 0.89
83 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (82 bp):
AAACCTAGCAGGCTAAGTGCCGGTGAAATGAATCAGCTTATAAACCTAGCAGGCTAAGCGCCGGT
GAATGGAATCAGGCTAT
Found at i:34331601 original size:2 final size:2
Alignment explanation
Indices: 34331594--34331623 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34331584 TAATATGCTG
34331594 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
34331624 ATTAATAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34338629 original size:41 final size:41
Alignment explanation
Indices: 34338535--34338720 Score: 304
Period size: 41 Copynumber: 4.6 Consensus size: 41
34338525 GACTTTAAGT
34338535 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTAT-AAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
34338575 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
34338616 CTAGCAGACTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
34338657 CTTGCAGGCTAAGTGTCGGTGAT-TGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGTTATAAAC
34338698 CTAGCAGGCTAAGTGCCGGTGAT
1 CTAGCAGGCTAAGTGCCGGTGAT
34338721 ATGTTAAATT
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 38 0.28
41 98 0.72
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:34338701 original size:82 final size:81
Alignment explanation
Indices: 34338481--34338720 Score: 308
Period size: 82 Copynumber: 2.9 Consensus size: 81
34338471 ATTGAAATTT
* ** * *
34338481 TCAGGTTTAAAACCTAGCAGGCTTAAG-GCCGGTGAAAT-AATTC-GGACTTTAAGTCTAGCAGG
1 TCAGG-TTATAACCTAGCAGGC-TAAGTGCCGGTGATCTGAA-TCAGG-CTATAAGCCTAGCAGG
34338543 CTAAGTGCCGGTGATCTGAA
62 CTAAGTGCCGGTGATCTGAA
* * *
34338563 TCAGGTTATAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAACCTAGCAGACTAA
1 TCAGGTTATAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAA
34338628 GTGCCGGTGATCTGAA
66 GTGCCGGTGATCTGAA
* *
34338644 TCAGGTTATAAACCTTGCAGGCTAAGTGTCGGTGAT-TGGAATCAGGCTATAAGCCTAGCAGGCT
1 TCAGGTTAT-AACCTAGCAGGCTAAGTGCCGGTGATCT-GAATCAGGCTATAAGCCTAGCAGGCT
34338708 AAGTGCCGGTGAT
64 AAGTGCCGGTGAT
34338721 ATGTTAAATT
Statistics
Matches: 140, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
80 4 0.03
81 67 0.48
82 69 0.49
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (81 bp):
TCAGGTTATAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAA
GTGCCGGTGATCTGAA
Found at i:34359446 original size:2 final size:2
Alignment explanation
Indices: 34359441--34359487 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
34359431 TTTATATATA
34359441 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34359483 TG TG T
1 TG TG T
34359488 TCTATTGTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:34359707 original size:33 final size:32
Alignment explanation
Indices: 34359666--34359826 Score: 115
Period size: 33 Copynumber: 4.8 Consensus size: 32
34359656 CAGTGTTTAT
*
34359666 ATGTAAGACCATAGTTAGGCTATGGCATTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
** * * *
34359698 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGTTGGGCTATGGCATTCTG
* * * * * * *
34359731 AACGTAAGACCATGGTTGGACCATGACAGTGTTTAT
1 -ATGTAAGACCATAGTTGGGCTATGGCA-T-TCT-G
*
34359767 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCATTCTG
* * *
34359799 ATGATAAGGCCATAATTGGGTTATGGCA
1 ATG-TAAGACCATAGTTGGGCTATGGCA
34359827 CTACGAATGT
Statistics
Matches: 94, Mismatches: 29, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
32 6 0.06
33 62 0.66
34 3 0.03
35 23 0.24
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (32 bp):
