Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008022.1 Hibiscus syriacus cultivar Beakdansim tig00110495_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: 1039607
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 3
Found at i:3743 original size:21 final size:21
Alignment explanation
Indices: 3704--3743 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3694 TTTGAAAATT
3704 AAAGAAATGAAATGGAAATGG
1 AAAGAAATGAAATGGAAATGG
*
3725 AAAGAATTGAAATGGAAAT
1 AAAGAAATGAAATGGAAAT
3744 AAATGTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (21 bp):
AAAGAAATGAAATGGAAATGG
Found at i:3874 original size:11 final size:11
Alignment explanation
Indices: 3839--3867 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
3829 GAATATCTTG
3839 ATGATGATTGA
1 ATGATGATTGA
3850 ATGATGATTGA
1 ATGATGATTGA
3861 ATGATGA
1 ATGATGA
3868 ATAAATGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (11 bp):
ATGATGATTGA
Found at i:3992 original size:36 final size:35
Alignment explanation
Indices: 3892--4003 Score: 136
Period size: 35 Copynumber: 3.2 Consensus size: 35
3882 ATTGGGGGTT
* * * *
3892 TTATAGGCGTGAAATCGTGATAGAAGATGGTTAGG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
* * *
3927 ATATAGGCGTGCAATAGTAATGGAAGATGGTGATG
1 TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
*
3962 TTATAGGCGTGAAAATGGTGATGGAAGATGGTGATG
1 TTATAGGCGTG-AAATAGTGATGGAAGATGGTGATG
3998 TT-TAGG
1 TTATAGG
4004 TAATATCTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 42 0.65
36 23 0.35
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (35 bp):
TTATAGGCGTGAAATAGTGATGGAAGATGGTGATG
Found at i:9655 original size:36 final size:35
Alignment explanation
Indices: 9556--9666 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
9546 TTGGGGGTAA
* * * *
9556 TATAGGCGTGAAATAGTGATAGAAGATGGTTAGGA
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
* * *
9591 TATAGGTGTGCAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
*
9626 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATAGTGATGGAAGATGGTGATGT
9662 T-TAGG
1 TATAGG
9667 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.03, G:0.36, T:0.29
Consensus pattern (35 bp):
TATAGGCGTGAAATAGTGATGGAAGATGGTGATGT
Found at i:11378 original size:2 final size:2
Alignment explanation
Indices: 11371--11397 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11361 AGTTATATTC
11371 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11398 GTTATTATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12154 original size:48 final size:46
Alignment explanation
Indices: 12098--12230 Score: 158
Period size: 46 Copynumber: 2.8 Consensus size: 46
12088 TGAGAGCATT
** *
12098 TGGTGCCAACATGAGGAAGCACATCACCATTCGGCCAAGTGGAGAAAA
1 TGGTGCCAACATGAACAAG--CATCACCATTCGGCCAAGGGGAGAAAA
*
12146 TGGTGCCAAGATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
1 TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
* * * * **
12192 TGGCGCCAATATTAACAAGAATTGCCATTCGGCCAAGGG
1 TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGG
12231 AGATGCCTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
46 59 0.79
48 16 0.21
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.16
Consensus pattern (46 bp):
TGGTGCCAACATGAACAAGCATCACCATTCGGCCAAGGGGAGAAAA
Found at i:25922 original size:23 final size:23
Alignment explanation
Indices: 25893--25940 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25883 CACTTGGATT
25893 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
25916 TGATGAATGAGTTTGAAAAATAA
1 TGATGAATGAGTTTGAAAAATAA
25939 TG
1 TG
25941 CATCCATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (23 bp):
TGATGAATGAGTTTGAAAAATAA
Found at i:30437 original size:20 final size:20
Alignment explanation
Indices: 30398--30459 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
30388 AGCATTTATC
*
30398 TTCATT-AAAATTAT-TATT
1 TTCATTAAAAATCATGTATT
30416 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
*
30436 TTCATTAAAAATCATGTCTT
1 TTCATTAAAAATCATGTATT
30456 TTCA
1 TTCA
30460 AAGGAGTTTC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.15
19 7 0.17
20 27 0.68
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:31231 original size:7 final size:6
Alignment explanation
Indices: 31212--31256 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
31202 GTGGTGCAAC
*
31212 AAAAAG AAAAAG AAAGAAG AAAAAC AAAATAG -AAAAG AAAAAG AA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAA-AG AAAAAG AAAAAG AA
31257 CTCCTACATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 2 0.06
6 25 0.74
7 7 0.21
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:34294 original size:16 final size:16
Alignment explanation
Indices: 34273--34320 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
34263 ATAAGTTACC
34273 TTCATTTTCTCTTTAT
1 TTCATTTTCTCTTTAT
*
34289 TTCATTTCCT-TTTAT
1 TTCATTTTCTCTTTAT
34304 TTCATATTT-TC-TTAT
1 TTCAT-TTTCTCTTTAT
34319 TT
1 TT
34321 ACTACCTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCATTTTCTCTTTAT
Found at i:34681 original size:17 final size:17
Alignment explanation
Indices: 34659--34692 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34649 TGCTTGATTT
34659 CCATACAGCTTTAAGAC
1 CCATACAGCTTTAAGAC
34676 CCATACAGCTTTAAGAC
1 CCATACAGCTTTAAGAC
34693 AAGTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (17 bp):
CCATACAGCTTTAAGAC
Found at i:41447 original size:19 final size:20
Alignment explanation
Indices: 41425--41467 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
41415 AGCATTTATC
* *
41425 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCAAGTATT
41444 TTCATTAAAAATCAAGTATT
1 TTCATTAAAAATCAAGTATT
41464 TTCA
1 TTCA
41468 AAGGGGTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCAAGTATT
Found at i:42304 original size:20 final size:20
Alignment explanation
Indices: 42262--42311 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
42252 ATCCAAGAGC
* * *
42262 ATGTATCTTC-TTTAAAATC
1 ATGTATTTTCATTAAAAATA
42281 ATGTATTTTCATTAAAAATA
1 ATGTATTTTCATTAAAAATA
42301 ATGTATTTTCA
1 ATGTATTTTCA
42312 AAAGGGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (20 bp):
ATGTATTTTCATTAAAAATA
Found at i:42887 original size:36 final size:35
Alignment explanation
Indices: 42783--42897 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
42773 ATGGTAATGG
* *
42783 GATGGTGAT-TATATAGGAGTGAAATGGTGATAGAA
1 GATGGTGATGT-TATAGGCGTGAAATGGTGATGGAA
* * *
42818 GATAGTGATGATATAGGCGTGCAATGGTGATGGAA
1 GATGGTGATGTTATAGGCGTGAAATGGTGATGGAA
42853 GATGGTGATGTTATAGGCGTGAAAATGGTGATGGAA
1 GATGGTGATGTTATAGGCGTG-AAATGGTGATGGAA
42889 GATGGTGAT
1 GATGGTGAT
42898 AAATAGATAG
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 48 0.69
36 22 0.31
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.28
Consensus pattern (35 bp):
GATGGTGATGTTATAGGCGTGAAATGGTGATGGAA
Found at i:50883 original size:21 final size:21
Alignment explanation
Indices: 50846--50890 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
50836 GATTTCTGGG
*
50846 CAAGGGGAATCAGTACCCATT
1 CAAGGGGAACCAGTACCCATT
*
50867 CAAGGGGAACC-GATACCCCTT
1 CAAGGGGAACCAG-TACCCATT
50888 CAA
1 CAA
50891 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCAGTACCCATT
Found at i:52596 original size:23 final size:23
Alignment explanation
