Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009592.1 Hibiscus syriacus cultivar Beakdansim tig00116971_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: 7920512
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 39
Found at i:1530921 original size:20 final size:20
Alignment explanation
Indices: 1530881--1530922 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1530871 ATTCCACCAC
* *
1530881 ATGCAACTATATGCTCTTAA
1 ATGCAACTATATGATCCTAA
*
1530901 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
1530921 AT
1 AT
1530923 CGGTTTTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1532158 original size:30 final size:32
Alignment explanation
Indices: 1532100--1532159 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
1532090 TATATGATTT
* *
1532100 ATATGAATATATGATTATGTGATAATATGAGA
1 ATATGAATATAAGATTATGTAATAATATGAGA
*
1532132 ATAT-AATATAAGA-TATGTAATTATATGA
1 ATATGAATATAAGATTATGTAATAATATGA
1532160 TCATAAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 8 0.32
32 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (32 bp):
ATATGAATATAAGATTATGTAATAATATGAGA
Found at i:1532813 original size:19 final size:21
Alignment explanation
Indices: 1532777--1532815 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1532767 AAATGACTTA
1532777 TATGATGATATAAGAATATGT
1 TATGATGATATAAGAATATGT
1532798 TATGA-GATAT-AGAATATG
1 TATGATGATATAAGAATATG
1532816 AATGTAAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TATGATGATATAAGAATATGT
Found at i:1536133 original size:31 final size:31
Alignment explanation
Indices: 1536090--1536161 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
1536080 ATCAACTAAG
* *
1536090 AGTATCTGAACTATTATTTTTATTTCGTTTT
1 AGTATCTAAACTATTACTTTTATTTCGTTTT
*
1536121 AGTATCTAAACTATTACTTTTGTTTCGTTTT
1 AGTATCTAAACTATTACTTTTATTTCGTTTT
*
1536152 ATTATCTAAA
1 AGTATCTAAA
1536162 TTTTCATTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.08, T:0.54
Consensus pattern (31 bp):
AGTATCTAAACTATTACTTTTATTTCGTTTT
Found at i:1537514 original size:18 final size:18
Alignment explanation
Indices: 1537491--1537527 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1537481 TCTTTTCTTC
1537491 AATATTAATAAATA-AATA
1 AATATTAA-AAATATAATA
1537509 AATATTAAAAATATAATA
1 AATATTAAAAATATAATA
1537527 A
1 A
1537528 TTTTTCCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTAAAAATATAATA
Found at i:1539360 original size:3 final size:3
Alignment explanation
Indices: 1539352--1539430 Score: 94
Period size: 3 Copynumber: 26.7 Consensus size: 3
1539342 TATTTATTTA
1539352 AAT AAT AAT AAT AAT -AT ATAT AAT AAT -AT AAGT AAT AAT AAT -AT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AA-T AAT AAT AAT AAT
*
1539396 ATT AAT AAT AAAT AAT AAT AAT AAT AA- AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
1539431 AATGAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
2 8 0.12
3 50 0.75
4 9 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1539368 original size:24 final size:25
Alignment explanation
Indices: 1539339--1539421 Score: 105
Period size: 27 Copynumber: 3.2 Consensus size: 25
1539329 TCTGGGCTTG
*
1539339 TAATATTTAT-TTAAATAATAATAA
1 TAATATTTATAATAAATAATAATAA
*
1539363 TAATATATATAATAATATAAGTAATAA
1 TAATATTTATAATAA-ATAA-TAATAA
1539390 TAATATATTAATAATAAATAATAATAA
1 TAATAT-TT-ATAATAAATAATAATAA
1539417 TAATA
1 TAATA
1539422 AAATAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
24 9 0.18
25 3 0.06
26 4 0.08
27 23 0.45
28 5 0.10
29 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (25 bp):
TAATATTTATAATAAATAATAATAA
Found at i:1539395 original size:27 final size:26
Alignment explanation
Indices: 1539353--1539429 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 26
1539343 ATTTATTTAA
1539353 ATAATAATAATAATATATATAATAAT
1 ATAATAATAATAATATATATAATAAT
1539379 ATAAGTAATAATAATATAT-TAATAAT
1 ATAA-TAATAATAATATATATAATAAT
*
1539405 A-AATAATAATAATA-ATAAAATAAT
1 ATAATAATAATAATATATATAATAAT
1539429 A
1 A
1539430 AAATGAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
23 2 0.04
24 18 0.38
25 2 0.04
26 12 0.25
27 14 0.29
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (26 bp):
ATAATAATAATAATATATATAATAAT
Found at i:1539426 original size:24 final size:25
Alignment explanation
Indices: 1539350--1539431 Score: 112
Period size: 27 Copynumber: 3.2 Consensus size: 25
1539340 AATATTTATT
*
1539350 TAAATAATAATAATAATATATATAA
1 TAAATAATAATAATAATATAAATAA
1539375 TAATATAAGTAATAATAATATATTAATAA
1 TAA-ATAA-TAATAATAATATA--AATAA
1539404 TAAATAATAATAATAATA-AAATAA
1 TAAATAATAATAATAATATAAATAA
1539428 TAAA
1 TAAA
1539432 ATGAAAAAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
24 9 0.17
25 3 0.06
26 5 0.10
27 24 0.46
28 4 0.08
29 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (25 bp):
TAAATAATAATAATAATATAAATAA
Found at i:1539438 original size:14 final size:14
Alignment explanation
Indices: 1539351--1539430 Score: 90
Period size: 14 Copynumber: 5.6 Consensus size: 14
1539341 ATATTTATTT
1539351 AAATAATAATAATA
1 AAATAATAATAATA
*
1539365 ATATATATAATAATA
1 AAATA-ATAATAATA
*
1539380 TAAGTAATAATAATA
1 -AAATAATAATAATA
* *
1539395 TATTAATAATAA-A
1 AAATAATAATAATA
*
1539408 TAATAATAATAATA
1 AAATAATAATAATA
1539422 AAATAATAA
1 AAATAATAA
1539431 AATGAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
13 12 0.21
14 23 0.41
15 18 0.32
16 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (14 bp):
AAATAATAATAATA
Found at i:1539682 original size:73 final size:73
Alignment explanation
Indices: 1539571--1539940 Score: 582
Period size: 73 Copynumber: 5.1 Consensus size: 73
1539561 CGAGTGATGG
* *
1539571 AAATTTCTATTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTAAAGAAAAACAATCTCA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
1539636 AGTGAGAT
66 AGTGAGAT
* * *
1539644 AAATTTCTGTTTCAAGTGAAATTGTCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
1539709 AGTGAGAT
66 AGTGAGAT
* *
1539717 AAATTTCTGTTTCGAGTGAAACTGTCTCATGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCG
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
1539782 AGTGAGAT
66 AGTGAGAT
* * *
1539790 AAATCGT-TGTTTCGAGGGAAACTGTCTCAAGCGAGACAAAGTTTGTTTTAAGAAAAACAATCTC
1 AAAT-TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTC
1539854 AAGTGAGAT
65 AAGTGAGAT
* * * *
1539863 AAATTAT-TGTTTCGAGGGAAACTGTCTCAAGCGATACAAAGTTTGTTTTAAGAAAAATAATCTC
1 AAATT-TCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTC
1539927 AAGTGAGAT
65 AAGTGAGAT
1539936 AAATT
1 AAATT
1539941 GCTATTTGAA
Statistics
Matches: 277, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
73 276 1.00
74 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (73 bp):
AAATTTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCA
AGTGAGAT
Found at i:1540255 original size:165 final size:164
Alignment explanation
Indices: 1539983--1540470 Score: 805
Period size: 164 Copynumber: 3.0 Consensus size: 164
1539973 ATGGATGTGG
* * * * *
1539983 GAAATAGTTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTCA
1 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTT-A
** *
1540048 GAAAAGATTGAATGAGAAACTATAGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
65 GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
1540113 GGGTAACATGCCCCAATCTCATGATAATGCTGTTA
130 GGGTAACATGCCCCAATCTCATGATAATGCTGTTA
1540148 GAAATAGTTTACTAAGTAAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTA
1 GAAATAGTTTACTAAGT-AAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTA
1540213 GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
65 GAAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATT
*
1540278 GGGTAACATGCCCCAATCTCATGATAATGCTGTTG
130 GGGTAACATGCCCCAATCTCATGATAATGCTGTTA
*
1540313 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTTG
1 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAG
* * * *
1540378 AAAAGATAAAATGAGAAACTATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGATTG
66 AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATTG
* * *
1540443 GATAACATGACCCAATCTCAAGATAATG
131 GGTAACATGCCCCAATCTCATGATAATG
1540471 TTCATTATTG
Statistics
Matches: 305, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
164 133 0.44
165 131 0.43
166 41 0.13
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (164 bp):
GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAG
AAAAGATAAAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTTAAAATAATATGTTGATTG
GGTAACATGCCCCAATCTCATGATAATGCTGTTA
Found at i:1541040 original size:22 final size:22
Alignment explanation
Indices: 1540988--1541041 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
1540978 AAAGTTTTCC
*
1540988 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
*
1541010 TCTTTGAAGAGATAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
1541032 TCTTTGAAGA
1 TCTTTGAAGA
1541042 ATGTAGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:1545695 original size:7 final size:7
Alignment explanation
Indices: 1545682--1545751 Score: 63
Period size: 7 Copynumber: 9.6 Consensus size: 7
1545672 TCCATTTTTC
1545682 CTTTTTT
1 CTTTTTT
1545689 -TTCTTTT
1 CTT-TTTT
1545696 CTTTTTT
1 CTTTTTT
1545703 CTTTTTTT
1 C-TTTTTT
1545711 CCTTTTTCAT
1 -CTTTTT--T
1545721 CTTTTTT
1 CTTTTTT
*
1545728 CTTTTCT
1 CTTTTTT
1545735 -TTTTTT
1 CTTTTTT
*
1545741 CTTCTTT
1 CTTTTTT
1545748 CTTT
1 CTTT
1545752 GCTGGATGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
6 7 0.13
7 24 0.46
8 13 0.25
9 7 0.13
10 1 0.02
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:1545710 original size:30 final size:30
Alignment explanation
Indices: 1545676--1545741 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
1545666 AATTTCTCCA
**
1545676 TTTTTCCTTTTTTTTCTTTTCTT-TTTTCTT
1 TTTTTCCTTTTTCATCTTTT-TTCTTTTCTT
1545706 TTTTTCCTTTTTCATCTTTTTTCTTTTCTT
1 TTTTTCCTTTTTCATCTTTTTTCTTTTCTT
1545736 TTTTTC
1 TTTTTC
1545742 TTCTTTCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTTTCCTTTTTCATCTTTTTTCTTTTCTT
Found at i:1545725 original size:8 final size:8
Alignment explanation
Indices: 1545684--1545747 Score: 62
Period size: 8 Copynumber: 8.4 Consensus size: 8
1545674 CATTTTTCCT
*
1545684 TTTTTTTC
1 TTTTCTTC
1545692 TTTTCTT-
1 TTTTCTTC
*
1545699 TTTTCTTT
1 TTTTCTTC
*
1545707 TTTTCCT-
1 TTTTCTTC
*
1545714 TTTTCATC
1 TTTTCTTC
1545722 TTTT-TTC
1 TTTTCTTC
*
1545729 TTTTCTTT
1 TTTTCTTC
1545737 TTTTCTTC
1 TTTTCTTC
1545745 TTT
1 TTT
1545748 CTTTGCTGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
7 19 0.40
8 28 0.60