ATGTAAGACCATAGTTGGGCTATGGCATTCTG
Found at i:34359775 original size:101 final size:101
Alignment explanation
Indices: 34359600--34359838 Score: 415
Period size: 101 Copynumber: 2.4 Consensus size: 101
34359590 GAATTGACGA
*
34359600 ATAAGACCATAACTGGGTTATGGCACTATGAATGTATGACCATGGTTGGACCATGACAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAGTGTTTA
*
34359665 TATGTAAGACCATAGTTAGGCTATGGCATTCTGATG
66 TATGTAAGACCATAGCTAGGCTATGGCATTCTGATG
*
34359701 ATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGACAGTGTTTA
1 ATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAGTGTTTA
*
34359766 TATGTAAGACCATAGCTGGGCTATGGCATTCTGATG
66 TATGTAAGACCATAGCTAGGCTATGGCATTCTGATG
* * *
34359802 ATAAGGCCATAATTGGGTTATGGCACTACGAATGTAA
1 ATAAGACCATAACTGGGTTATGGCACTATGAATGTAA
34359839 AGGATGAAAA
Statistics
Matches: 130, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 130 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (101 bp):
ATAAGACCATAACTGGGTTATGGCACTATGAATGTAAGACCATGGTTGGACCATGACAGTGTTTA
TATGTAAGACCATAGCTAGGCTATGGCATTCTGATG
Found at i:34381940 original size:22 final size:22
Alignment explanation
Indices: 34381915--34381960 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34381905 TATTTTATTC
34381915 TTTTGGTTTGGTAACTCAACAA
1 TTTTGGTTTGGTAACTCAACAA
34381937 TTTTGGTTTGGTAACTCAACAA
1 TTTTGGTTTGGTAACTCAACAA
34381959 TT
1 TT
34381961 CAACTCTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (22 bp):
TTTTGGTTTGGTAACTCAACAA
Found at i:34386105 original size:30 final size:30
Alignment explanation
Indices: 34386071--34386130 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
34386061 TCTCCTTCAA
*
34386071 GCTCTCACCATTCCTGTCACCACTATAGCT
1 GCTCTCAACATTCCTGTCACCACTATAGCT
** *
34386101 GCTCTCAACATTGTTGTGACCACTATAGCT
1 GCTCTCAACATTCCTGTCACCACTATAGCT
34386131 ATTTAGTAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.33, G:0.13, T:0.32
Consensus pattern (30 bp):
GCTCTCAACATTCCTGTCACCACTATAGCT
Found at i:34391255 original size:9 final size:9
Alignment explanation
Indices: 34391237--34391294 Score: 64
Period size: 9 Copynumber: 6.4 Consensus size: 9
34391227 TTCGGTTAAA
34391237 AATTAACCG
1 AATTAACCG
*
34391246 AATTACCCG
1 AATTAACCG
*
34391255 AATTAACCT
1 AATTAACCG
34391264 AATT-ACTCG
1 AATTAAC-CG
* *
34391273 AATTATCCT
1 AATTAACCG
34391282 AATTAACCG
1 AATTAACCG
34391291 AATT
1 AATT
34391295 GAATCACTAC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
8 2 0.05
9 36 0.92
10 1 0.03
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:34391260 original size:18 final size:18
Alignment explanation
Indices: 34391237--34391294 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
34391227 TTCGGTTAAA
*
34391237 AATTAACCGAATTACCCG
1 AATTAACCTAATTACCCG
*
34391255 AATTAACCTAATTACTCG
1 AATTAACCTAATTACCCG
* *
34391273 AATTATCCTAATTAACCG
1 AATTAACCTAATTACCCG
34391291 AATT
1 AATT
34391295 GAATCACTAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (18 bp):
AATTAACCTAATTACCCG
Found at i:34391345 original size:6 final size:6
Alignment explanation
Indices: 34391334--34391362 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34391324 ACTTTTAGAC
34391334 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
34391363 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:34391386 original size:20 final size:20
Alignment explanation
Indices: 34391318--34391375 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
34391308 ATTAAATTAT