Indices: 52566--52625 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
52556 ATTATTATAT
52566 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
52589 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
52612 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
52626 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:67273 original size:19 final size:20
Alignment explanation
Indices: 67227--67275 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
67217 TAATAAAGGG
67227 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
67247 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
67266 AATAAAATAA
1 AATAAAATAA
67276 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:67574 original size:279 final size:278
Alignment explanation
Indices: 67074--67629 Score: 988
Period size: 279 Copynumber: 2.0 Consensus size: 278
67064 GCACCATGAG
67074 TGATGTAAGGCGAATCTACACACTTTGGTGAGAAGAGTAGATAGCCTTATTGTGTCCCGATCTAG
1 TGATGTAAGGCGAATCTACACACTTTGGTGAGAAGAGTAGATAGCCTTATTGTGTCCCGATCTAG
* *
67139 GATTGACAAGTACTGATGTCCTTGAATTTATAAGTTTGGGCTGCAAAATAAGATAAGAAATATGA
66 GATTGACAAGTACTGATGTCCTCGAATTTATAAGTTTGGACTGCAAAATAAGATAAGAAATATGA
67204 TTAATAATGGACTTAATAAAGGGAATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAAT
131 TTAATAATGGACTTAATAAAGGG-ATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAAT
* * *
67269 AAAATAAAGAAAGGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTTGTTGATGAA
195 AAAATAAAAAAAAGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAA
67334 ATGGAAATGGTGGTGATAT
260 ATGGAAATGGTGGTGATAT
*
67353 TGATGTAAGGCGAATCTACACACTTTGGTGAGAATAGTAGATAGCCTTATTGTGTCCCGATCTAG
1 TGATGTAAGGCGAATCTACACACTTTGGTGAGAAGAGTAGATAGCCTTATTGTGTCCCGATCTAG
67418 GATTGACAAGTACTGATGTCCTCGAATTTATAAGTTTGGACTGCAAAATAAGATAAGAAAATATG
66 GATTGACAAGTACTGATGTCCTCGAATTTATAAGTTTGGACTGCAAAATAAGATAAG-AAATATG
*
67483 TTTAATAATGGACTTAATAAAGGG-TAATAATATAAGTAATGAAAATAAATAATAAGAATGAAAT
130 ATTAATAATGGACTTAATAAAGGGATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAAT
* *
67547 GAAATAAATAAAAAGATAGAGATGGCTGCGGAATTGATGGAAGTGATGGATGATGTTGATGATGA
195 AAAATAAA-AAAAAGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGA
*
67612 AATGGCAATGGTGGTGAT
259 AATGGAAATGGTGGTGAT
67630 GTTGTATCTC
Statistics
Matches: 265, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
278 47 0.18
279 188 0.71
280 30 0.11
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (278 bp):
TGATGTAAGGCGAATCTACACACTTTGGTGAGAAGAGTAGATAGCCTTATTGTGTCCCGATCTAG
GATTGACAAGTACTGATGTCCTCGAATTTATAAGTTTGGACTGCAAAATAAGATAAGAAATATGA
TTAATAATGGACTTAATAAAGGGATAATAATATAAGTAATGAAAATAAATAATAAGAATGAAATA
AAATAAAAAAAAGATAGAGATGGCTGCGGAATTGATGGAAGAGATGGATGATGTTGATGATGAAA
TGGAAATGGTGGTGATAT
Found at i:71803 original size:13 final size:13
Alignment explanation
Indices: 71774--71819 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
71764 ACTTCTCTTT
71774 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
71787 TTCTTTTCTTCTT-
1 TTCTTTTCTT-TTC
*
71800 TTC-TGTCTTTTC
1 TTCTTTTCTTTTC
71812 ATTCTTTT
1 -TTCTTTT
71820 TGCACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.07
12 5 0.19
13 16 0.59
14 4 0.15
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.74
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:71817 original size:9 final size:8
Alignment explanation
Indices: 71779--71819 Score: 64
Period size: 8 Copynumber: 4.9 Consensus size: 8
71769 TCTTTTTCTT
71779 TTCTTTTC
1 TTCTTTTC
71787 TTCTTTTC
1 TTCTTTTC
71795 TTCTTTTC
1 TTCTTTTC
71803 TGTCTTTTC
1 T-TCTTTTC
71812 ATTCTTTT
1 -TTCTTTT
71820 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 17 0.55
9 13 0.42
10 1 0.03
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (8 bp):
TTCTTTTC
Found at i:78645 original size:8 final size:8
Alignment explanation
Indices: 78634--78679 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
78624 TCATTTTCTT
78634 TTCTTTTA
1 TTCTTTTA
78642 TTCTTTTA
1 TTCTTTTA
*
78650 TTCTTTTC
1 TTCTTTTA
78658 TT-TTTTA
1 TTCTTTTA
78665 TT-TTTCTA
1 TTCTTT-TA
78673 TTCTTTT
1 TTCTTTT
78680 TACACTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 9 0.26
8 22 0.65
9 3 0.09
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (8 bp):
TTCTTTTA
Found at i:78983 original size:19 final size:20
Alignment explanation
Indices: 78937--78985 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
78927 TAATAAAGGG
78937 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
78957 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
78976 AATAAAATAA
1 AATAAAATAA
78986 AGAAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:83724 original size:13 final size:13
Alignment explanation
Indices: 83702--83736 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
83692 AAAGCAACAA
83702 AAAG-AGAAAAAC
1 AAAGAAGAAAAAC
83714 AAAGAAGAAAAAC
1 AAAGAAGAAAAAC
83727 AAA-AAGAAAA
1 AAAGAAGAAAA
83737 GAAAAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAC
Found at i:83742 original size:12 final size:12
Alignment explanation
Indices: 83701--83736 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
83691 AAAAGCAACA
83701 AAAAGAGAAAAAC
1 AAAA-AGAAAAAC
83714 AAAGAAGAAAAAC
1 AAA-AAGAAAAAC
83727 AAAAAGAAAA
1 AAAAAGAAAA
83737 GAAAAAGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 14 0.64
14 1 0.05
ACGTcount: A:0.81, C:0.06, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAC
Found at i:85324 original size:50 final size:50
Alignment explanation
Indices: 85258--85378 Score: 215
Period size: 50 Copynumber: 2.4 Consensus size: 50
85248 AGGATTAGAT
* *
85258 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAATATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAATATTATTTTTAGTTA
85308 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAATATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGATGAGTTAAAATATTATTTTTAGTTA
*
85358 TTATTATTTAATTAGGAATTA
1 TTATTATTTTATTAGGAATTA
85379 GAGTTAAGAC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (50 bp):
TTATTATTTTATTAGGAATTAAGGATGAGTTAAAATATTATTTTTAGTTA
Found at i:92441 original size:19 final size:20
Alignment explanation
Indices: 92409--92453 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
92399 TTTTTTCAAT
*
92409 AAAAAACATTAAAAAACAAA
1 AAAAAACATAAAAAAACAAA
**
92429 AAAAAACA-AAAAAGGCAAA
1 AAAAAACATAAAAAAACAAA
92448 AAAAAA
1 AAAAAA
92454 GTCAAAATTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.82, C:0.09, G:0.04, T:0.04
Consensus pattern (20 bp):
AAAAAACATAAAAAAACAAA
Found at i:110293 original size:58 final size:57
Alignment explanation
Indices: 110223--110340 Score: 182
Period size: 58 Copynumber: 2.1 Consensus size: 57
110213 CCAGGTTGTT
*
110223 GCAAACATGTACCATGCTATTTTGTGCAAAAGAAATGTTGAAATGTGCAGTATTATGG
1 GCAAACATGTACCATGCTATTTTGTGCAAAAGAAATGTTGAAATGTACAG-ATTATGG
* * * *
110281 GCAAACATGTACCTTGTTGTTTTGTGCAAAAGAAATGTTGAAATGTATAGATTATGG
1 GCAAACATGTACCATGCTATTTTGTGCAAAAGAAATGTTGAAATGTACAGATTATGG
110338 GCA
1 GCA
110341 TGTATGATCT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 10 0.18
58 45 0.82
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (57 bp):
GCAAACATGTACCATGCTATTTTGTGCAAAAGAAATGTTGAAATGTACAGATTATGG
Found at i:115317 original size:33 final size:33
Alignment explanation