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTC
Found at i:1548803 original size:20 final size:20
Alignment explanation
Indices: 1548761--1548805 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1548751 ATGCAAATGC
** *
1548761 AAATGTAAATGTAAAAATGA
1 AAATGTAAATACAAAAATAA
*
1548781 AAATGTAAATACAAACATAA
1 AAATGTAAATACAAAAATAA
1548801 AAATG
1 AAATG
1548806 CAAAAATGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.22
Consensus pattern (20 bp):
AAATGTAAATACAAAAATAA
Found at i:1550955 original size:56 final size:55
Alignment explanation
Indices: 1550869--1550973 Score: 201
Period size: 56 Copynumber: 1.9 Consensus size: 55
1550859 TTATGCAGGG
1550869 TTTTGGTTCTAAGGGTAAAGGTACTTGAACTGTCCTTGTTGATGCCCCCTTGGAGC
1 TTTTGGTTCTAAGGGTAAAGGTACTTGAACTG-CCTTGTTGATGCCCCCTTGGAGC
1550925 TTTTGGTTCTAAGGGTAAAGGTACTTGAACTGCCTTGTTGATGCCCCCT
1 TTTTGGTTCTAAGGGTAAAGGTACTTGAACTGCCTTGTTGATGCCCCCT
1550974 GGACTACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 17 0.35
56 32 0.65
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (55 bp):
TTTTGGTTCTAAGGGTAAAGGTACTTGAACTGCCTTGTTGATGCCCCCTTGGAGC
Found at i:1551278 original size:21 final size:20
Alignment explanation
Indices: 1551253--1551300 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
1551243 GATAATAAAT
1551253 AATAAAATTTAATACTTGAAA
1 AATAAAATTTAATACTTG-AA
1551274 AATAAAA-TTAATACTTGAA
1 AATAAAATTTAATACTTGAA
1551293 AATAAAAT
1 AATAAAAT
1551301 AAAACATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.35
20 10 0.38
21 7 0.27
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAATACTTGAA
Found at i:1551296 original size:19 final size:20
Alignment explanation
Indices: 1551253--1551300 Score: 80
Period size: 19 Copynumber: 2.4 Consensus size: 20
1551243 GATAATAAAT
1551253 AATAAAATTTAATACTTGAAA
1 AATAAAA-TTAATACTTGAAA
1551274 AATAAAATTAATACTTG-AA
1 AATAAAATTAATACTTGAAA
1551293 AATAAAAT
1 AATAAAAT
1551301 AAAACATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 10 0.37
20 10 0.37
21 7 0.26
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (20 bp):
AATAAAATTAATACTTGAAA
Found at i:1551986 original size:18 final size:18
Alignment explanation
Indices: 1551963--1551998 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1551953 TCTTTTCTTC
1551963 AATATTAATAAATA-AATA
1 AATATTAA-AAATATAATA
1551981 AATATTAAAAATATAATA
1 AATATTAAAAATATAATA
1551999 TTTTTCCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATTAAAAATATAATA
Found at i:1556144 original size:90 final size:90
Alignment explanation
Indices: 1556044--1556210 Score: 255
Period size: 90 Copynumber: 1.8 Consensus size: 90
1556034 CAAGATGCAT
* * * *
1556044 GTGTGTTTGTTTCTTTATTTTTAAAGGTATTCATGTTCAATT-TGTTCTTGTTCGTTTATTTATT
1 GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTCTGGTCGTGTTCATTTATTTA-T
1556108 TTTGAAGGTGTTCGCGAACATGATTG
65 TTTGAAGGTGTTCGCGAACATGATTG
* *
1556134 GTGTGTTTGTTTTTTTATTTTTAAAGGCATTCATGTTCAATTCGTGGTCGTGTTCATTTTTTTAT
1 GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTC-TGGTCGTGTTCATTTATTTAT
1556199 TTTGAAGGTGTT
65 TTTGAAGGTGTT
1556211 TATGAACATG
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
90 40 0.58
91 13 0.19
92 16 0.23
ACGTcount: A:0.17, C:0.08, G:0.20, T:0.54
Consensus pattern (90 bp):
GTGTGTTTGTTTCTTTATTTTTAAAGGCATTCATGTTCAATTCTGGTCGTGTTCATTTATTTATT
TTGAAGGTGTTCGCGAACATGATTG
Found at i:1558544 original size:18 final size:19
Alignment explanation
Indices: 1558523--1558569 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
1558513 GTAAAAAGAT
*
1558523 ATTAAAAT-AATAAAAGTG
1 ATTAAAATAAATAAAAGTA
1558541 ATT-AAATAAATAAAAGTA
1 ATTAAAATAAATAAAAGTA
*
1558559 ATTAAAGTAAA
1 ATTAAAATAAA
1558570 AATAAGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (19 bp):
ATTAAAATAAATAAAAGTA
Found at i:1558848 original size:64 final size:63
Alignment explanation
Indices: 1558726--1558855 Score: 226
Period size: 66 Copynumber: 2.0 Consensus size: 63
1558716 CTTGTATACC
1558726 GAACACCAAGACATCTTTGATTCCAGCTTCGATAATTGATTCTAAAACGACATCAATTGTCGTA
1 GAACACCAAGACATCTTTGATTCCAGCTTCGATAATTGATTCT-AAACGACATCAATTGTCGTA
1558790 GAACACCCAAGACAATCTTTGATTCCAGCTTCGATAATTGATTCT-AACGACATCAATTGTCGTA
1 GAACA-CCAAGAC-ATCTTTGATTCCAGCTTCGATAATTGATTCTAAACGACATCAATTGTCGTA
1558854 GA
1 GA
1558856 TCAATTACCG
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
64 26 0.41
65 7 0.11
66 31 0.48
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (63 bp):
GAACACCAAGACATCTTTGATTCCAGCTTCGATAATTGATTCTAAACGACATCAATTGTCGTA
Found at i:1561368 original size:25 final size:22
Alignment explanation
Indices: 1561341--1561383 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1561331 TATTGTATTA
1561341 TATAATA--TTTTATTAATAAG
1 TATAATATTTTTTATTAATAAG
*
1561361 TATAATATTTTTTATTTATAAG
1 TATAATATTTTTTATTAATAAG
1561383 T
1 T
1561384 GAAGAGTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TATAATATTTTTTATTAATAAG
Found at i:1561433 original size:39 final size:41
Alignment explanation
Indices: 1561390--1561468 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 41
1561380 AAGTGAAGAG
* *
1561390 TATGATATAAAATT-TATAATATAATTT-ATTTTAT-TATAT
1 TATGAAATAAAATTAT-TAAAATAATTTGATTTTATATATAT
* *
1561429 TATGAAATTAAATTATTAAAATTATTTGATTTTATATATA
1 TATGAAATAAAATTATTAAAATAATTTGATTTTATATATA
1561469 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
39 21 0.64
40 8 0.24
41 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (41 bp):
TATGAAATAAAATTATTAAAATAATTTGATTTTATATATAT
Found at i:1562535 original size:24 final size:25
Alignment explanation
Indices: 1562508--1562557 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1562498 TTCCTCTTCT
1562508 TGATCTCCATTCTC-TTTTCAGCTG
1 TGATCTCCATTCTCTTTTTCAGCTG
1562532 TGATCTCCATTCTCTTTTTCAGCTG
1 TGATCTCCATTCTCTTTTTCAGCTG
1562557 T
1 T
1562558 TTCACATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.12, C:0.28, G:0.12, T:0.48
Consensus pattern (25 bp):
TGATCTCCATTCTCTTTTTCAGCTG
Found at i:1568680 original size:19 final size:20
Alignment explanation
Indices: 1568656--1568703 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1568646 GAAAAAACTG
*
1568656 AAGAAAAAGAGA-GAACTTT
1 AAGAAAAAGACATGAACTTT
*
1568675 AAGAAAAAAACATGAACTTT
1 AAGAAAAAGACATGAACTTT
*
1568695 AAGCAAAAG
1 AAGAAAAAG
1568704 GGCAAGTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.60, C:0.08, G:0.17, T:0.15
Consensus pattern (20 bp):
AAGAAAAAGACATGAACTTT
Found at i:1573285 original size:33 final size:34
Alignment explanation
Indices: 1573248--1573311 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1573238 GCTAAATCTA
1573248 AAAAAATA-AAAAATAGTT-TAGGGACTAAAATGC
1 AAAAAATATAAAAA-AGTTATAGGGACTAAAATGC
**
1573281 AAAAAATATGCAAAAGTTATAGGGACTAAAA
1 AAAAAATATAAAAAAGTTATAGGGACTAAAA
1573312 GCTAATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 12 0.44
34 15 0.56
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.20
Consensus pattern (34 bp):
AAAAAATATAAAAAAGTTATAGGGACTAAAATGC
Found at i:1574607 original size:24 final size:23
Alignment explanation
Indices: 1574545--1574608 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
1574535 GGCTAGGGTA
*
1574545 GGCTCCAGGTCAGGTTTGGTTTG
1 GGCTCCAGGTCAGGTTTAGTTTG
* * *
1574568 GGCTCCGGGTCGGGTTCTATTTTG
1 GGCTCCAGGTCAGGTT-TAGTTTG
*
1574592 GGCTCCAGGTAAGGTTT
1 GGCTCCAGGTCAGGTTT
1574609 TGGTTGGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.09, C:0.19, G:0.38, T:0.34
Consensus pattern (23 bp):
GGCTCCAGGTCAGGTTTAGTTTG
Found at i:1575166 original size:140 final size:139
Alignment explanation
Indices: 1574838--1575422 Score: 697
Period size: 140 Copynumber: 4.3 Consensus size: 139
1574828 CAAGCTACGG
* * * * ** * * *
1574838 GTTCTTCTCATCATGAACTCTCTACTGGAAATATCGACCCCTCGAGTGAGGCG-TCCCTGATTCA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTTCACTGATTCA
* * *
1574902 ACTCCAAATACGATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATGAA-TTTCTTCCTCT
66 ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCCCTCT
*
1574966 ATCGGATGA
131 ATCAGATGA
* * * *
1574975 GTTCTTCTTATTATAAACTCTCTATTGGAAATGTTAATCCCTCAAGTGAGGCGTTGA-TGATTCA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTTCACTGATTCA
** *
1575039 ACTCCATATGTGATGAATTGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCT
66 ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAAC-T-TTCTCCCT
1575104 CTATCAGATGA
129 CTATCAGATGA
* *
1575115 GTTATTCTCATTATGAACT-TCCCATTGGAAATGTTAATCCCTCAAGTGAGGCG-TCACTGATTT
1 GTTCTTCTCATTATGAACTCT-CCATTGGAAATGTTAATCCCTCAAGTGAGGCGTTCACTGATTC
* *
1575178 AACTCCATATACAATGAGTCGAGAAAAGGTTGAACAAG---TTCTCA-TATGAAC-TTCTCCCTC
65 AACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCCCTC
1575238 TATCAGATGA
130 TATCAGATGA
* *
1575248 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGC-ATAACTGATTCA
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTTCACTGATTCA
* ** * * *
1575312 ACTCAATATGTGATGAATCGAGCAAAGGTTGAACAAGTTCTTCTCATTATTAACTTCTTCTCCCC
66 ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAAC-T-TTCTCCCT
* *
1575377 CTATCGGACGA
129 CTATCAGATGA
* * * * *
1575388 GTTCTTATCGTTGTGAACTTTCCACTGGAAATGTT
1 GTTCTTCTCATTATGAACTCTCCATTGGAAATGTT
1575423 GATTGGTTTA
Statistics
Matches: 386, Mismatches: 47, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
133 108 0.28
134 1 0.00
136 13 0.03
137 111 0.29
138 1 0.00
139 4 0.01
140 148 0.38
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (139 bp):
GTTCTTCTCATTATGAACTCTCCATTGGAAATGTTAATCCCTCAAGTGAGGCGTTCACTGATTCA
ACTCCATATACGATGAATCGAGAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTCTCCCTCT
ATCAGATGA
Found at i:1575341 original size:273 final size:275
Alignment explanation
Indices: 1574876--1575422 Score: 785
Period size: 273 Copynumber: 2.0 Consensus size: 275
1574866 AAATATCGAC
* * * *
1574876 CCCTCGAGTGAGGCGTCCCTGATTCAACTCCAAATACGATGAATCGAGCAAAGGTTGAACAAGTT
1 CCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAG-T
* * * * *
1574941 CTTCTCATTATGAATTTCTTCCTCTATCGGATGAGTTCTTCTTATTATAAACTCTCTATTGGAAA
65 -TTCTCATTATGAACTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAA
* * * *
1575006 TGTTAATCCCTCAAGTGAGGCGTTGATGATTCAACTCCATATGTGATGAATTGAGAAAAGGTTGA
129 TGTTAATCCCTCAAGTGAGGCGATAATGATTCAACTCAATATGTGATGAATCGAGAAAAGGTTGA
* * *
1575071 ACAAGTTCTTCTCATTATGAACTTATTCTCCCTCTATCAGATGAGTTATTCTCATTATGAACTTC
194 ACAAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAACTTC
*
1575136 CCATTGGAAATGTTAAT
259 CCACTGGAAATGTTAAT
* * *
1575153 CCCTCAAGTGAGGCGTCACTGATTTAACTCCATATACAATGAGTCGAGAAAAGGTTGAACAAG-T