* *
34391318 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
34391339 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
34391357 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
34391376 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:34391876 original size:32 final size:32
Alignment explanation
Indices: 34391830--34391890 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
34391820 GGGGTCTTCT
34391830 TTGGCGGCCATTCTTTATTAATTAATTACTAC
1 TTGGCGGCCATTCTTTATTAATTAATTACTAC
*
34391862 TTGGCGGCCCTTCTTTATTAATTAATTAC
1 TTGGCGGCCATTCTTTATTAATTAATTAC
34391891 AATATTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.44
Consensus pattern (32 bp):
TTGGCGGCCATTCTTTATTAATTAATTACTAC
Found at i:34402186 original size:5 final size:5
Alignment explanation
Indices: 34402169--34402215 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
34402159 ACCTAAGATG
* * *
34402169 TGAAT TGAGT TGAAT TGAAT ATGAAT TGAAT TAAAT TGAGT TGAAT T
1 TGAAT TGAAT TGAAT TGAAT -TGAAT TGAAT TGAAT TGAAT TGAAT T
34402216 TACTCGTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.40
Consensus pattern (5 bp):
TGAAT
Found at i:34402680 original size:24 final size:24
Alignment explanation
Indices: 34402653--34402736 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
34402643 GGCTATTCGG
34402653 AGCTTCCCGTTAATGGCTCTTTGT
1 AGCTTCCCGTTAATGGCTCTTTGT
* * * *
34402677 AGCTACTCGTTATTGGCTCGTATG-
1 AGCTTCCCGTTAATGGCTC-TTTGT
**
34402701 AGCTTCATGATT-ATGGCTCTTAT-T
1 AGCTTCCCG-TTAATGGCTCTT-TGT
34402725 AGCTTCCCGTTA
1 AGCTTCCCGTTA
34402737 TACAGCTCGG
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
23 3 0.07
24 36 0.82
25 5 0.11
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.40
Consensus pattern (24 bp):
AGCTTCCCGTTAATGGCTCTTTGT
Found at i:34402769 original size:25 final size:25
Alignment explanation
Indices: 34402725--34402795 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
34402715 GGCTCTTATT
** *
34402725 AGCTTCCCGTTATACAGCTCGGATA
1 AGCTTCCCGTTATATGGCTCGCATA
*
34402750 AGCTTCCCGTTATATGGCTCACATA
1 AGCTTCCCGTTATATGGCTCGCATA
* *
34402775 AACTTCCTGTTATATGGCTCG
1 AGCTTCCCGTTATATGGCTCG
34402796 AGAGAGGGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGTTATATGGCTCGCATA
Found at i:34407528 original size:43 final size:43
Alignment explanation
Indices: 34407423--34407539 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
34407413 TGAGTATTTG
* * * *
34407423 TGTAAGACCATGTCTGGGACGTTGGCA-TCAATTTGAGGTTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATTGAATTTGA-G-TTACA
34407467 TGTAAGACC-CTGTCTGGGACATTGGCATTGACATTTGA-TTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATTGA-ATTTGAGTTACA
*
34407510 TGTAAGACCACGTCTGGGACATTGACATTG
1 TGTAAGACCACGTCTGGGACATTGGCATTG
34407540 TCTCCGAATG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
43 31 0.48
44 25 0.39
45 2 0.03
46 6 0.09
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATTGAATTTGAGTTACA
Found at i:34416553 original size:29 final size:30
Alignment explanation
Indices: 34416516--34416572 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34416506 TCTGAGCCTT
*
34416516 GGGGAAAAA-TGTAATTATGTAAAAGTTTA
1 GGGGAAAAATTGTAATTATGAAAAAGTTTA
* *
34416545 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAATTGTAATTATGAAAAAGTT
34416573 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.42, C:0.02, G:0.25, T:0.32
Consensus pattern (30 bp):
GGGGAAAAATTGTAATTATGAAAAAGTTTA
Done.