Indices: 115261--115326 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
115251 GATTGTGACA
*
115261 CCATAACCGACTCAGTTACAGAATGTTCAGGTG
1 CCATAACCGACTCAGCTACAGAATGTTCAGGTG
** *
115294 CCATAACCGGGTCAGCTATAGAATGTTCAGGTG
1 CCATAACCGACTCAGCTACAGAATGTTCAGGTG
115327 GGTGAGATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (33 bp):
CCATAACCGACTCAGCTACAGAATGTTCAGGTG
Found at i:119360 original size:11 final size:11
Alignment explanation
Indices: 119344--119375 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
119334 TACCATGGAG
119344 ATTGTGAGCTA
1 ATTGTGAGCTA
119355 ATTGTGAGCTA
1 ATTGTGAGCTA
119366 ATTGTGAGCT
1 ATTGTGAGCT
119376 GCCATATAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (11 bp):
ATTGTGAGCTA
Found at i:123364 original size:22 final size:21
Alignment explanation
Indices: 123338--123378 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
123328 GCTGTGGAAA
123338 TGATGGT-CTTGATGGATGAAGT
1 TGATGGTGC-TGAT-GATGAAGT
123360 TGATGGTGCTGATGATGAA
1 TGATGGTGCTGATGATGAA
123379 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 11 0.61
23 1 0.06
ACGTcount: A:0.24, C:0.05, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTGCTGATGATGAAGT
Found at i:126395 original size:24 final size:24
Alignment explanation
Indices: 126368--126418 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
126358 TGTGGATCAC
* *
126368 CAAAAGTCATGTCTATTGATTCTT
1 CAAAAGACATGTCTATTGAATCTT
* *
126392 CAAAAGACATGTTTCTTGAATCTT
1 CAAAAGACATGTCTATTGAATCTT
126416 CAA
1 CAA
126419 CTTGAAGTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (24 bp):
CAAAAGACATGTCTATTGAATCTT
Found at i:127640 original size:22 final size:22
Alignment explanation
Indices: 127594--127645 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
127584 TTTTCTCTTT
*
127594 TTTCTTTTTTGGGTGCTTTCAA
1 TTTCTTTTTTGAGTGCTTTCAA
* *
127616 TTTCTTCTTTTGAGTGCTTTGAT
1 TTTCTT-TTTTGAGTGCTTTCAA
127639 TTTCTTT
1 TTTCTTT
127646 GCTGGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.08, C:0.13, G:0.15, T:0.63
Consensus pattern (22 bp):
TTTCTTTTTTGAGTGCTTTCAA
Found at i:129123 original size:20 final size:20
Alignment explanation
Indices: 129095--129141 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
129085 TATAGTGATG
*
129095 TGAGTTATATTTGAAGCTCA
1 TGAGCTATATTTGAAGCTCA
*
129115 TGAGCTATATTTGAAGGTCA
1 TGAGCTATATTTGAAGCTCA
129135 TGAGCTA
1 TGAGCTA
129142 ATTATATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (20 bp):
TGAGCTATATTTGAAGCTCA
Found at i:134870 original size:28 final size:30
Alignment explanation
Indices: 134812--134873 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
134802 TCACTCTTCC
*
134812 TTTCTTTACTTTCATTTTCCTTGTCTTAAACCT
1 TTTCTTTACTTTCATTTTACTTG---TAAACCT
134845 TTTCTTTACTTTCA-TTTACTTG-AAACCT
1 TTTCTTTACTTTCATTTTACTTGTAAACCT
134873 T
1 T
134874 GTTTCTACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 7 0.25
32 7 0.25
33 14 0.50
ACGTcount: A:0.18, C:0.23, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTCTTTACTTTCATTTTACTTGTAAACCT
Found at i:139277 original size:24 final size:23
Alignment explanation
Indices: 139227--139277 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
139217 TTTCTTTGTT
* * *
139227 TTTTCTTCTTTTGAGTGCTGGAT
1 TTTTCTTATTTTGAGTGCTGCAC
*
139250 TTTTCTTTATTTTGAGTGCTTCAC
1 TTTTC-TTATTTTGAGTGCTGCAC
139274 TTTT
1 TTTT
139278 TTTTCTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.10, C:0.14, G:0.16, T:0.61
Consensus pattern (23 bp):
TTTTCTTATTTTGAGTGCTGCAC
Found at i:144209 original size:13 final size:13
Alignment explanation
Indices: 144187--144216 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
144177 ACTAAACACC
144187 TTTC-ACATACCT
1 TTTCAACATACCT
144199 TTTCAACATACCT
1 TTTCAACATACCT
144212 TTTCA
1 TTTCA
144217 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:146964 original size:5 final size:5
Alignment explanation
Indices: 146954--146989 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
146944 CTTCAACTTC
146954 TTTCT TTTCT TTTCT TTTCT TTTC- TTT-T TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
146990 TGAGTGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.21
5 23 0.79
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:146974 original size:15 final size:13
Alignment explanation
Indices: 146954--146989 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
146944 CTTCAACTTC
146954 TTTCTTTTCTTTTCT
1 TTTCTTTTC-TTT-T
146969 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
146982 TTTCTTTT
1 TTTCTTTT
146990 TGAGTGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 9 0.43
14 3 0.14
15 9 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:150071 original size:22 final size:23
Alignment explanation
Indices: 150043--150094 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
150033 ATTTATAAGT
150043 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
150065 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
150088 TGGTGAT
1 TGGTGAT
150095 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:150086 original size:36 final size:37
Alignment explanation
Indices: 150045--150160 Score: 143
Period size: 36 Copynumber: 3.2 Consensus size: 37
150035 TTATAAGTTG
*
150045 GTGATAATATAGGCGTGA-TATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
150081 GTGAT-A-AT-GGTGATGGACTATGGTGATGATATAGGC
1 GTGATAATATAGGTG-T-GACTATGGTGATGATATAGGC
** *
150117 GTGATAATGGAGATG-GACTATGGTGATGATATAGGC
1 GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
150153 GTGATAAT
1 GTGATAAT
150161 GGTGATGGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
33 3 0.04
34 3 0.04
35 3 0.04
36 57 0.81
37 1 0.01
39 3 0.04
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.30
Consensus pattern (37 bp):
GTGATAATATAGGTGTGACTATGGTGATGATATAGGC
Found at i:150161 original size:36 final size:36
Alignment explanation
Indices: 150063--150170 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
150053 ATAGGCGTGA
150063 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
150099 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
150135 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
150171 ATATTGTATC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.29, C:0.06, G:0.36, T:0.30
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:151578 original size:19 final size:20
Alignment explanation
Indices: 151540--151578 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
151530 ACCATTCACT
*
151540 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
151560 TGCATAATATATG-TTTTCA
1 TGCATAATATATGATTTTCA
151579 CATCTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:152575 original size:19 final size:21
Alignment explanation
Indices: 152551--152602 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
152541 CGGCCAAGAG
*
152551 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
152570 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
152591 CATGTATTTTCA
1 CATGTATTTTCA
152603 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:152972 original size:13 final size:13
Alignment explanation
Indices: 152954--152998 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
152944 CATTGCCATT
*
152954 TCATCATCATCCA
1 TCATCAACATCCA
*
152967 TCATCAACATCCT
1 TCATCAACATCCA
*
152980 TCATCAAGA-CCA