1 CCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAGTT
*
1575217 TCTCA-TATGAACTTCTCCCTCTATCAGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAATG
66 TCTCATTATGAACTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAATG
*
1575281 TTAATCCCTCAAGTGAGGC-ATAACTGATTCAACTCAATATGTGATGAATCGAGCAAAGGTTGAA
131 TTAATCCCTCAAGTGAGGCGATAA-TGATTCAACTCAATATGTGATGAATCGAGAAAAGGTTGAA
* * * * * * *
1575345 CAAGTTCTTCTCATTATTAACTTCTTCTCCCCCTATCGGACGAGTTCTTATCGTTGTGAACTTTC
195 CAAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAACTTCC
1575410 CACTGGAAATGTT
260 CACTGGAAATGTT
1575423 GATTGGTTTA
Statistics
Matches: 240, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
272 2 0.01
273 176 0.73
274 6 0.03
277 56 0.23
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (275 bp):
CCCTCAAGTGAGGCGTCACTGATTCAACTCCAAATACAATGAATCGAGAAAAGGTTGAACAAGTT
TCTCATTATGAACTTCTCCCTCTATCAGATGAGTTCTTCTCATTATAAACTCTCCATTGGAAATG
TTAATCCCTCAAGTGAGGCGATAATGATTCAACTCAATATGTGATGAATCGAGAAAAGGTTGAAC
AAGTTCTTCTCATTATGAACTTATTCTCCCCCTATCAGACGAGTTATTATCATTATGAACTTCCC
ACTGGAAATGTTAAT
Found at i:1579479 original size:14 final size:15
Alignment explanation
Indices: 1579455--1579483 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1579445 CCTTGAACCC
1579455 TTTTCTCTTTTCTTT
1 TTTTCTCTTTTCTTT
1579470 TTTTCT-TTTTCTTT
1 TTTTCTCTTTTCTTT
1579484 CTTAGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTCTTTTCTTT
Found at i:1580317 original size:186 final size:189
Alignment explanation
Indices: 1580003--1580383 Score: 723
Period size: 186 Copynumber: 2.0 Consensus size: 189
1579993 GTAGTCTTCG
*
1580003 TAATGATCATTTTGATGTTTTTGTTCGCTACTTGTACTGTCCCATTCATTTTCGGGTGGTAGGTC
1 TAATGATCATTTTGATGTTTTTGTTCGCTACTTGTACTGCCCCATTCATTTTCGGGTGGTAGGTC
1580068 ACAAAATTGGCATGTTTTATCTTAAACTGCATACATAGTTCATCCATCATCTTGTTATTCAGATT
66 ACAAAATTGGCATGTTTTATCTTAAACTGCATACATAGTTCATCCATCATCTTGTTATTCAGATT
1580133 AGTGTCATTATCTTT-GTGATTCTTTCTGGCAATCCACATCGACAAA-TATTTCT-TTT
131 AGTGTCATTATCTTTAGTGATTCTTTCTGGCAATCCACATCGACAAATTATTTCTCTTT
1580189 TAATGATCATTTTGATGTTTTTGTTCGCTACTTGTACTGCCCCATTCATTTTCGGGTGGTAGGTC
1 TAATGATCATTTTGATGTTTTTGTTCGCTACTTGTACTGCCCCATTCATTTTCGGGTGGTAGGTC
1580254 ACAAAATTGGCATGTTTTATCTTAAACTGCATACATAGTTCATCCATCATCTTGTTATTCAGATT
66 ACAAAATTGGCATGTTTTATCTTAAACTGCATACATAGTTCATCCATCATCTTGTTATTCAGATT
1580319 AGTGTCATTATCTTTAGTGATTCTTTCTGGCAATCCACATCGACAAATTATTTCTCTTT
131 AGTGTCATTATCTTTAGTGATTCTTTCTGGCAATCCACATCGACAAATTATTTCTCTTT
*
1580378 TTATGA
1 TAATGA
1580384 ATTTGCAAAC
Statistics
Matches: 190, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
186 144 0.76
187 31 0.16
188 7 0.04
189 8 0.04
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.43
Consensus pattern (189 bp):
TAATGATCATTTTGATGTTTTTGTTCGCTACTTGTACTGCCCCATTCATTTTCGGGTGGTAGGTC
ACAAAATTGGCATGTTTTATCTTAAACTGCATACATAGTTCATCCATCATCTTGTTATTCAGATT
AGTGTCATTATCTTTAGTGATTCTTTCTGGCAATCCACATCGACAAATTATTTCTCTTT
Found at i:1588829 original size:61 final size:61
Alignment explanation
Indices: 1588759--1588883 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
1588749 AAATCAAACT
1588759 TTTTAGTTGAGACCATGAGATCCCATCACCCTGGATATACTCTTCGACCCATTTTTTAGTC
1 TTTTAGTTGAGACCATGAGATCCCATCACCCTGGATATACTCTTCGACCCATTTTTTAGTC
1588820 TTTTAGTTGAGACCATGAGATCCCATCACCCTGGATATACTCTTCGACCCATTTTTTAGTC
1 TTTTAGTTGAGACCATGAGATCCCATCACCCTGGATATACTCTTCGACCCATTTTTTAGTC
1588881 TTT
1 TTT
1588884 CCCATTAGAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (61 bp):
TTTTAGTTGAGACCATGAGATCCCATCACCCTGGATATACTCTTCGACCCATTTTTTAGTC
Found at i:1598158 original size:23 final size:23
Alignment explanation
Indices: 1598104--1598167 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1598094 CAGCTCATAT
*
1598104 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACGTAG
* * *
1598127 AATTACACCTAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACGTAG
*
1598150 AAATGCACCAAAATGCCA
1 AAATGCACCAAAGTGCCA
1598168 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.16
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACGTAG
Found at i:1599434 original size:59 final size:63
Alignment explanation
Indices: 1599360--1599482 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 63
1599350 ATTTAATACA
*
1599360 TACTATAATATATATCACATATACCC-AATC-ATCA-A-CATATGATCATACATTCATGCCTT
1 TACTATAATATATATCACATATACCCAAATCAAACATAGCATATGATCATACATTCATGCCTT
1599419 TACTATAATATATATCACATATACCCAAATCAAACATATGCATATGATCATACATTCATGCCTT
1 TACTATAATATATATCACATATACCCAAATCAAACATA-GCATATGATCATACATTCATGCCTT
1599483 CTCAAATAGG
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
59 26 0.45
60 4 0.07
61 3 0.05
62 1 0.02
64 24 0.41
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (63 bp):
TACTATAATATATATCACATATACCCAAATCAAACATAGCATATGATCATACATTCATGCCTT
Found at i:1608060 original size:30 final size:30
Alignment explanation
Indices: 1608026--1608107 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
1608016 TTAAAAAAAT
1608026 AAATACAATTAAATCAAAATTTTATGTATA
1 AAATACAATTAAATCAAAATTTTATGTATA
*
1608056 AAATAATCAA--AAATTAAAATTTTATGTATA
1 AAAT-A-CAATTAAATCAAAATTTTATGTATA
* * *
1608086 TACTA-ACATTAGATCAAAATTT
1 AAATACA-ATTAAATCAAAATTT
1608108 ATGCATCACA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
27 1 0.02
28 1 0.02
29 1 0.02
30 35 0.83
31 1 0.02
32 3 0.07
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATACAATTAAATCAAAATTTTATGTATA
Found at i:1608517 original size:3 final size:3
Alignment explanation
Indices: 1608499--1608541 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
1608489 TCTACAAAAA
1608499 TAT TA- TAT TA- TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1608542 TGTAGGCCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1609143 original size:19 final size:19
Alignment explanation
Indices: 1609112--1609157 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1609102 AATGCAATTG
*
1609112 TTTTT-TTT-TTTTTTTTCA
1 TTTTTATTTATTTTGTTT-A
1609130 TTTTTATTTATTTTGTTTA
1 TTTTTATTTATTTTGTTTA
1609149 TTTTTATTT
1 TTTTTATTT
1609158 TTACTTAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 5 0.20
19 13 0.52
20 7 0.28
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.85
Consensus pattern (19 bp):
TTTTTATTTATTTTGTTTA
Found at i:1611558 original size:199 final size:199
Alignment explanation
Indices: 1611107--1611748 Score: 1036
Period size: 199 Copynumber: 3.2 Consensus size: 199
1611097 GCCTAAAATA
* * *
1611107 TTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCATGCACCTCGTTGGGCATTA
1 TTTTTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTC
*
1611171 ATTCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATATATTATGTAGACCTATTTTCT
64 ATTCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCT
* * *
1611236 CATAAAAACCGGTATATTTATGCTGGTTACATTGTAAATTTACCTATTATATTATAATTATAGGT
129 CAT-AAAACCGGTATATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGT
*
1611301 TTCGATT
193 TTCGATG
* * *
1611308 TTTTTTGGATCGATACAATTTTAAATGTATCGACACTATATGCGCGCACCTCGTTGGGCATTCAT
1 TTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
*
1611373 TCTGGACAAAAAGTATCGACACAAATTTAGAAAGTATCGATACATTATGTAGACCTATTTTCTCA
66 TCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
*
1611438 TAAAACCGGTATATTTCTACTGGTTACATTGTAAATTTACATATTACATTATAATTATAGGTTTC
131 TAAAACCGGTATATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTC
1611503 GATG
196 GATG
1611507 TTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
1 TTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
* *
1611572 TCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATACATTAAGTAGACATATTTTCTCA
66 TCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
* * * *
1611637 TAAAACCGATATATTTCTACCGGTTGCATTGTAAATTTACCTATTACATTATAATTATCGGTTTC
131 TAAAACCGGTATATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTC
*
1611702 AATG
196 GATG
*
1611706 TTTTTGGGATCGATACAATTTTAAAAAT-TATCGATACTTTATG
1 TTTTTGGGATCGATACAATTTT--AAATGTATCGACACTTTATG
1611749 TTTACCTATT
Statistics
Matches: 412, Mismatches: 26, Indels: 7
0.93 0.06 0.02
Matches are distributed among these distances:
199 272 0.66
200 118 0.29
201 19 0.05
202 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCAT
TCTGGACAAAAAGTATCGACACAAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCA
TAAAACCGGTATATTTCTACTGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTC
GATG
Found at i:1613247 original size:24 final size:24
Alignment explanation
Indices: 1613192--1613247 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1613182 CGAAATTTAT
*
1613192 ATTGAAACTCAAACTCAAATTGAA
1 ATTGAAATTCAAACTCAAATTGAA
* *
1613216 ATTTAAATTCAAACTCCAATT-AA
1 ATTGAAATTCAAACTCAAATTGAA
1613239 ATATGAAAT
1 AT-TGAAAT
1613248 GAACATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (24 bp):
ATTGAAATTCAAACTCAAATTGAA
Found at i:1616145 original size:20 final size:20
Alignment explanation
Indices: 1616120--1616158 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1616110 CTGGTATATT
*
1616120 TATACCGGTTACATTGTAAA
1 TATACCGATTACATTGTAAA
*
1616140 TATACCTATTACATTGTAA
1 TATACCGATTACATTGTAA
1616159 TTACCAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.38
Consensus pattern (20 bp):
TATACCGATTACATTGTAAA
Found at i:1621070 original size:25 final size:24
Alignment explanation
Indices: 1621040--1621088 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1621030 ACCTGCATTT
*
1621040 ATAATTAAATTTATCATTTTATATA
1 ATAATTAAA-CTATCATTTTATATA
*
1621065 ATAATTATACTATCATTTTATATA
1 ATAATTAAACTATCATTTTATATA
1621089 TAAAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (24 bp):
ATAATTAAACTATCATTTTATATA
Found at i:1623299 original size:161 final size:161
Alignment explanation
Indices: 1623123--1623579 Score: 547
Period size: 162 Copynumber: 2.7 Consensus size: 161
1623113 TCGAGACCGG
*
1623123 TTTTGTCATATTTTTAC-TGTTATATTATTATGGATCGATATATTTTTATAAAATATCGACAATT
1 TTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACAATT
* * *
1623187 TATTGGCTCTATTATTGCATCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
66 TATAGGCGCTATTACTGCATCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
*
1623252 CACTTTCAACATATCCAGTAGCGTTTTACCAA
131 CACTTTCAACATAT-CAGTAGCGCTTTACCAA
* * *
1623284 TTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTT
1 TTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACAATT
* *
1623349 TATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATATTTATATTAAAGTATCGA
66 TATAGGCGCTATTACTGCATCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
* **
1623414 CACTTTCAACATATCGGTAGCGCTTTACCGG
131 CACTTTCAACATATCAGTAGCGCTTTACCAA
* *
1623445 TTTTGTCATTTCTAGACGGTTTTGTCATATTTTACCTATTATATTATTATGGATCGATACATTTT
1 TTTTG-----TC---A--------T-AT-TTTTACATGTTATATTATTATGGATCGATACATTTT
* * * * * *
1623510 TATAAAGTATCGACACTTTATACGCGCTATTACTGCTTATCTTTTAAATTCCATAAGTGTCGATA
48 TATAAAATATCGACAATTTATAGGCGCTATTACTGCATCTCTTTTAAATTCCAAAAGTGTCGATA
1623575 CTTAT
113 CTTAT
1623580 TTCAATAGAA
Statistics
Matches: 257, Mismatches: 20, Indels: 20
0.87 0.07 0.07
Matches are distributed among these distances:
161 35 0.14
162 117 0.46
166 2 0.01
169 1 0.00
177 1 0.00
178 2 0.01
179 99 0.39
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.44
Consensus pattern (161 bp):
TTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTTATAAAATATCGACAATT
TATAGGCGCTATTACTGCATCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAAGTATCGA
CACTTTCAACATATCAGTAGCGCTTTACCAA
Found at i:1626114 original size:3 final size:3
Alignment explanation
Indices: 1626108--1626177 Score: 54
Period size: 3 Copynumber: 22.3 Consensus size: 3
1626098 TTTTTTTAAA
* * *
1626108 TAT TATT TATT TATT TAT TAT TAT AAT TAT TAT AAT TAT AAT TA- TAT
1 TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1626155 TAT TATT TAT TATT TAT T-T TAT T
1 TAT TA-T TAT TA-T TAT TAT TAT T
1626178 TTGCAGGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 35 0.62
4 17 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1626126 original size:15 final size:16
Alignment explanation
Indices: 1626108--1626176 Score: 76
Period size: 15 Copynumber: 4.6 Consensus size: 16
1626098 TTTTTTTAAA
*
1626108 TATTATT-TATTTATT
1 TATTATTATAATTATT
1626123 TATTATTATAATTA-T
1 TATTATTATAATTATT
*
1626138 TATAATTATAATTATAT
1 TATTATTATAATTAT-T
1626155 TATTATT-T-ATTATT
1 TATTATTATAATTATT
1626169 TATT-TTAT
1 TATTATTAT
1626177 TTTGCAGGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
13 2 0.04
14 6 0.13
15 26 0.55
16 6 0.13
17 7 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATAATTATT
Found at i:1626164 original size:12 final size:11
Alignment explanation
Indices: 1626107--1626168 Score: 60
Period size: 11 Copynumber: 5.7 Consensus size: 11
1626097 ATTTTTTTAA
1626107 ATATTATTTATT
1 ATATTA-TTATT
1626119 -TATTTATTATT
1 ATA-TTATTATT
1626130 ATA--ATTATT
1 ATATTATTATT
*
1626139 ATAATTATAATT
1 AT-ATTATTATT
1626151 ATATTATTATT
1 ATATTATTATT
1626162 -TATTATT
1 ATATTATT
1626169 TATTTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 8 0.19
10 8 0.19
11 15 0.35
12 12 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTATT
Found at i:1627137 original size:10 final size:9
Alignment explanation
Indices: 1627101--1627144 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
1627091 AGTTTTTAAT
1627101 ATTTTTTTA
1 ATTTTTTTA
* *
1627110 TTTTTGTTTT
1 ATTTT-TTTA
1627120 ATTTTTTTA
1 ATTTTTTTA
1627129 ATTTATTTTA
1 ATTT-TTTTA
1627139 ATTTTT
1 ATTTTT
1627145 CCTTTGATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:1627137 original size:18 final size:19
Alignment explanation
Indices: 1627100--1627144 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1627090 GAGTTTTTAA
* *
1627100 TATTTTTTTATTTTTGTTT
1 TATTTTTTTATATTTATTT
1627119 TATTTTTTTA-ATTTATTT
1 TATTTTTTTATATTTATTT
1627137 TAATTTTT
1 T-ATTTTT
1627145 CCTTTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (19 bp):
TATTTTTTTATATTTATTT
Found at i:1627142 original size:19 final size:19
Alignment explanation
Indices: 1627094--1627144 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1627084 ACGAGAGAGT
* *
1627094 TTTTAATATTTTTTTATTTT
1 TTTTAAT-TTTTTTAATTTA
*
1627114 TGTTTTATTTTTTTAATTTA
1 T-TTTAATTTTTTTAATTTA
1627134 TTTTAATTTTT
1 TTTTAATTTTT
1627145 CCTTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.35
20 12 0.46
21 5 0.19
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTAATTTTTTTAATTTA
Found at i:1627965 original size:22 final size:21
Alignment explanation
Indices: 1627940--1627994 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1627930 CAATTGGAAT
* *
1627940 TTTGGGATTTAGAGTTTTCAGA
1 TTTGGGATTT-GAGTTTTAAAA
1627962 TTTGGAGATTTGAGTTTTAAAA
1 TTTGG-GATTTGAGTTTTAAAA
1627984 TTTAGGGATTT
1 TTT-GGGATTT
1627995 TGACAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 22 0.76
23 7 0.24
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.47
Consensus pattern (21 bp):
TTTGGGATTTGAGTTTTAAAA
Found at i:1629497 original size:2 final size:2
Alignment explanation
Indices: 1629492--1629534 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1629482 TACGAAGGAA
1629492 AT AT AT AT 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 AT AT AT AT
1629534 A
1 A
1629535 ATAATAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1630985 original size:37 final size:37
Alignment explanation
Indices: 1630822--1631149 Score: 291
Period size: 37 Copynumber: 8.8 Consensus size: 37
1630812 AATAAAAAAT
* * * *
1630822 AAAATATTTTTTTAAAACTATATTTTATATATGATTTTTA
1 AAAATA-TTTTTAAAAACTATATATTATATA--AGTTTTC
* * *
1630862 AAAATATTTTTCAAAACCATATAATATAATATA-TTTTC
1 AAAATATTTTTAAAAACTATATATTAT-ATA-AGTTTTC
* * *
1630900 AAAAAAATATTTT-AAAATTATATATTATAT-ATTTTTCC
1 -AAAATAT-TTTTAAAAACTATATATTATATAAGTTTT-C
* *
1630938 AAAAT-GTTTTAAAAATTATATATTATATAAGTTTTC
1 AAAATATTTTTAAAAACTATATATTATATAAGTTTTC
1630974 AAAATATTTTTAAAAACTATATATTATATAAGTTTTC
1 AAAATATTTTTAAAAACTATATATTATATAAGTTTTC
* *
1631011 AAAATGTTTTTAAAAA--ACTATATTATGTAAGTTTTC
1 AAAATATTTTTAAAAACTA-TATATTATATAAGTTTTC
* * *
1631047 TAAAT-GTTTTAAAAACTATATATTATATATATTTTTTC
1 AAAATATTTTTAAAAACTATATATTATATA-A-GTTTTC
* *
1631085 AAAA-ATGTTTTAAAAATTTTATATTATATAAGTTTTC
1 AAAATAT-TTTTAAAAACTATATATTATATAAGTTTTC
1631122 AAAA-ATATTTT--AAACTATATATTATATA
1 AAAATAT-TTTTAAAAACTATATATTATATA
1631150 TATTCAAAAT
Statistics
Matches: 244, Mismatches: 29, Indels: 35
0.79 0.09 0.11
Matches are distributed among these distances:
35 29 0.12
36 55 0.23
37 74 0.30
38 16 0.07
39 57 0.23
40 13 0.05
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.48
Consensus pattern (37 bp):
AAAATATTTTTAAAAACTATATATTATATAAGTTTTC
Found at i:1632096 original size:84 final size:84
Alignment explanation
Indices: 1631826--1632621 Score: 976
Period size: 84 Copynumber: 9.5 Consensus size: 84
1631816 AAATATGGCA
* * * * * * *
1631826 TGCCCTTGAGCTGAATGGAATTGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTATCG-CTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1631889 AGCTATACTGCAAATGATG
66 AGTTATGCTGCAAATGATG
* * * * * * * *
1631908 TTCCTTTGACCTGACTGTAATCGAACTCGAAGGTC-TTGGTTGACAGAAAACCCTTCTCACCTTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1631972 AGTTATGTTGTAAATTGGATG
66 AGTTATGCTGCAAA-T-GATG
* * * *
1631993 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTATTGGCAGATAGCCCTTCTCGCCTAG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
*
1632058 AGCTATGCTGCAAATGATG
66 AGTTATGCTGCAAATGATG
* **
1632077 TGCCTTGGAGCTGAGTGTAATAAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* * *
1632142 AGCTATGTTGTAAATGATG
66 AGTTATGCTGCAAATGATG
* * *
1632161 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGATAACCCTTCTAGCCCTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
**
1632226 AGTTATATTGCAAATGATG
66 AGTTATGCTGCAAATGATG
* * * *
1632245 TGCCTTTGAGCTGAGTGTAATCCAACTCGAAGGTC-TTGGTTGACAGATAACCATTCTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
**
1632309 AGTTATGCTATAAATGATG
66 AGTTATGCTGCAAATGATG
* * * * *
1632328 TGCCTTGGAGCTAAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAGATAGCCCTTTTCGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
* *
1632393 AGCTATGCTGTAAATGATG
66 AGTTATGCTGCAAATGATG
* * * *
1632412 TGCCTTTGAGCTGAGTGTAATCGAAATCGAAGGTCTTGTGTTGGCAGATAACCTTTCTAGCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
*
1632477 AGTTATACTGCAAATGATG
66 AGTTATGCTGCAAATGATG
* * * *
1632496 TGCCTTTGAGTTGAGTGTAATCAAACTCGAAGGTC-TTTCTTGAG-AGATAACCCTTCTAGCCTT
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTG-GCAGATAACCCTTCTCGCCTT
* *
1632559 GAGTTATGTTG-TAATGATG
65 GAGTTATGCTGCAAATGATG
1632578 TGCCTTTGAGCTGAGTGTAATCAGAACTCGAAGGTCTTTTGTTG
1 TGCCTTTGAGCTGAGTGTAATC-GAACTCGAAGGTCTTTTGTTG
1632622 AAGGTGCTTT
Statistics
Matches: 612, Mismatches: 93, Indels: 16
0.85 0.13 0.02
Matches are distributed among these distances:
82 76 0.12
83 126 0.21
84 341 0.56
85 37 0.06
86 32 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTG
AGTTATGCTGCAAATGATG
Found at i:1632360 original size:251 final size:251
Alignment explanation
Indices: 1631829--1632621 Score: 1094
Period size: 251 Copynumber: 3.2 Consensus size: 251
1631819 TATGGCATGC
* * * * *
1631829 CCTT-GAGCTGAATGGAATTGAACTCGAAGGT-ATTTGTTGACAGATAACCCTTATCG-CTTGAG
1 CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAG
* * * * * *
1631891 CTATACTGCAAATGATGTTCCTTTGACCTGACTGTAATCGAACTCGAAGGTCTTG-GTTGACAGA
66 CTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGA
* * * * * *
1631955 AAACCCTTCTCA-CCTTTAGTTATGTTGTAAATTGGATGTGCCTTTGAGCTGAATGTAATCGAAC
131 TAACCCTTCT-AGCCTTGAGTTATATTGCAAA-T-GATGTGCCTTTGAGCTGAGTGTAATCAAAC
* * * * *
1632019 TCGAAGGTCTTTTATTGGCAGATAGCCCTTCTCGCCTAGAGCTATGCTGCAAATGATGTG
193 TCGAAGGTC-TTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTG
** *
1632079 CCTTGGAGCTGAGTGTAATAAAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGCCTTGAG
1 CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAG
*
1632144 CTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGA
66 CTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGA
* *
1632209 TAACCCTTCTAGCCCTGAGTTATATTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCCAACTCG
131 TAACCCTTCTAGCCTTGAGTTATATTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCG
** * *
1632274 AAGGTCTTGGTTGACAGATAACCATTCTCGCCTTGAGTTATGCTATAAATGATGTG
196 AAGGTCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTG
* * * *
1632330 CCTTGGAGCTAAGTGTAATCGAACTCGAAGGTTTTTTGTTGGCAGATAGCCCTTTTCGCCTTGAG
1 CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAG
*
1632395 CTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAAATCGAAGGTCTTGTGTTGGCAGA
66 CTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGA
* * *
1632460 TAACCTTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGTTGAGTGTAATCAAACTCG
131 TAACCCTTCTAGCCTTGAGTTATATTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCG
* * * *
1632525 AAGGTCTTTCTTGAGAGATAACCCTTCTAGCCTTGAGTTATGTTGT-AATGATGTG