1 TCATCAACATCCA
152992 TCATCAA
1 TCATCAA
152999 TTCCATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.27
Consensus pattern (13 bp):
TCATCAACATCCA
Found at i:153343 original size:26 final size:25
Alignment explanation
Indices: 153313--153365 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
153303 TGTAGAGTGC
153313 AAAAATAAAGAAAAAGACA-AAAAGAA
1 AAAAATAAAG-AAAAGA-AGAAAAGAA
**
153339 AAAAATTCAGAAAAGAAGAAAAGAA
1 AAAAATAAAGAAAAGAAGAAAAGAA
153364 AA
1 AA
153366 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 15 0.62
26 8 0.33
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (25 bp):
AAAAATAAAGAAAAGAAGAAAAGAA
Found at i:153352 original size:18 final size:17
Alignment explanation
Indices: 153332--153383 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 17
153322 GAAAAAGACA
153332 AAAAGAAAAAAATTCAG
1 AAAAGAAAAAAATTCAG
*
153349 AAAAG-AAGAAA---AG
1 AAAAGAAAAAAATTCAG
153362 AAAAGAAAAAAATTCA-
1 AAAAGAAAAAAATTCAG
153378 AAAAGA
1 AAAAGA
153384 GAAAGCAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.24
14 5 0.17
16 11 0.38
17 6 0.21
ACGTcount: A:0.75, C:0.04, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAGAAAAAAATTCAG
Found at i:153354 original size:31 final size:29
Alignment explanation
Indices: 153319--153388 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 29
153309 GTGCAAAAAT
153319 AAAGAAAAAGACAAAAAGAAAAAAATTCAGA
1 AAAGAAAAAGA-AAAAAGAAAAAAATTCA-A
*
153350 AAAGAAGAAA-AGAAAAGAAAAAAATTCAA
1 AAAGAA-AAAGAAAAAAGAAAAAAATTCAA
*
153379 AAAGAGAAAG
1 AAAGAAAAAG
153389 CAAGCCAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 3 0.09
29 6 0.17
30 16 0.46
31 7 0.20
32 3 0.09
ACGTcount: A:0.74, C:0.04, G:0.16, T:0.06
Consensus pattern (29 bp):
AAAGAAAAAGAAAAAAGAAAAAAATTCAA
Found at i:153367 original size:30 final size:28
Alignment explanation
Indices: 153332--153387 Score: 94
Period size: 30 Copynumber: 1.9 Consensus size: 28
153322 GAAAAAGACA
153332 AAAAGAAAAAAATTCAGAAAAGAAGAAAAG
1 AAAAGAAAAAAATTCA-AAAAG-AGAAAAG
153362 AAAAGAAAAAAATTCAAAAAGAGAAA
1 AAAAGAAAAAAATTCAAAAAGAGAAA
153388 GCAAGCCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 5 0.19
29 5 0.19
30 16 0.62
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (28 bp):
AAAAGAAAAAAATTCAAAAAGAGAAAAG
Found at i:156128 original size:90 final size:90
Alignment explanation
Indices: 156006--156183 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
155996 TAATCCCGAA
* * * * * *
156006 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
156071 TAGGGTAACTTGTATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
156096 TATTAAATTCCAATTAATTAAATATACATTTAATTTATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
156161 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
156184 GTGCGTTAGG
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATACATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:165391 original size:24 final size:24
Alignment explanation
Indices: 165341--165393 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
165331 TTTCCTTTTT
* *
165341 TTTCTTTTAAGTGCAGTATTTTTC
1 TTTCTTTTAAGTGCAGTACTTTCC
* **
165365 TTTCTTTTGAGTGCTTTACTTTCC
1 TTTCTTTTAAGTGCAGTACTTTCC
165389 TTTCT
1 TTTCT
165394 GATTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.60
Consensus pattern (24 bp):
TTTCTTTTAAGTGCAGTACTTTCC
Found at i:172627 original size:24 final size:27
Alignment explanation
Indices: 172596--172668 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 27
172586 AAAATTCGGC
*
172596 AAAG-AAATTGAAGCACTCAAAAG-A-
1 AAAGAAAATTCAAGCACTCAAAAGAAG
172620 AAA-AAAATTCAAGCACTCAAAAAGAAG
1 AAAGAAAATTCAAGCACTC-AAAAGAAG
172647 AAAGAAAAGTTCAAGCACTCAA
1 AAAGAAAA-TTCAAGCACTCAA
172669 CAATAAGTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 16 0.38
25 5 0.12
26 1 0.02
27 3 0.07
28 6 0.14
29 11 0.26
ACGTcount: A:0.59, C:0.15, G:0.14, T:0.12
Consensus pattern (27 bp):
AAAGAAAATTCAAGCACTCAAAAGAAG
Found at i:176446 original size:22 final size:22
Alignment explanation
Indices: 176406--176447 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
176396 AAATATGTGG
*
176406 TTCATAATAATAACTTCATACA
1 TTCATAATAATAACATCATACA
* *
176428 TTCATAATATTATCATCATA
1 TTCATAATAATAACATCATA
176448 ACTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATAACATCATACA
Found at i:177388 original size:19 final size:21
Alignment explanation
Indices: 177358--177409 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
177348 CGGCCAAGAG
*
177358 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
*
177377 CATGTTTTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
177398 CATGTATTTTCA
1 CATGTATTTTCA
177410 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:181110 original size:19 final size:21
Alignment explanation
Indices: 181086--181137 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
181076 CGGCCAAGAG
*
181086 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
181105 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
181126 CATGTATTTTCA
1 CATGTATTTTCA
181138 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:186379 original size:19 final size:21
Alignment explanation
Indices: 186355--186406 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
186345 CGGCCAAGAG
*
186355 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
186374 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
186395 CATGTATTTTCA
1 CATGTATTTTCA
186407 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:186841 original size:18 final size:20
Alignment explanation
Indices: 186818--186856 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
186808 TATCATTTAT
186818 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
186836 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
186856 T
1 T
186857 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:186859 original size:22 final size:20
Alignment explanation
Indices: 186814--186862 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
186804 TCTCTATCAT
186814 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
186833 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
186853 TTATATTATT
1 TTATATTATT
186863 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:189703 original size:18 final size:20
Alignment explanation
Indices: 189680--189718 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
189670 TATCATTTAT
189680 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
189698 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
189718 T
1 T
189719 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:189721 original size:22 final size:20
Alignment explanation
Indices: 189676--189724 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
189666 TCTCTATCAT
189676 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
189695 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
189715 TTATATTATT
1 TTATATTATT
189725 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:190019 original size:19 final size:18
Alignment explanation
Indices: 189988--190052 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
189978 AATTGGATTG
189988 CAAAAAGAA-AGAAAAAGA
1 CAAAAAGAAGAGAAAAA-A
*
190006 CAAAAAGAAGAGAAAAAT
1 CAAAAAGAAGAGAAAAAA
*
190024 CATAAAAGAAGAAAAGAAAA
1 CA-AAAAGAAGAGAA-AAAA
*
190044 GAAAAAGAA
1 CAAAAAGAA
190053 TTAAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 11 0.28
19 25 0.62
20 4 0.10
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (18 bp):
CAAAAAGAAGAGAAAAAA
Found at i:201569 original size:17 final size:15
Alignment explanation
Indices: 201539--201573 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
201529 GAATATAAAA
201539 AAAAGGAAATGATAAG
1 AAAAGGAAATGAT-AG
201555 AAAAGGAAATGGATAG
1 AAAAGGAAAT-GATAG
201571 AAA
1 AAA
201574 TGATATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (15 bp):
AAAAGGAAATGATAG
Found at i:207600 original size:15 final size:16
Alignment explanation
Indices: 207577--207613 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
207567 AGTGCTTTAA
*
207577 CTTTCTTTCTTTTATT
1 CTTTTTTTCTTTTATT
207593 -TTTTTTTCTTTTATT
1 CTTTTTTTCTTTTATT
207608 CTTTTT
1 CTTTTT
207614 GAGTGCTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTTTTCTTTTATT
Found at i:216379 original size:19 final size:20
Alignment explanation
Indices: 216338--216388 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
216328 GAAACCCCTT
*
216338 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
216358 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
216377 TGAAGATACATG
1 TGAAAATACATG
216389 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:217324 original size:30 final size:31
Alignment explanation
Indices: 217285--217344 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
217275 ACATGCTGCC
**
217285 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
217316 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
217345 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:219815 original size:8 final size:8
Alignment explanation
Indices: 219802--219831 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
219792 TATTCTGCTT
219802 TTTTTTTC
1 TTTTTTTC
219810 TTTTTTTC
1 TTTTTTTC
219818 TTTTCTTTC
1 TTTT-TTTC
219827 TTTTT
1 TTTTT
219832 GCACGCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:219830 original size:26 final size:25
Alignment explanation
Indices: 219768--219831 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
219758 TCTTTTTGGA
219768 ATTCTTCTTTTTTTTCTTTACTTCT
1 ATTCTTCTTTTTTTTCTTTACTTCT
* **
219793 ATTCTGCTTTTTTTTTCTTTTTTTCT
1 ATTCTTC-TTTTTTTTCTTTACTTCT
*
219819 TTTCTTTCTTTTT
1 ATTC-TTCTTTTT
219832 GCACGCCAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 6 0.19
26 24 0.75
27 2 0.06
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (25 bp):
ATTCTTCTTTTTTTTCTTTACTTCT
Found at i:220568 original size:19 final size:20
Alignment explanation
Indices: 220527--220569 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
220517 GAAACCCCTT
* *
220527 TGAAAATACATGATTTTTGA
1 TGAAAATACATGAGTTTTAA
220547 TGAAAATACATG-GTTTTAA
1 TGAAAATACATGAGTTTTAA
220566 TGAA
1 TGAA
220570 GAACATGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGAGTTTTAA
Found at i:221510 original size:30 final size:31
Alignment explanation
Indices: 221471--221530 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
221461 ACATGCTGCC
**
221471 ATGATATCTAAATGATATGCAAACAAAATAA
1 ATGATATCTAAAACATATGCAAACAAAATAA
* *
221502 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACAAAATA
221531 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACAAAATAA
Found at i:222124 original size:18 final size:20
Alignment explanation
Indices: 222101--222139 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
222091 TATCTTTTAT
222101 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
222119 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
222139 T
1 T
222140 ATTATTACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:222142 original size:22 final size:20
Alignment explanation
Indices: 222097--222145 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
222087 TCTCTATCTT
222097 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
222116 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
222136 TTATATTATT
1 TTATATTATT
222146 ACCCTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:223122 original size:24 final size:25
Alignment explanation
Indices: 223094--223141 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
223084 GCTTATTTTT
* *
223094 GATGAAGAATCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
223118 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
223142 GATCATGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.52, C:0.10, G:0.23, T:0.15
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:226655 original size:11 final size:11
Alignment explanation
Indices: 226639--226664 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
226629 AATTATTGGC
226639 CACACGCCTAG
1 CACACGCCTAG
226650 CACACGCCTAG
1 CACACGCCTAG
226661 CACA
1 CACA
226665 TGCACAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.46, G:0.15, T:0.08
Consensus pattern (11 bp):
CACACGCCTAG
Found at i:233144 original size:19 final size:20
Alignment explanation
Indices: 233097--233147 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
233087 GAAACCCCTT
**
233097 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
233117 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
233136 TGAAGATACATG
1 TGAAAATACATG
233148 CTCTTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:237727 original size:8 final size:8
Alignment explanation
Indices: 237714--237762 Score: 64
Period size: 8 Copynumber: 5.9 Consensus size: 8
237704 TCTTTTTATT
237714 TTCTTTTC
1 TTCTTTTC
237722 TTCTTTTTC
1 TTC-TTTTC
237731 TTCTTTTC
1 TTCTTTTC
237739 TTCTTTT-
1 TTCTTTTC
237746 TGTCTTTTC
1 T-TCTTTTC
237755 TTTCTTTT
1 -TTCTTTT
237763 TGTACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 1 0.03
8 21 0.57
9 14 0.38
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:237727 original size:33 final size:33
Alignment explanation
Indices: 237686--237764 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 33
237676 CTTGGCTTGC
*
237686 TTTC-TCTTTTTGAACTTCTCTT-TTTATTTTCT
1 TTTCTTCTTTTTGAACTTCTCTTCTTT-TTGTCT
*** *
237718 TTTCTTCTTTTTCTTCTTTTCTTCTTTTTGTCT
1 TTTCTTCTTTTTGAACTTCTCTTCTTTTTGTCT
237751 TTTCTTTCTTTTTG
1 TTTC-TTCTTTTTG
237765 TACTCCAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
32 4 0.11
33 23 0.61
34 11 0.29
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.73
Consensus pattern (33 bp):
TTTCTTCTTTTTGAACTTCTCTTCTTTTTGTCT
Found at i:237731 original size:9 final size:9
Alignment explanation
Indices: 237717--237763 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
237707 TTTTATTTTC
237717 TTTTCTTCT
1 TTTTCTTCT
237726 TTTTCTTC-
1 TTTTCTTCT
237734 TTTTCTTCT
1 TTTTCTTCT
*
237743 TTTT-GTC-
1 TTTTCTTCT
237750 TTTTCTTTCT
1 TTTTC-TTCT
237760 TTTT
1 TTTT
237764 GTACTCCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 4 0.12
8 10 0.31
9 14 0.44
10 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:237736 original size:17 final size:16
Alignment explanation
Indices: 237712--237763 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 16
237702 TCTCTTTTTA
237712 TTTTCTTTTCTTCTTT
1 TTTTCTTTTCTTCTTT
237728 TTCTTCTTTTCTTCTTT
1 TT-TTCTTTTCTTCTTT
*
237745 TTGTCTTTTCTTTCTTT
1 TTTTCTTTTC-TTCTTT
237762 TT
1 TT
237764 GTACTCCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTCTTCTTT
Found at i:238499 original size:19 final size:20
Alignment explanation
Indices: 238458--238508 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
238448 GAAACCCCTT
*
238458 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
238478 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
238497 TGAAGATACATG
1 TGAAAATACATG
238509 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:239836 original size:19 final size:17
Alignment explanation
Indices: 239799--239845 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
239789 TGGACTTAAT
239799 AAAGTAAATAATAAATGA
1 AAAG-AAATAATAAATGA
239817 AAAGAAATAATAAGAATGA
1 AAAGAAATAAT-A-AATGA
*
239836 AATGAAATAA
1 AAAGAAATAA
239846 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.19
Consensus pattern (17 bp):
AAAGAAATAATAAATGA
Found at i:242842 original size:15 final size:16
Alignment explanation
Indices: 242815--242851 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
242805 CTTTATTATC
242815 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
242831 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
242846 TTATTT
1 TTATTT
242852 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:243240 original size:9 final size:9
Alignment explanation
Indices: 243228--243268 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
243218 AAAAAAAAAA
243228 AAAAAAGCC
1 AAAAAAGCC
*
243237 AAAAAAGCAA
1 AAAAAAGC-C
243247 AAAAAAGCC
1 AAAAAAGCC
*
243256 AAAAAATCC
1 AAAAAAGCC
243265 AAAA
1 AAAA
243269 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.73, C:0.17, G:0.07, T:0.02
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:243240 original size:10 final size:10
Alignment explanation
Indices: 243227--243261 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
243217 AAAAAAAAAA
243227 AAAAAAAGCC
1 AAAAAAAGCC
*
243237 -AAAAAAGCA
1 AAAAAAAGCC
243246 AAAAAAAGCC
1 AAAAAAAGCC
243256 AAAAAA
1 AAAAAA
243262 TCCAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.77, C:0.14, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:243240 original size:19 final size:19
Alignment explanation
Indices: 243203--243261 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
243193 ATTTTTTTTC
243203 AAAAAAAAAAAAAAA---A
1 AAAAAAAAAAAAAAAGCCA
243219 AAAAAAAAAAAAAAAGCCA
1 AAAAAAAAAAAAAAAGCCA
**
243238 AAAAAGCAAAAAAAAGCCA
1 AAAAAAAAAAAAAAAGCCA
243257 AAAAA
1 AAAAA
243262 TCCAAAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
16 15 0.39
19 23 0.61
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAGCCA
Found at i:243252 original size:1 final size:1
Alignment explanation
Indices: 243203--243233 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
243193 ATTTTTTTTC
243203 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
243234 GCCAAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:254683 original size:26 final size:25
Alignment explanation
Indices: 254654--254721 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 25
254644 CTTTTTAAAC
* *
254654 TTCTCTTTTTCTTTTCTTTTCTTATT
1 TTCTATTTTTCTTTTCTCTTCTT-TT
254680 TTCTGATTTTT-TTTTCTCTTCTTTT
1 TTCT-ATTTTTCTTTTCTCTTCTTTT
*
254705 TGTCTTTTCTTTCTTTT
1 T-TCTATT-TTTCTTTT
254722 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
25 5 0.14
26 21 0.60
27 9 0.26
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (25 bp):
TTCTATTTTTCTTTTCTCTTCTTTT
Found at i:254714 original size:13 final size:12
Alignment explanation
Indices: 254665--254716 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
254655 TCTCTTTTTC
254665 TTTTCTTTTCTT
1 TTTTCTTTTCTT
254677 ATTTTCTGATTT-TT
1 -TTTTCT--TTTCTT
*
254691 TTTTCTCTTCTT
1 TTTTCTTTTCTT
254703 TTTGTCTTTTCTT
1 TTT-TCTTTTCTT
254716 T
1 T
254717 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 21 0.64
14 2 0.06
15 3 0.09
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:264242 original size:23 final size:24
Alignment explanation
Indices: 264203--264259 Score: 82
Period size: 23 Copynumber: 2.5 Consensus size: 24
264193 TTCTTTCTTT
264203 TTTCTTCTGTTTGAGTGCTTTCAA
1 TTTCTTCTGTTTGAGTGCTTTCAA
* *
264227 TTTCTTCT-TTTGAGTGCTTTTAT
1 TTTCTTCTGTTTGAGTGCTTTCAA
264250 TTTCTT-TGTT
1 TTTCTTCTGTT
264260 GATTTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 21 0.70
24 8 0.27
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (24 bp):
TTTCTTCTGTTTGAGTGCTTTCAA
Found at i:272472 original size:36 final size:36
Alignment explanation
Indices: 272420--272528 Score: 166
Period size: 36 Copynumber: 3.0 Consensus size: 36
272410 ATAAGATTCA
272420 ATCTGTCCATCACCATTATCACGCCTATATCATCACC
1 ATCT-TCCATCACCATTATCACGCCTATATCATCACC
*
272457 ATCTTCCATCACCATTATCACGTCTATATCATCACC
1 ATCTTCCATCACCATTATCACGCCTATATCATCACC
** *
272493 ATAGTCCATCACCA-TATCATGCCTATATCATCACC
1 ATCTTCCATCACCATTATCACGCCTATATCATCACC
272528 A
1 A
272529 AATTCCATTT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 20 0.30
36 43 0.64
37 4 0.06
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
ATCTTCCATCACCATTATCACGCCTATATCATCACC
Found at i:272709 original size:20 final size:20
Alignment explanation
Indices: 272686--272723 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
272676 TCCATTTCAA
272686 TTCTTTCCTTTTTCCATTAT
1 TTCTTTCCTTTTTCCATTAT
272706 TTCTTTCCTTTTTCCATT
1 TTCTTTCCTTTTTCCATT
272724 TCAATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (20 bp):
TTCTTTCCTTTTTCCATTAT
Found at i:273034 original size:14 final size:15
Alignment explanation
Indices: 273000--273046 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
272990 AATTTGGAGT
273000 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
273015 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
273029 TCAAAAGTAAAAGAAAA
1 GCAAAAG--AAAGAAAA
273046 G
1 G
273047 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:276682 original size:35 final size:36
Alignment explanation
Indices: 276571--276682 Score: 190
Period size: 36 Copynumber: 3.1 Consensus size: 36
276561 ATACAATCTG
*
276571 TCCATCACCATTATCACGCCTATATCATCACCATCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
276607 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
276643 TCCATCACCA-TATCACGCCTATATCATCACCAAAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
276678 TCCAT
1 TCCAT
276683 TTTCCATTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 28 0.39
36 44 0.61
ACGTcount: A:0.30, C:0.38, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:280018 original size:32 final size:33
Alignment explanation
Indices: 279957--280023 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
279947 AAGTAATTAA
279957 AAGAAAGAAATGATTAAAATGGAATATGGA-AG
1 AAGAAAGAAATGATTAAAATGGAATATGGATAG
*
279989 AAGAAAGGAAATGA-TAAGAATTGAA-ATGGATAG
1 AAGAAA-GAAATGATTAA-AATGGAATATGGATAG
280022 AA
1 AA
280024 AATGTTATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (33 bp):
AAGAAAGAAATGATTAAAATGGAATATGGATAG
Found at i:280564 original size:19 final size:19
Alignment explanation
Indices: 280540--280589 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
280530 GAAACCCCTT
* **
280540 TGAAAATACATGTTTTTTA
1 TGAAAATACATGATTTAAA
280559 TGAAAATACATGATTTAAA
1 TGAAAATACATGATTTAAA
*
280578 TGAAGATACATG
1 TGAAAATACATG
280590 CTCTTGGACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:281767 original size:19 final size:21