196 AAGGTCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTG
*
1632580 CCTTTGAGCTGAGTGTAATCAGAACTCGAAGGTCTTTTGTTG
1 CCTTGGAGCTGAGTGTAATC-GAACTCGAAGGTCTTTTGTTG
1632622 AAGGTGCTTT
Statistics
Matches: 484, Mismatches: 53, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
250 31 0.06
251 305 0.63
252 59 0.12
253 57 0.12
254 32 0.07
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (251 bp):
CCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTATCGCCTTGAG
CTATGCTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGGCAGA
TAACCCTTCTAGCCTTGAGTTATATTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCG
AAGGTCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTG
Found at i:1634785 original size:40 final size:40
Alignment explanation
Indices: 1634740--1634828 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 40
1634730 GTTTACATTC
* *
1634740 CAAACGCCACAAAATG-GTA-ACTTTAGCGGCGTTTTTATA
1 CAAACGCCACAAAA-GAGTAGACTTTAGCGACATTTTTATA
* *
1634779 CAAAACGCCACGACAGAGTAGTACTTTAGCGACATTTTTATA
1 C-AAACGCCACAAAAGAGTAG-ACTTTAGCGACATTTTTATA
1634821 CAAACGCC
1 CAAACGCC
1634829 GCAATAGGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
39 2 0.05
40 14 0.33
41 7 0.17
42 19 0.45
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (40 bp):
CAAACGCCACAAAAGAGTAGACTTTAGCGACATTTTTATA
Found at i:1634899 original size:41 final size:41
Alignment explanation
Indices: 1634861--1635156 Score: 310
Period size: 41 Copynumber: 7.2 Consensus size: 41
1634851 CATTTTTTCA
* *
1634861 ACAAACGTCG-TGATAGAGTAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGTCGCT-ATAGACTCGTACTTTAGTGGCGTTTTTAT
* ** * *
1634902 AAAAACAACGCTATAGA-TGCGTATTTTAGTGGCGTTTTGAT
1 ACAAACGTCGCTATAGACT-CGTACTTTAGTGGCGTTTTTAT
* * * *
1634943 ACAAACGCCGTTATATACTCGTACTTTAGTGGCGTTTGTGTTT
1 ACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTT-T-TAT
* * **
1634986 ACAAACGCCACTATAGACTCGTACGGTAGTGGCGTTTTTAT
1 ACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* *
1635027 ACAAACGTCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
1 ACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* * *
1635068 ATAAACGTCGCTATTGACTCTTACTTTAGTGGCGTTTTTAT
1 ACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
* * * *
1635109 AAAAATGCCGCTAAAGACTCGT-CTTTTAGTGGCGTTTTTAT
1 ACAAACGTCGCTATAGACTCGTAC-TTTAGTGGCGTTTTTAT
1635150 ACAAACG
1 ACAAACG
1635157 CCACAAATTT
Statistics
Matches: 210, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.01
41 171 0.81
42 4 0.02
43 33 0.16
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
ACAAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTTAT
Found at i:1635021 original size:125 final size:123
Alignment explanation
Indices: 1634887--1635155 Score: 310
Period size: 125 Copynumber: 2.2 Consensus size: 123
1634877 AGTAGTACTT
* * * *
1634887 TAGTGGCGTTTTTATAAAAACAACGCTATAGA-TGCGTATTTTAGTGGCGTTTTGATACAAACGC
1 TAGTGGCGTTTTTATACAAACAACGCTAAAGACT-CGTACTTTAGTGGCATTTTGATACAAACGC
* * * *
1634951 CGTTATAT-ACTCGTACTTTAGTGGCGTTTGTGTTTACAAACGCCACTATAGACTCGTAC-GG
65 CGCTAT-TGACTCGTACTTTAGTGGCGTTT-T-TATAAAAACGCCACTAAAGACTCGT-CTGG
** * * *
1635012 TAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTACTTTAGTGGCATTTTTATATAAACGTC
1 TAGTGGCGTTTTTATACAAACAACGCTAAAGACTCGTACTTTAGTGGCATTTTGATACAAACGCC
* * * **
1635077 GCTATTGACTCTTACTTTAGTGGCGTTTTTATAAAAATGCCGCTAAAGACTCGTCTTT
66 GCTATTGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCACTAAAGACTCGTCTGG
1635135 TAGTGGCGTTTTTATACAAAC
1 TAGTGGCGTTTTTATACAAAC
1635156 GCCACAAATT
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
122 1 0.01
123 41 0.33
124 2 0.02
125 78 0.63
126 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (123 bp):
TAGTGGCGTTTTTATACAAACAACGCTAAAGACTCGTACTTTAGTGGCATTTTGATACAAACGCC
GCTATTGACTCGTACTTTAGTGGCGTTTTTATAAAAACGCCACTAAAGACTCGTCTGG
Found at i:1638992 original size:43 final size:43
Alignment explanation
Indices: 1638881--1639420 Score: 698
Period size: 43 Copynumber: 12.7 Consensus size: 43
1638871 AAGGTAATTA
* *
1638881 GCGGCGTTTGT-TCCAAAAACGCCGCTATATATATGACCATTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
1638923 GCGGCATTTGT-TCCAAAAACGTCGCTATAGATATAACGTTCT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
1638965 ACGGCGTTTGTATCCAAAAACACCGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
1639008 GCGGCGTTTGT-TTCAAAAACGCTGCTACAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
*
1639050 GCGGCGTTTGTATCCAAAAATGCCGCTATAG-TATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
*
1639092 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGATCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * *
1639134 TCGGAGTTTGTATCCAAAAACGCCACTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
1639177 GTGGCGTTTGT-TCCAAAAACGCTGCTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
1639219 GCGGCATTTGAATCCAAAAAAGTCGCTATAAATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
1639262 GCGGCATATGTATCCAAAAACTCCGCTATAGATATTACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
1639305 GTGGCGTTTGTATCCAAAAACGCCACTATAGATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
** ** *
1639348 GCGGCGTTTGTATAAAAAAAAACCGCTATAAATATGACCTTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
* *
1639391 GCGGTGTTTGT-TCCAAAAACGTCGCTATAG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAG
1639421 TTTTTGACCT
Statistics
Matches: 425, Mismatches: 68, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
41 18 0.04
42 173 0.41
43 234 0.55
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:1639025 original size:85 final size:84
Alignment explanation
Indices: 1638881--1639420 Score: 656
Period size: 85 Copynumber: 6.4 Consensus size: 84
1638871 AAGGTAATTA
* * *
1638881 GCGGCGTTTGT-TCCAAAAACGCCGCTATATATATGACCATTTGCGGCATTTGTTCCAAAAACGT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACG-
* *
1638945 CGCTATAGATATAACGTTCT
65 CGCTATAGATATAACCTTTT
* * *
1638965 ACGGCGTTTGTATCCAAAAACACCGCTATAGATATGACCTTTTGCGGCGTTTGTTTCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
* *
1639030 TGCTACAGATATGACCTTTT
66 -GCTATAGATATAACCTTTT
*
1639050 GCGGCGTTTGTATCCAAAAATGCCGCTATAG-TATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACG-
* *
1639114 CGCTATAGATATGATCTTTT
65 CGCTATAGATATAACCTTTT
* * * *
1639134 TCGGAGTTTGTATCCAAAAACGCCACTATAGATATGACCTTTTGTGGCGTTTGTTCCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
*
1639199 TGCTATAGATATGACCTTTT
66 -GCTATAGATATAACCTTTT
* * * * * * *
1639219 GCGGCATTTGAATCCAAAAAAGTCGCTATAAATATGACCTTTTGCGGCATATGTATCCAAAAACT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT-TCCAAAAAC-
* *
1639284 CCGCTATAGATATTACCTTTT
64 GCGCTATAGATATAACCTTTT
* * **
1639305 GTGGCGTTTGTATCCAAAAACGCCACTATAGATATGACCTTTTGCGGCGTTTGTATAAAAAAAAA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT-T--CCAAAAA
* *
1639370 C-CGCTATAAATATGACCTTTT
63 CGCGCTATAGATATAACCTTTT
* *
1639391 GCGGTGTTTGT-TCCAAAAACGTCGCTATAG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAG
1639421 TTTTTGACCT
Statistics
Matches: 395, Mismatches: 52, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
84 87 0.22
85 200 0.51
86 101 0.26
87 1 0.00
88 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (84 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
GCTATAGATATAACCTTTT
Found at i:1642078 original size:4 final size:4
Alignment explanation
Indices: 1642069--1642099 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1642059 AAAACCGTGA
1642069 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1642100 AATAAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1642721 original size:17 final size:16
Alignment explanation
Indices: 1642699--1642733 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
1642689 TGTAAATGAT
1642699 AAAAAATGAAAAAGAAA
1 AAAAAATG-AAAAGAAA
1642716 AAAAAATGAAAAGAAA
1 AAAAAATGAAAAGAAA
1642732 AA
1 AA
1642734 GTTAGTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAATGAAAAGAAA
Found at i:1643639 original size:6 final size:6
Alignment explanation
Indices: 1643628--1643655 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1643618 TTAAATCGCG
1643628 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
1643656 AAACCGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:1645233 original size:38 final size:37
Alignment explanation
Indices: 1645062--1645364 Score: 289
Period size: 36 Copynumber: 8.0 Consensus size: 37
1645052 AAATAAATAT
* * *
1645062 TTTTTAAAACTATATTTTATATAT-GATTTTTAAAACTG
1 TTTTAAAAACTATATATTATATATAG-TTTTCAAAA-TG
* * * *
1645100 TTTTTCAAAACCATATAATATAATATA-TTTTCAAAACAAATA
1 -TTTTAAAAACTATATATTAT-ATATAGTTTTC---A-AAATG
*
1645142 TTTT-AAAATTATATATTATATATA-TTTTCCAAAATG
1 TTTTAAAAACTATATATTATATATAGTTTT-CAAAATG
*
1645178 TTTTAAAAATTATATATTATATA-AGTTTTCAAAATG
1 TTTTAAAAACTATATATTATATATAGTTTTCAAAATG
*
1645214 TTTTTAAAAAACTATATATTATATA-AGTTTTCCAAATG
1 -TTTT-AAAAACTATATATTATATATAGTTTTCAAAATG
1645252 TTTTAAAAACTATATATTATATATA-TATATTCAAAAATG
1 TTTTAAAAACTATATATTATATATAGT-T-TTC-AAAATG
*
1645291 TTTTAAAAACTATATATTATATA-AGTTTTCAAAATA
1 TTTTAAAAACTATATATTATATATAGTTTTCAAAATG
** *
1645327 TTTTTTAAACTATATATTATATATATATTTTCAAAATG
1 TTTTAAAAACTATATATTATATATA-GTTTTCAAAATG
1645365 ACTTTAAACT
Statistics
Matches: 228, Mismatches: 18, Indels: 37
0.81 0.06 0.13
Matches are distributed among these distances:
36 62 0.27
37 37 0.16
38 45 0.20
39 58 0.25
40 17 0.07
41 4 0.02
42 2 0.01
43 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATAGTTTTCAAAATG
Found at i:1645350 original size:113 final size:109
Alignment explanation
Indices: 1645062--1645379 Score: 336
Period size: 113 Copynumber: 2.8 Consensus size: 109
1645052 AAATAAATAT
* * * * * * * *
1645062 TTTTTAAAACTATATTTTATATATGATTTTTAAAACTGTTTTTCAAAACCATATAATATAATATA
1 TTTTAAAAACTATATATTATATAAG-TTTTCAAAA-TATTTTTAAAAACTATATATTAT-ATATA
* * *
1645127 TTTTCAAAACAAATATTTTAAAATTATATATTATATATATTTTCCAAAATG
63 TTTTC----CAAATGTTTTAAAACTATATATTATATATATTTTCAAAAATG
* *
1645178 TTTTAAAAATTATATATTATATAAGTTTTCAAAATGTTTTTAAAAAACTATATATTATATA-AGT
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTT-AAAAACTATATATTATATATA-T
1645242 TTTCCAAATGTTTTAAAAACTATATATTATATATATATATTCAAAAATG
64 TTTCCAAATGTTTT-AAAACTATATATTATATATAT-T-TTCAAAAATG
*
1645291 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTT-TAAACTATATATTATATATATAT
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTTAAAAACTATATA-T-TATATATAT
* *
1645355 TTTCAAAATGACTTT-AAACTATATA
64 TTTCCAAATG-TTTTAAAACTATATA
1645380 ATATGTGCAC