Alignment explanation
Indices: 281724--281775 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
281714 GAAACCCCTT
281724 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
281745 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
281764 TGAAGATACATG
1 TGAAAATACATG
281776 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:283661 original size:35 final size:37
Alignment explanation
Indices: 283614--283692 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
283604 TTTGAGAATT
* *
283614 TGGTGATGATATAGGTGTGAT-AT-GATGATGGACTA
1 TGGTGATAATATAGGTGTGATAATGGAAGATGGACTA
*
283649 TGGTGATAATATAGGTGTGATAATGGAAGATGGATTA
1 TGGTGATAATATAGGTGTGATAATGGAAGATGGACTA
283686 TGGTGAT
1 TGGTGAT
283693 GGAAATAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 20 0.51
36 2 0.05
37 17 0.44
ACGTcount: A:0.30, C:0.01, G:0.34, T:0.34
Consensus pattern (37 bp):
TGGTGATAATATAGGTGTGATAATGGAAGATGGACTA
Found at i:288113 original size:11 final size:12
Alignment explanation
Indices: 288092--288140 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
288082 TTGAGAATTT
288092 GGTGATGATATA
1 GGTGATGATATA
288104 GGTG-TGATAT-
1 GGTGATGATATA
*
288114 GATGATGGACTAT-
1 GGTGAT-GA-TATA
288127 GGTGATGATATA
1 GGTGATGATATA
288139 GG
1 GG
288141 CGTGATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 3 0.10
11 10 0.32
12 10 0.32
13 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:288137 original size:35 final size:37
Alignment explanation
Indices: 288091--288170 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
288081 TTTGAGAATT
* *
288091 TGGTGATGATATAGGTGTGAT-AT-GATGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
288126 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
288163 TGGTGATG
1 TGGTGATG
288171 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 2 0.05
37 18 0.45
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:291439 original size:19 final size:21
Alignment explanation
Indices: 291393--291440 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
291383 TAAAAGGGAT
*
291393 AATATATAAGTAATGAAAATA
1 AATAAATAAGTAATGAAAATA
291414 AAT-AATAAG-AATG-AAATA
1 AATAAATAAGTAATGAAAATA
291432 AATAAATAA
1 AATAAATAA
291441 ATAAAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 5 0.20
21 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (21 bp):
AATAAATAAGTAATGAAAATA
Found at i:291872 original size:19 final size:21
Alignment explanation
Indices: 291829--291872 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
291819 GAAACCCCTT
*
291829 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTGTAAA
291850 TGAAAATACATGA-TTGT-AA
1 TGAAAATACATGACTTGTAAA
291869 TGAA
1 TGAA
291873 GATTCATGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 13 0.59
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.32
Consensus pattern (21 bp):
TGAAAATACATGACTTGTAAA
Found at i:292955 original size:15 final size:15
Alignment explanation
Indices: 292944--292972 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
292934 ACTCAAAAAG
292944 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
292959 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
292973 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:293775 original size:158 final size:156
Alignment explanation
Indices: 293494--293796 Score: 572
Period size: 157 Copynumber: 1.9 Consensus size: 156
293484 TAGAATGGAA
293494 GAAGAAGAAATCGAAGAAGAGAGGCTGAAGTAACATCAGTAGCAGAAGAGATGTTCATCAAAATC
1 GAAGAAGAAATCGAAGAAGAGAGGCTGAAGTAACATCAGTAGCAGAAGAGATGTTCATCAAAATC
293559 AGAATGACAACTTTAGCAACATTGAGTGACCATTCCTCCATTTCAAGGTTGAACTGAT-CAGAAG
66 AGAATGACAACTTTAGCAACATTGAGTGACCATTCCTCCATTTCAAGGTTGAACTGATCCAGAAG
293623 CCTATCTTGATTGGGGCCCTATAATG
131 CCTATCTTGATTGGGGCCCTATAATG
293649 GAAGAAGAAATCGAAGAAGAAGAGGCTGAAGTAACATCAGTAGCCAGAAGAGATGTTCATCAAAA
1 GAAGAAGAAATCGAAGAAG-AGAGGCTGAAGTAACATCAGTAG-CAGAAGAGATGTTCATCAAAA
293714 TCAGAATGACAACTTTAGCAACATTGAAGTGACCATTCCTCCATTTCAAGGTTGAACTGATCCAG
64 TCAGAATGACAACTTTAGCAACATTG-AGTGACCATTCCTCCATTTCAAGGTTGAACTGATCCAG
293779 AAGCCTATCTTGATTGGG
128 AAGCCTATCTTGATTGGG
293797 TAATCAAGAT
Statistics
Matches: 144, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
155 19 0.13
156 23 0.16
157 47 0.33
158 34 0.24
159 21 0.15
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (156 bp):
GAAGAAGAAATCGAAGAAGAGAGGCTGAAGTAACATCAGTAGCAGAAGAGATGTTCATCAAAATC
AGAATGACAACTTTAGCAACATTGAGTGACCATTCCTCCATTTCAAGGTTGAACTGATCCAGAAG
CCTATCTTGATTGGGGCCCTATAATG
Found at i:301527 original size:8 final size:8
Alignment explanation
Indices: 301516--301555 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
301506 GAGAAAAATC
301516 AGAAAAGA
1 AGAAAAGA
301524 AGAAAAGA
1 AGAAAAGA
301532 AGAAAAGA
1 AGAAAAGA
*
301540 A-AAAAAA
1 AGAAAAGA
301547 AGAATAAGA
1 AGAA-AAGA
301556 GAAGTTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 6 0.21
8 19 0.68
9 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.03
Consensus pattern (8 bp):
AGAAAAGA
Found at i:305309 original size:8 final size:8
Alignment explanation
Indices: 305298--305338 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
305288 GAGAAAAATC
305298 AGAAAAGA
1 AGAAAAGA
305306 AGAAAAGA
1 AGAAAAGA
305314 AGAAAAGA
1 AGAAAAGA
* *
305322 AAAAAAAA
1 AGAAAAGA
305330 AGAATAAGA
1 AGAA-AAGA
305339 GAAGTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 25 0.89
9 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (8 bp):
AGAAAAGA
Found at i:312158 original size:11 final size:12
Alignment explanation
Indices: 312137--312257 Score: 71
Period size: 11 Copynumber: 10.2 Consensus size: 12
312127 TTTATAAGTT
*
312137 GGTGATAATATA
1 GGTGATGATATA
312149 GGTG-TGATAT-
1 GGTGATGATATA
312159 GGTGATGGA-ATA
1 GGTGAT-GATATA
312171 TGGTGATGATATA
1 -GGTGATGATATA
*
312184 GGCG-TGATA-A
1 GGTGATGATATA
312194 TGGTGATGGACTATA
1 -GGTGAT-GA-TATA
312209 -GTGATGATATA
1 GGTGATGATATA
*
312220 GGAG-TGATA-A
1 GGTGATGATATA
*
312230 TGGAGATGGACTAT-
1 -GGTGAT-GA-TATA
312244 GGTGATGATATA
1 GGTGATGATATA
312256 GG
1 GG
312258 CGTGATAATG
Statistics
Matches: 87, Mismatches: 5, Indels: 34
0.69 0.04 0.27
Matches are distributed among these distances:
10 6 0.07
11 32 0.37
12 21 0.24
13 23 0.26
14 4 0.05
15 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:312196 original size:23 final size:22
Alignment explanation
Indices: 312168--312273 Score: 74
Period size: 23 Copynumber: 4.5 Consensus size: 22
312158 TGGTGATGGA
312168 ATATGGTGATGATATAGGCGTG
1 ATATGGTGATGATATAGGCGTG
*
312190 ATAATGGTGATGGACTATAGTG-ATG
1 AT-ATGGTGAT-GA-TATAG-GCGTG
* *
312215 ATATAG-GAGTGATA-ATGGAGATGG
1 ATATGGTGA-TGATATA-GGCG-T-G
312239 ACTATGGTGATGATATAGGCGTG
1 A-TATGGTGATGATATAGGCGTG
312262 ATAATGGTGATG
1 AT-ATGGTGATG
312274 GACAGATTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
21 2 0.03
22 6 0.09
23 24 0.36
24 9 0.14
25 21 0.32
26 4 0.06
ACGTcount: A:0.31, C:0.04, G:0.35, T:0.30
Consensus pattern (22 bp):
ATATGGTGATGATATAGGCGTG
Found at i:312213 original size:36 final size:36
Alignment explanation
Indices: 312136--312276 Score: 221
Period size: 36 Copynumber: 3.9 Consensus size: 36
312126 ATTTATAAGT
* * *
312136 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
312171 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* * *
312207 TAGTGATGATATAGGAGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
312243 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
312277 AGATTGTATC
Statistics
Matches: 96, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 19 0.20
36 77 0.80
ACGTcount: A:0.30, C:0.04, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:312250 original size:13 final size:12
Alignment explanation
Indices: 312154--312275 Score: 55
Period size: 13 Copynumber: 10.2 Consensus size: 12
312144 ATATAGGTGT
312154 GATATGGTGATG
1 GATATGGTGATG
312166 GAATATGGTGAT-
1 G-ATATGGTGATG
*
312178 GATATAGGCG-T-
1 GATAT-GGTGATG
312189 GATAATGGTGATG
1 GAT-ATGGTGATG
*
312202 GACTATAGTGAT-
1 GA-TATGGTGATG
*
312214 GATATAG-GA-G
1 GATATGGTGATG
*
312224 TGATAATGGAGATG
1 -GAT-ATGGTGATG
312238 GACTATGGTGAT-
1 GA-TATGGTGATG
*
312250 GATATAGGCG-T-
1 GATAT-GGTGATG
312261 GATAATGGTGATG
1 GAT-ATGGTGATG
312274 GA
1 GA
312276 CAGATTGTAT
Statistics
Matches: 87, Mismatches: 7, Indels: 31
0.70 0.06 0.25
Matches are distributed among these distances:
10 2 0.02
11 29 0.33
12 21 0.24
13 32 0.37
14 3 0.03
ACGTcount: A:0.31, C:0.03, G:0.36, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:318078 original size:19 final size:18
Alignment explanation
Indices: 318056--318094 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
318046 ATTGTCTAAG
*
318056 AATTTACAATTAGAAGTTT
1 AATTTACAATT-GAAATTT
*
318075 AATTTGCAATTGAAATTT
1 AATTTACAATTGAAATTT
318093 AA
1 AA
318095 GAATTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (18 bp):
AATTTACAATTGAAATTT
Found at i:318540 original size:13 final size:12
Alignment explanation
Indices: 318521--318642 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 12
318511 ATATAGGCGT
318521 GATATGGTGATG
1 GATATGGTGATG
318533 GAATATGGTGAT-
1 G-ATATGGTGATG
*
318545 GATATAGGCG-T-
1 GATAT-GGTGATG
318556 GATAATGGTGATG
1 GAT-ATGGTGATG
318569 GACTATGGTGAT-
1 GA-TATGGTGATG
*
318581 GATATAGGCG-T-
1 GATAT-GGTGATG
*
318592 GATAATGGAGATG
1 GAT-ATGGTGATG
318605 GACTATGGTGAT-
1 GA-TATGGTGATG
*
318617 GATATAGGCG-T-
1 GATAT-GGTGATG
318628 GATAATGGTGATG
1 GAT-ATGGTGATG
318641 GA
1 GA
318643 CAGATTGTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
11 31 0.35
12 24 0.27
13 31 0.35
14 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:318565 original size:23 final size:23
Alignment explanation
Indices: 318535--318640 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 23
318525 TGGTGATGGA
318535 ATATGGTGATGATATAGGCG-TG
1 ATATGGTGATGATATAGGCGATG
*
318557 ATAATGGTGATGGACTAT-GGTGATG
1 AT-ATGGTGAT-GA-TATAGGCGATG
* *
318582 ATATAGGCG-TGATA-ATGGAGATGG
1 ATAT-GGTGATGATATA-GGCGAT-G
318606 ACTATGGTGATGATATAGGCG-TG
1 A-TATGGTGATGATATAGGCGATG
318629 ATAATGGTGATG
1 AT-ATGGTGATG
318641 GACAGATTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.07
23 26 0.39
24 14 0.21
25 21 0.31
26 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (23 bp):
ATATGGTGATGATATAGGCGATG
Found at i:318576 original size:36 final size:36
Alignment explanation
Indices: 318503--318643 Score: 248
Period size: 36 Copynumber: 3.9 Consensus size: 36
318493 ATTTATAAGT
* *
318503 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
318538 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
318574 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
318610 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
318644 AGATTGTATC
Statistics
Matches: 101, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 20 0.20
36 81 0.80
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:321148 original size:5 final size:5
Alignment explanation
Indices: 321138--321163 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
321128 CTTCAACTTC
321138 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
321164 CTTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:325431 original size:24 final size:21
Alignment explanation
Indices: 325396--325438 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
325386 GGCACATTCT
*
325396 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
325419 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
325439 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:326306 original size:15 final size:15
Alignment explanation
Indices: 326295--326323 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
326285 ACTCAAAAAG
326295 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
326310 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
326324 GTTGAAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:327650 original size:13 final size:13
Alignment explanation
Indices: 327628--327657 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
327618 ACTAAACACC
327628 TTTC-ACATACCT
1 TTTCAACATACCT
327640 TTTCAACATACCT
1 TTTCAACATACCT
327653 TTTCA
1 TTTCA
327658 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:335267 original size:36 final size:36
Alignment explanation
Indices: 335215--335318 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
335205 GATACTATTT
* *
335215 TCATCACCATAATCCATCTCCGTTATCACACCTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
* *
335251 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACACCTATA
* *
335287 TCATCACCATATTCCATTACCATT-TCATCACC
1 TCATCACCATAATCCATCACCATTATCA-CACC
335319 ATTAAATCAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 3 0.05
36 57 0.95
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.31
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACACCTATA
Found at i:335713 original size:24 final size:24
Alignment explanation
Indices: 335673--335719 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
335663 AAAGTGCTAC
335673 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
335698 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
335720 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:335966 original size:23 final size:24
Alignment explanation
Indices: 335935--335983 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
335925 TTTCTTACTA
*
335935 TTTCATTTC-TTATTCTT-TCATCT
1 TTTCATTTCATTA-CCTTATCATCT
*
335958 TTTCTTTTCATTACCTTATCATCT
1 TTTCATTTCATTACCTTATCATCT
335982 TT
1 TT
335984 CTTAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTCATTACCTTATCATCT
Found at i:339853 original size:36 final size:36
Alignment explanation
Indices: 339801--339883 Score: 139
Period size: 36 Copynumber: 2.3 Consensus size: 36
339791 GATACTATTT
*
339801 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
339837 TCATCACCATAGTCCATCACCATTTTCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
339873 TCATCACCATA
1 TCATCACCATA
339884 TTCTATTACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:339895 original size:36 final size:36
Alignment explanation
Indices: 339801--339897 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 36
339791 GATACTATTT
*
339801 TCATCACCATAATCCATCT-CCATTATCACGCCTATA
1 TCATCACCATAATCCAT-TACCATTTTCACGCCTATA
* *
339837 TCATCACCATAGTCCATCACCATTTTCACGCCTATA
1 TCATCACCATAATCCATTACCATTTTCACGCCTATA
* *
339873 TCATCACCATATTCTATTACCATTT
1 TCATCACCATAATCCATTACCATTT
339898 CATCACCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (36 bp):
TCATCACCATAATCCATTACCATTTTCACGCCTATA
Done.