Statistics
Matches: 177, Mismatches: 16, Indels: 22
0.82 0.07 0.10
Matches are distributed among these distances:
110 9 0.05
111 30 0.17
112 12 0.07
113 65 0.37
114 19 0.11
115 21 0.12
116 21 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (109 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTTAAAAACTATATATTATATATATTT
TCCAAATGTTTTAAAACTATATATTATATATATTTTCAAAAATG
Found at i:1645371 original size:75 final size:75
Alignment explanation
Indices: 1645062--1645379 Score: 326
Period size: 75 Copynumber: 4.2 Consensus size: 75
1645052 AAATAAATAT
* * * * * * *
1645062 TTTTTAAAACTATATTTTATATATGATTTTTAAAACTGTTTTTCAAAACCATATAATATA-ATAT
1 TTTTAAAAACTATATATTATATAAG-TTTTCAAAA-TG-TTTTAAAAACTATATATTATATATAT
**
1645126 ATTTTCAAAACAAA
63 ATTTTCAAAA-TGA
* * *
1645140 TATTTTAAAATTATATATTATATATA-TTTTCCAAAATGTTTTAAAAATTATATATTATATA-A-
1 T-TTTAAAAACTATATATTATATA-AGTTTT-CAAAATGTTTTAAAAACTATATATTATATATAT
* *
1645202 GTTTTCAAAATGT
63 ATTTTCAAAATGA
*
1645215 TTTTAAAAAACTATATATTATATAAGTTTTCCAAATGTTTTAAAAACTATATATTATATATATAT
1 TTTT-AAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATTATATATATAT
*
1645280 ATTCAAAAATG-
65 TTTC-AAAATGA
* **
1645291 TTTTAAAAACTATATATTATATAAGTTTTCAAAATATTTTTTAAACTATATATTATATATATATT
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATTATATATATATT
1645356 TTCAAAATGA
66 TTCAAAATGA
*
1645366 CTTT--AAACTATATA
1 TTTTAAAAACTATATA
1645380 ATATGTGCAC
Statistics
Matches: 206, Mismatches: 24, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
73 10 0.05
74 38 0.18
75 85 0.41
76 17 0.08
77 24 0.12
78 8 0.04
79 24 0.12
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (75 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATTATATATATATT
TTCAAAATGA
Found at i:1646292 original size:19 final size:19
Alignment explanation
Indices: 1646270--1646310 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1646260 TTAATCTACG
*
1646270 ATTATAATTGTAA-ATTTTT
1 ATTATAATT-TAAGATATTT
1646289 ATTATAATTTAAGATATTT
1 ATTATAATTTAAGATATTT
1646308 ATT
1 ATT
1646311 TTTGAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTATAATTTAAGATATTT
Found at i:1647856 original size:2 final size:2
Alignment explanation
Indices: 1647849--1647903 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1647839 AACACTTATG
1647849 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1647891 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1647904 GATACTACGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1652170 original size:19 final size:20
Alignment explanation
Indices: 1652128--1652170 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1652118 GAGAATGAAG
* *
1652128 AAAATCAGGGTTTTTATCAG
1 AAAATAAGGGTTTTTATCAC
1652148 AAAATAAGGGTTTTTATC-C
1 AAAATAAGGGTTTTTATCAC
1652167 AAAA
1 AAAA
1652171 ACCCGACGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (20 bp):
AAAATAAGGGTTTTTATCAC
Found at i:1652171 original size:20 final size:20
Alignment explanation
Indices: 1652126--1652165 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1652116 GAGAGAATGA
*
1652126 AGAAAATCAGGGTTTTTATC
1 AGAAAATAAGGGTTTTTATC
1652146 AGAAAATAAGGGTTTTTATC
1 AGAAAATAAGGGTTTTTATC
1652166 CAAAAACCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (20 bp):
AGAAAATAAGGGTTTTTATC
Found at i:1652215 original size:23 final size:22
Alignment explanation
Indices: 1652181--1652261 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 22
1652171 ACCCGACGGA
1652181 TGCATCGATGCACATTCAAGGCG
1 TGCATCGATGCACATTCAAGG-G
* * *
1652204 TGCATCGGTGCACCTTC-ATGG
1 TGCATCGATGCACATTCAAGGG
*
1652225 TGTATCGATGCACATTCAAAGGG
1 TGCATCGATGCACATTC-AAGGG
1652248 ATGCATCGATGCAC
1 -TGCATCGATGCAC
1652262 TGTTAGTGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 15 0.32
22 2 0.04
23 18 0.38
24 12 0.26
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGG
Found at i:1660111 original size:21 final size:21
Alignment explanation
Indices: 1660085--1660125 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1660075 TTCATTACTG
*
1660085 TAGTAGTGCATCGATACACTA
1 TAGTAGTGAATCGATACACTA
*
1660106 TAGTAGTGAATCGGTACACT
1 TAGTAGTGAATCGATACACT
1660126 GTAGCAGTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (21 bp):
TAGTAGTGAATCGATACACTA
Found at i:1660405 original size:18 final size:19
Alignment explanation
Indices: 1660359--1660414 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
1660349 ATATTTAATG
* *
1660359 AAAAAGACATTAATTGTTTC
1 AAAAAGATATCAATTG-TTC
*
1660379 AAAAGGATATCAATTGTT-
1 AAAAAGATATCAATTGTTC
*
1660397 AAAAAGATACCAATTGTT
1 AAAAAGATATCAATTGTT
1660415 GGAAAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 16 0.52
19 2 0.06
20 13 0.42
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (19 bp):
AAAAAGATATCAATTGTTC
Found at i:1662479 original size:34 final size:33
Alignment explanation
Indices: 1662432--1662499 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
1662422 TTACAACTGT
*
1662432 CTAGTTTTTCACGGGATAAACTAGAACATTTCC
1 CTAGTTTTACACGGGATAAACTAGAACATTTCC
* ** *
1662465 CTAGATTTTACACGGGCTATGCTAGAACCTTTCC
1 CTAG-TTTTACACGGGATAAACTAGAACATTTCC
1662499 C
1 C
1662500 CTTTACAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (33 bp):
CTAGTTTTACACGGGATAAACTAGAACATTTCC
Found at i:1663414 original size:139 final size:139
Alignment explanation
Indices: 1663163--1663836 Score: 698
Period size: 139 Copynumber: 4.8 Consensus size: 139
1663153 TCAATCTGGA
* * * * *
1663163 GATAATTTGGTGACAACACAGTTCCTACGTGATGAGGAAGTTTGATTGTCTGAGGGTGACACTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGC
* * * * * * *
1663228 TCCTTA-TCATTGA-GAGGATCT-AGTTGGTGGACGACAATGTTCCTACGTGATGAGGACATCTA
66 T-CATACGCATTGAGGA-GATCTGA-TCGGTAGACAACATTGTTCCTACGTGATGAGGACGTCTA
1663290 GCCGTCTTTAGG
128 GCCGTCTTTAGG
* ** * * *
1663302 GATAATTTGGCGACAACATTGTTCCTACGTGATTGA-GAAATCTGATTGTCTGAGGATGACACTA
1 GATAATTTGGAGACAACACGGTTCCTACGTGA-TGAGGAAGTCTGATTATCTGAGGATGACACTG
* * * * * *
1663366 CTCTTTCGCGTTGAGGAGATCT-AGTCGATAGACGACATTGTTCATACGTGATGAGGACGTCTAG
65 CTCATACGCATTGAGGAGATCTGA-TCGGTAGACAACATTGTTCCTACGTGATGAGGACGTCTAG
1663430 CCGTCTTTAGG
129 CCGTCTTTAGG
* * * * *
1663441 GATAATTTGGAGACAACATGGTTCCTACGTGATGAGTAAGTCTGGTTATCAGAGGATGACGCTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGC
* * * * **
1663506 TCATACGCATTGAGGAGATCTGATCGG-AGAACAACATTGTTTCTACTTTATGAGGATGTCTAAT
66 TCATACGCATTGAGGAGATCTGATCGGTAG-ACAACATTGTTCCTACGTGATGAGGACGTCTAGC
*
1663570 TGTCTTTAGG
130 CGTCTTTAGG
* * *
1663580 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGGTTATATGAGGATGACGCTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGC
** * * * *
1663645 TCATACGTGTTGAGGAGATATGATTGGTGGACAACATTGTTCCTACGTGATAAGGACGTCTAGCC
66 TCATACGCATTGAGGAGATCTGATCGGTAGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
1663710 GTCTTTAGG
131 GTCTTTAGG
* * * * *
1663719 GATAATTTGGAGACAACACGGTTCATACATGATGAGGAAGTCTGGTTATATGAGGATGACGA-TC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGAC-ACTG
* * * * * * * *
1663783 CTCCTACGCGTTAAGGATATCTAATCAGTGGA-ATACATTGTTCCTATGTGATGA
65 CTCATACGCATTGAGGAGATCTGATCGGTAGACA-ACATTGTTCCTACGTGATGA
1663837 TAACGGCGGC
Statistics
Matches: 457, Mismatches: 69, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
138 9 0.02
139 441 0.96
140 7 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (139 bp):
GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGC
TCATACGCATTGAGGAGATCTGATCGGTAGACAACATTGTTCCTACGTGATGAGGACGTCTAGCC
GTCTTTAGG
Found at i:1673822 original size:17 final size:17
Alignment explanation
Indices: 1673800--1673835 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1673790 TATTGGTTCG
1673800 TGCAAAAGGAAATAAGT
1 TGCAAAAGGAAATAAGT
1673817 TGCAAAAGGAAATAAGT
1 TGCAAAAGGAAATAAGT
1673834 TG
1 TG
1673836 GTGCTTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (17 bp):
TGCAAAAGGAAATAAGT
Found at i:1674849 original size:60 final size:60
Alignment explanation
Indices: 1674769--1674902 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
1674759 TAGAACGTTC
** * * * *
1674769 AAAAAGTTTTGGGACCAATTTAGAAA-GAG-GTTCATAGTTTAGGGATGAAATTGAAATATT
1 AAAAAGTTTAAGGACCAATTT-GAAATGAGAG-TCATAATTTAAGGATAAAATTAAAATATT
* * *
1674829 CATAAGTTTAAGGACTAATTTGAAATGAGAGTCATAATTTAAGGATAAAATTAAAATATT
1 AAAAAGTTTAAGGACCAATTTGAAATGAGAGTCATAATTTAAGGATAAAATTAAAATATT
1674889 AAAAAGTTTAAGGA
1 AAAAAGTTTAAGGA
1674903 TAGTTTAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
59 4 0.07
60 56 0.92
61 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.31
Consensus pattern (60 bp):
AAAAAGTTTAAGGACCAATTTGAAATGAGAGTCATAATTTAAGGATAAAATTAAAATATT
Found at i:1674851 original size:29 final size:29
Alignment explanation
Indices: 1674799--1674904 Score: 92
Period size: 29 Copynumber: 3.6 Consensus size: 29
1674789 TAGAAAGAGG
* *
1674799 TTCAT-AGTTTAGGGATGAAATTGAAATA
1 TTCATAAGTTTAAGGATAAAATTGAAATA
*
1674827 TTCATAAGTTTAAGGACT-AATTTGAAATGAGA
1 TTCATAAGTTTAAGGA-TAAAATTGAAAT---A
* *
1674859 GTCATAA-TTTAAGGATAAAATTAAAATA
1 TTCATAAGTTTAAGGATAAAATTGAAATA
* *
1674887 TTAAAAAGTTTAAGGATA
1 TTCATAAGTTTAAGGATA
1674905 GTTTAAAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
28 10 0.16
29 28 0.44
30 2 0.03
31 16 0.25
32 7 0.11
ACGTcount: A:0.45, C:0.04, G:0.17, T:0.34
Consensus pattern (29 bp):
TTCATAAGTTTAAGGATAAAATTGAAATA
Found at i:1676514 original size:5 final size:5
Alignment explanation
Indices: 1676360--1676495 Score: 168
Period size: 5 Copynumber: 26.0 Consensus size: 5
1676350 AGCATACATA
*
1676360 TATAT TATAT TATAT AGTACAT TATA- TA-AT TATAAGTT TATAT TATAT
1 TATAT TATAT TATAT --TATAT TATAT TATAT TAT-A--T TATAT TATAT
*
1676408 AGTATAAA TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 --TAT-AT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1676456 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1676496 GTTTATACTA
Statistics
Matches: 117, Mismatches: 4, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
3 1 0.01
4 4 0.03
5 95 0.81
6 4 0.03
7 8 0.07
8 5 0.04
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:1676560 original size:16 final size:17
Alignment explanation
Indices: 1676541--1676584 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
1676531 ATTGTGTATT
*
1676541 TATATTTTAT-AATACA
1 TATATTATATCAATACA
*
1676557 TATATTATATCAGTACA
1 TATATTATATCAATACA
1676574 TATTATTATAT
1 TA-TATTATAT
1676585 ATTACTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.38
17 7 0.29
18 8 0.33
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATTATATCAATACA
Found at i:1683798 original size:39 final size:39
Alignment explanation
Indices: 1683755--1683843 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
1683745 ATTTGGTCAC
*
1683755 AGGCCCAGTGACTACGACTCCAGTTATAGATGGGGTAAT
1 AGGCCCAGTGACTACGACTCCAGCTATAGATGGGGTAAT
1683794 AGGCCCAGTGACTACGACTCCAGCTATAGATGGGGTAAT
1 AGGCCCAGTGACTACGACTCCAGCTATAGATGGGGTAAT
*
1683833 AGGCCTAGTGA
1 AGGCCCAGTGA
1683844 TTACTCCCGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (39 bp):
AGGCCCAGTGACTACGACTCCAGCTATAGATGGGGTAAT
Found at i:1683857 original size:18 final size:18
Alignment explanation
Indices: 1683834--1683886 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1683824 TGGGGTAATA
*
1683834 GGCCTAGTGATTACTCCC
1 GGCCTAGCGATTACTCCC
1683852 GGCCTAGCGATTACTCCC
1 GGCCTAGCGATTACTCCC
*
1683870 GACCTAGCGATTACTCC
1 GGCCTAGCGATTACTCC
1683887 AGATGGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.36, G:0.21, T:0.25
Consensus pattern (18 bp):
GGCCTAGCGATTACTCCC
Found at i:1686592 original size:4 final size:4
Alignment explanation
Indices: 1686583--1686673 Score: 119
Period size: 4 Copynumber: 22.8 Consensus size: 4
1686573 TGCTCTTTAT
*
1686583 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG GTGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
* * * * * *
1686631 GTGG ATGG GTGG ATGG GTGG ATGG GTGG GTGG ATGG GTGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATG
1686674 TGTGTATGTG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 75 1.00
ACGTcount: A:0.18, C:0.00, G:0.57, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:1686682 original size:8 final size:8
Alignment explanation
Indices: 1686671--1686743 Score: 82
Period size: 8 Copynumber: 9.6 Consensus size: 8
1686661 GGATGGGTGG
1686671 ATGTGTGT
1 ATGTGTGT
1686679 ATGTGTGT
1 ATGTGTGT
1686687 A--TGTG-
1 ATGTGTGT
1686692 -TGTGTGT
1 ATGTGTGT
1686699 ATGTGTGT
1 ATGTGTGT
1686707 ATGTGTGT
1 ATGTGTGT
1686715 ATGTGTGT
1 ATGTGTGT
* *
1686723 GTGTATGT
1 ATGTGTGT
* *
1686731 GTGTATGT
1 ATGTGTGT
1686739 ATGTG
1 ATGTG
1686744 CCATATCATT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
6 8 0.14
8 49 0.86
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.49
Consensus pattern (8 bp):
ATGTGTGT
Found at i:1686697 original size:12 final size:12
Alignment explanation
Indices: 1686676--1686743 Score: 91
Period size: 12 Copynumber: 5.7 Consensus size: 12
1686666 GGTGGATGTG
1686676 TGTATGTGTGTA
1 TGTATGTGTGTA
*
1686688 TGTGTGTGTGTA
1 TGTATGTGTGTA
* * *
1686700 TGTGTGTATGTG
1 TGTATGTGTGTA
*
1686712 TGTATGTGTGTG
1 TGTATGTGTGTA
1686724 TGTATGTGTGTA
1 TGTATGTGTGTA
1686736 TGTATGTG
1 TGTATGTG
1686744 CCATATCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (12 bp):
TGTATGTGTGTA
Found at i:1686697 original size:20 final size:20
Alignment explanation
Indices: 1686676--1686743 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
1686666 GGTGGATGTG
*
1686676 TGTATGTGTGTATGTGTGTG
1 TGTATGTGTGTATGTGTGTA
1686696 TGTATGTGTGTATGTGTGTA
1 TGTATGTGTGTATGTGTGTA
*
1686716 TGTGTGTGTGTATGTGTGTA
1 TGTATGTGTGTATGTGTGTA
1686736 TGTATGTG
1 TGTATGTG
1686744 CCATATCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (20 bp):
TGTATGTGTGTATGTGTGTA
Found at i:1686711 original size:28 final size:28
Alignment explanation
Indices: 1686671--1686738 Score: 136
Period size: 28 Copynumber: 2.4 Consensus size: 28
1686661 GGATGGGTGG
1686671 ATGTGTGTATGTGTGTATGTGTGTGTGT
1 ATGTGTGTATGTGTGTATGTGTGTGTGT
1686699 ATGTGTGTATGTGTGTATGTGTGTGTGT
1 ATGTGTGTATGTGTGTATGTGTGTGTGT
1686727 ATGTGTGTATGT
1 ATGTGTGTATGT
1686739 ATGTGCCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (28 bp):
ATGTGTGTATGTGTGTATGTGTGTGTGT
Found at i:1693394 original size:18 final size:17
Alignment explanation
Indices: 1693368--1693405 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1693358 CAAAGCTCTC
1693368 GAAAGGAAGAGGAAGAG
1 GAAAGGAAGAGGAAGAG
1693385 GAAGAGGAAGAGGAA-AG
1 GAA-AGGAAGAGGAAGAG
1693402 GAAA
1 GAAA
1693406 AGTGGAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 8 0.40
18 11 0.55
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (17 bp):
GAAAGGAAGAGGAAGAG
Found at i:1693407 original size:6 final size:6
Alignment explanation
Indices: 1693371--1693404 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
1693361 AGCTCTCGAA
1693371 AGGAAG AGGAAG AGGAAG AGGAAG AGGAA- AGGAA
1 AGGAAG AGGAAG AGGAAG AGGAAG AGGAAG AGGAA
1693405 AAGTGGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:1694724 original size:32 final size:32
Alignment explanation
Indices: 1694687--1694748 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
1694677 TCAAACATCA
*
1694687 TTATTAAATTAATAACTTAATAATATAATTCG
1 TTATTAAATTAACAACTTAATAATATAATTCG
*
1694719 TTATTAAATTAACGACTTAATAATATAATT
1 TTATTAAATTAACAACTTAATAATATAATT
1694749 AAAACAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (32 bp):
TTATTAAATTAACAACTTAATAATATAATTCG
Found at i:1696178 original size:21 final size:21
Alignment explanation
Indices: 1696154--1696249 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
1696144 TTCAAAGAAA
1696154 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1696175 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1696189 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
1696210 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
1696224 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
1696245 CATTT
1 CATTT
1696250 TTTCAAAGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 28
0.64 0.04 0.31
Matches are distributed among these distances:
14 10 0.18
15 14 0.25
16 2 0.04
19 2 0.04
20 14 0.25
21 15 0.26
ACGTcount: A:0.44, C:0.21, G:0.05, T:0.30
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:1696188 original size:35 final size:35
Alignment explanation
Indices: 1696106--1696250 Score: 238
Period size: 35 Copynumber: 4.1 Consensus size: 35
1696096 CCATTATCAT
* * *
1696106 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAACCA
1696141 TTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1696177 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1696212 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1696247 TTTT
1 TTTT
1696251 TTCAAAGTTG
Statistics
Matches: 105, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
35 74 0.70
36 11 0.10
37 20 0.19
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:1696266 original size:70 final size:70
Alignment explanation
Indices: 1696121--1696285 Score: 228
Period size: 70 Copynumber: 2.3 Consensus size: 70
1696111 AACAAACATC
*
1696121 TACCAAACTTTGAAAAACTATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 TACCAAACTTTGAAAAACCA-TTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAG
*
1696186 AAACATT
65 -AACAGT
1696193 TACCAAACTTTG-AAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTTTCAAA
1 TACCAAACTTTGAAAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCA--TTTTCAAA
***
1696257 G-TTGGT
64 GAACAGT
1696263 TACCAAAC-TTGAAAAACCATTTT
1 TACCAAACTTTGAAAAACCATTTT
1696286 AATACTTTCA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
69 3 0.04
70 55 0.65
71 6 0.07
72 21 0.25
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.32
Consensus pattern (70 bp):
TACCAAACTTTGAAAAACCATTTTCAAAGAAACATTTACCAAACTTTGAAAACCATTTTCAAAGA
ACAGT
Found at i:1700794 original size:37 final size:34
Alignment explanation
Indices: 1700732--1700850 Score: 152
Period size: 34 Copynumber: 3.4 Consensus size: 34
1700722 ATCTCATTAT
*
1700732 CATTTTTCAACA-AACAATTACCAAACTTTGAAAAA
1 CATTTTTCAA-AGAACATTTACCAAACTTTG-AAAA
1700767 CTATTTTTCAAAGATACATTTACCAAACTTTGAAAA
1 C-ATTTTTCAAAGA-ACATTTACCAAACTTTGAAAA
1700803 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAA
1 CATTTTTCAAAG-AACATTTACCAAACTTTGAAAA
1700837 CCATTTTTTCAAAG
1 -CA-TTTTTCAAAG
1700851 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 1, Indels: 12
0.85 0.01 0.13
Matches are distributed among these distances:
34 30 0.39
35 6 0.08
36 15 0.20
37 25 0.33
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (34 bp):
CATTTTTCAAAGAACATTTACCAAACTTTGAAAA
Found at i:1701006 original size:41 final size:37
Alignment explanation
Indices: 1700949--1701028 Score: 106
Period size: 41 Copynumber: 2.1 Consensus size: 37
1700939 GTTTGTTGTA
1700949 GCCTGAAGGGCAAGTCTAAACATATTGTTGCTTTTAAGTTG
1 GCCTGAAGGGCAAGTCTAAAC----TGTTGCTTTTAAGTTG
* *
1700990 GCCTGAATGTCAAGTCTAAACTGTTGCTTTTAAGTTG
1 GCCTGAAGGGCAAGTCTAAACTGTTGCTTTTAAGTTG
1701027 GC
1 GC
1701029 TAATATACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
37 18 0.49
41 19 0.51
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (37 bp):
GCCTGAAGGGCAAGTCTAAACTGTTGCTTTTAAGTTG
Found at i:1701940 original size:20 final size:21
Alignment explanation
Indices: 1701897--1701940 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1701887 CTATTTCTAA
*
1701897 ATTAAATTCAATATTTTTTGT
1 ATTAAATTCAATATTTTTTAT
* *
1701918 ATTAAATTTATTA-TTTTTAT
1 ATTAAATTCAATATTTTTTAT
1701938 ATT
1 ATT
1701941 TCTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTAAATTCAATATTTTTTAT
Found at i:1702043 original size:20 final size:20
Alignment explanation
Indices: 1702018--1702065 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1702008 AAGTATGAAT
*
1702018 AAATATTGAATTTAATTTTA
1 AAATATTAAATTTAATTTTA
*
1702038 AAATATAAAATTTAATTTTA
1 AAATATTAAATTTAATTTTA
*
1702058 AATTATTA
1 AAATATTA
1702066 TTTTGGGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAATATTAAATTTAATTTTA
Found at i:1708314 original size:17 final size:18
Alignment explanation
Indices: 1708280--1708317 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1708270 AAAAAATTGC
1708280 TAACGAAAACTAATAAAA
1 TAACGAAAACTAATAAAA
1708298 TAAC-AAAATCTAA-AAAA
1 TAACGAAAA-CTAATAAAA
1708315 TAA
1 TAA
1708318 AATAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.11, G:0.03, T:0.18
Consensus pattern (18 bp):
TAACGAAAACTAATAAAA
Found at i:1708333 original size:22 final size:22
Alignment explanation
Indices: 1708291--1708333 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1708281 AACGAAAACT
**
1708291 AATAAAATAACAAAATCTAAAA
1 AATAAAATAACAAAAAATAAAA
1708313 AATAAAATAA-AATAAAATAAA
1 AATAAAATAACAA-AAAATAAA
1708334 TGAACTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.19
Consensus pattern (22 bp):
AATAAAATAACAAAAAATAAAA
Found at i:1709131 original size:23 final size:23
Alignment explanation
Indices: 1709086--1709149 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
1709076 CAACTCATAT
1709086 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
** * * **
1709109 ATTTTCACCGAAGTGTCGTGTAG
1 AAATGCACCGAAGTGCCACGTAG
1709132 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1709150 TATAAGATGT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:1715955 original size:23 final size:23
Alignment explanation
Indices: 1715920--1715980 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
1715910 CAACTCATAT
*
1715920 AAATGCACCGAAGTGACACGTAG
1 AAATACACCGAAGTGACACGTAG
** * * *
1715943 ATTTTCACCGAAGTGTCGCGTAG
1 AAATACACCGAAGTGACACGTAG
1715966 AAATACACCGAAGTG
1 AAATACACCGAAGTG
1715981 CCATATAAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATACACCGAAGTGACACGTAG
Found at i:1721620 original size:41 final size:41
Alignment explanation
Indices: 1721575--1721676 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
1721565 AAGGTCTTAT
* * *
1721575 AGATGGCCCAAAGGACTTATGATCTTGCTCGAAAGACTGAC
1 AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* * *
1721616 AGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTGAC
* *
1721658 TGATGGCCTGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
1721677 CCAATTTTGG
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:1721795 original size:256 final size:257
Alignment explanation
Indices: 1721328--1722071 Score: 1125
Period size: 256 Copynumber: 2.9 Consensus size: 257
1721318 AAAAAGCTCT
* * * *
1721328 AAAGGTCTTATCATCTTGCTTGAAATACTGACAGATGACCTGAAGAATTTAATCATCATGCTCGA
1 AAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATCATCATGCTCGA
* * * *
1721393 AAGACTTACTGATGGCTTGAAGGACTTGCAAATTTTGGAAATAGTTGACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* * *
1721458 GAAATCGTTTTCTCACTTTTCAAAAATTTCATTTTCTGAAAATTCTAAATGATAAACTTTGAAAA
131 GAAATCATTTTCTCACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGAAAA
*
1721523 TCACTTTCTCATTTTTCAAATTATATGAAAGCAACTTGCCCAAAGGTCTTATAGATGGCCC-
196 TCACTTTCTCATTTTTCAAATTATATGAAAGCAACTTGCCCAAAGGTCTTATAGATGACCCG
* *
1721584 AAAGGACTTATGATCTTGCTCGAAAGACTGACAGATGACCCGAAGGATTTAATCATCATGCTCGA
1 AAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATCATCATGCTCGA
**
1721649 AAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTAA
66 AAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* * *
1721714 GAAATTACTTTCTCACTTTTCAAAAATTTTATTTTCTGAAAATACTAAATGAGAAACTTTGAAAA
131 GAAATCATTTTCTCACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGAAAA
*
1721779 TCACTTTCTCATTTTTCAAATTATATG-AAGTCATCTTGCCCAAAGGTCTTATAGATGACCCG
196 TCACTTTCTCATTTTTCAAATTATATGAAAG-CAACTTGCCCAAAGGTCTTATAGATGACCCG
* * * * *
1721841 AAA-GACTTATCATCTTGCTCGAAAGACTAACAAATGACCCGAAGTATTTAATCATCATGTTCAA
1 AAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATCATCATGCTCGA
* ** * * *
1721905 AAGACTTACTGATTGCCCAAAAGACTTATCACTTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
66 AAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
* *
1721970 GAAATCATTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACAAAATGAGAAACTTTGAAAA
131 GAAATCATTTTCTCACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGAAAA
* * * *
1722035 CCGCTTTCTCATTTTTCAAATTATATAAAAACAACTT
196 TCACTTTCTCATTTTTCAAATTATATGAAAGCAACTT
1722072 AATGGTCGGG
Statistics
Matches: 441, Mismatches: 44, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
255 3 0.01
256 433 0.98
257 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (257 bp):
AAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGAATTTAATCATCATGCTCGA
AAGACTTACTGATGGCCTGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTG
GAAATCATTTTCTCACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGAAAA
TCACTTTCTCATTTTTCAAATTATATGAAAGCAACTTGCCCAAAGGTCTTATAGATGACCCG
Found at i:1723970 original size:30 final size:30
Alignment explanation
Indices: 1723936--1723996 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1723926 TTTGAACCAT
*
1723936 TTGTACTTGATGAACCTTGTGGGTTGAGAC
1 TTGTACTTGATGAACCTTGTGGCTTGAGAC
1723966 TTGTACTTGATGAACCTTGTGGCTTGAGAC
1 TTGTACTTGATGAACCTTGTGGCTTGAGAC
1723996 T
1 T
1723997 CAATGAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (30 bp):
TTGTACTTGATGAACCTTGTGGCTTGAGAC
Found at i:1724053 original size:7 final size:7
Alignment explanation
Indices: 1724029--1724087 Score: 52
Period size: 7 Copynumber: 8.6 Consensus size: 7
1724019 ACTTGATCTA
1724029 TTTTCTT
1 TTTTCTT
*
1724036 TCTTC-T
1 TTTTCTT
*
1724042 ATTTCTT
1 TTTTCTT
*
1724049 TTTTCTCC
1 TTTTCT-T
1724057 TTTTC--
1 TTTTCTT
1724062 TTTTCTT
1 TTTTCTT
1724069 TTTTCTT
1 TTTTCTT
1724076 TTTTCTCT
1 TTTTCT-T
1724084 TTTT
1 TTTT
1724088 TTGAATAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
5 5 0.12
6 4 0.10
7 23 0.55
8 10 0.24
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTCTT
Found at i:1724054 original size:20 final size:18
Alignment explanation
Indices: 1724029--1724078 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 18
1724019 ACTTGATCTA
1724029 TTTTCTTTCTTCTATTTCTT
1 TTTTCTTT-TTCT-TTTCTT
1724049 TTTTCTCCTTTTCTTTTCTT
1 TTTTCT--TTTTCTTTTCTT
1724069 TTTTCTTTTT
1 TTTTCTTTTT
1724079 TCTCTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 4 0.14
20 18 0.64
21 4 0.14
22 2 0.07
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTCTT
Found at i:1724077 original size:27 final size:28
Alignment explanation
Indices: 1724029--1724087 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
1724019 ACTTGATCTA
1724029 TTTTCTTTCTTCTATTTCTTTTTTCTCC
1 TTTTCTTTCTTCTATTTCTTTTTTCTCC
*
1724057 TTTTCTTTTCTT-T-TTTCTTTTTTCTCT
1 TTTTC-TTTCTTCTATTTCTTTTTTCTCC
1724084 TTTT
1 TTTT
1724088 TTGAATAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 17 0.59
28 6 0.21
29 6 0.21
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTCTTTCTTCTATTTCTTTTTTCTCC
Found at i:1724761 original size:205 final size:208
Alignment explanation
Indices: 1724390--1724802 Score: 724
Period size: 205 Copynumber: 2.0 Consensus size: 208
1724380 TTCAGGCTCA
*
1724390 AATGGGGACAACAAGAGATATATATTTTTCTCCTTTTTGTGAATGGATATTGAAAGAAATTCATT
1 AATGGGGACAACAAGAGATATATATTTTTCTCCATTTTGTGAATGGATATTGAAAGAAATTCATT
* *
1724455 CATCATTTCGTACATAGAAGTCCTTGAAAAAAGAGGTATCCCCAGGGGGATGAATATTCATGATT
66 CATCATTTCATACACAGAAGTCCTTGAAAAAAGAGGTATCCCCAGGGGGATGAATATTCATGATT
1724520 AACTTTTATTTACATGAAAACAATGTAATTAATACATGATAAAATATTTAAATCATTCCCTCTTA
131 AACTTTTATTTACATGAAAACAATGTAATTAATACATGATAAAATATTTAAATCATTCCCTCTTA
1724585 TTTCTT-TTCTTC
196 TTTCTTCTTCTTC
* *
1724597 AATGGGGACAATAAGAGATATATATTTTTCT-CATTTTGTGAATGGATATTGAAAGAAATTCGTT
1 AATGGGGACAACAAGAGATATATATTTTTCTCCATTTTGTGAATGGATATTGAAAGAAATTCATT
**
1724661 CATCATTTCATACACAGAAGTCCTTGAAAAAAGAGGT-TTTCCAGGGGGATGAATATTCATGATT
66 CATCATTTCATACACAGAAGTCCTTGAAAAAAGAGGTATCCCCAGGGGGATGAATATTCATGATT
* *
1724725 AACTTTTATTTACATGAAAACAATGTAATTAATACATGATAGAATATTTAAATCATTCCCTTTTA
131 AACTTTTATTTACATGAAAACAATGTAATTAATACATGATAAAATATTTAAATCATTCCCTCTTA
1724790 TTTCTTCTTCTTC
196 TTTCTTCTTCTTC
1724803 TTGCTTAGAG
Statistics
Matches: 196, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
205 94 0.48
206 72 0.37
207 30 0.15
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (208 bp):
AATGGGGACAACAAGAGATATATATTTTTCTCCATTTTGTGAATGGATATTGAAAGAAATTCATT
CATCATTTCATACACAGAAGTCCTTGAAAAAAGAGGTATCCCCAGGGGGATGAATATTCATGATT
AACTTTTATTTACATGAAAACAATGTAATTAATACATGATAAAATATTTAAATCATTCCCTCTTA
TTTCTTCTTCTTC
Found at i:1728868 original size:32 final size:32
Alignment explanation
Indices: 1728816--1728908 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
1728806 ACATAGGTCA
* *
1728816 CTGTCCATATGTCCCTAAGGACATAGGTAATC
1 CTGTCCATATATCCCAAAGGACATAGGTAATC
* *
1728848 CTGTCTATATATCCCAAAGGACATAGGTAA-A
1 CTGTCCATATATCCCAAAGGACATAGGTAATC
* * *
1728879 CTATCCATATGTCTCGAAA-GACATAGGTAA
1 CTGTCCATATATC-CCAAAGGACATAGGTAA
1728909 CCCTCGACTC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
31 21 0.40
32 31 0.60
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (32 bp):
CTGTCCATATATCCCAAAGGACATAGGTAATC
Found at i:1729244 original size:23 final size:24
Alignment explanation
Indices: 1729200--1729244 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
1729190 ATCTCTTATG
1729200 TTCATATATCACATAATCATACCA
1 TTCATATATCACATAATCATACCA
1729224 TTCATTATATCA-AT-ATCATAC
1 TTCA-TATATCACATAATCATAC
1729245 GACTTATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (24 bp):
TTCATATATCACATAATCATACCA
Found at i:1738950 original size:140 final size:140
Alignment explanation
Indices: 1738698--1738977 Score: 551
Period size: 140 Copynumber: 2.0 Consensus size: 140
1738688 AAGAGGTAAA
1738698 GCAAACAGAAATACCACGACATGTTGATTTAGGTCGGTTAAGTTGGCATAAATTCCTTTACTAGA
1 GCAAACAGAAATACCACGACATGTTGATTTAGGTCGGTTAAGTTGGCATAAATTCCTTTACTAGA
1738763 GAGGCATTCATATTATCTGGATGCTTGGCAAAGGTTTTCCATTGGTGCTGATGAACGATGTCCAT
66 GAGGCATTCATATTATCTGGATGCTTGGCAAAGGTTTTCCATTGGTGCTGATGAACGATGTCCAT
1738828 GACATCACTG
131 GACATCACTG
1738838 GCAAACAGAAATACCACGACATGTTGATTTAGGTCGGTTAAGTTGGCATAAATTCCTTTACTAGA
1 GCAAACAGAAATACCACGACATGTTGATTTAGGTCGGTTAAGTTGGCATAAATTCCTTTACTAGA
*
1738903 GAGGCATTCATATTATCTGGATGCTTGGCAAAGTTTTTCCATTGGTGCTGATGAACGATGTCCAT
66 GAGGCATTCATATTATCTGGATGCTTGGCAAAGGTTTTCCATTGGTGCTGATGAACGATGTCCAT
1738968 GACATCACTG
131 GACATCACTG
1738978 TCGAGATCAA
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (140 bp):
GCAAACAGAAATACCACGACATGTTGATTTAGGTCGGTTAAGTTGGCATAAATTCCTTTACTAGA
GAGGCATTCATATTATCTGGATGCTTGGCAAAGGTTTTCCATTGGTGCTGATGAACGATGTCCAT
GACATCACTG
Found at i:1739119 original size:78 final size:77
Alignment explanation
Indices: 1739020--1739174 Score: 301
Period size: 78 Copynumber: 2.0 Consensus size: 77
1739010 GAAGATTAAC
1739020 TCAAATAAAACCCAGCGGTTTTTGAGGCTTTAAAACCTTTCTTGCGCCTCTTCATCAACAAAACA
1 TCAAATAAAACCCAGCGGTTTTTGAGGCTTTAAAACCTTTCTTG-GCCTCTTCATCAACAAAACA
1739085 TGATGGAGATGAT
65 TGATGGAGATGAT
1739098 TCAAATAAAACCCAGCGGTTTTTGAGGCTTTAAAACCTTTCTTGGCCTCTTCATCAACAAAACAT
1 TCAAATAAAACCCAGCGGTTTTTGAGGCTTTAAAACCTTTCTTGGCCTCTTCATCAACAAAACAT
1739163 GATGGAGATGAT
66 GATGGAGATGAT
1739175 GGAGTCATGC
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 33 0.43
78 44 0.57
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (77 bp):
TCAAATAAAACCCAGCGGTTTTTGAGGCTTTAAAACCTTTCTTGGCCTCTTCATCAACAAAACAT
GATGGAGATGAT
Found at i:1746111 original size:21 final size:20
Alignment explanation
Indices: 1746082--1746120 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1746072 TAAGGCATTA
*
1746082 AACATCATAAATAAAACAAAT
1 AACAACATAAA-AAAACAAAT
*
1746103 AACAACATACAAAAACAA
1 AACAACATAAAAAAACAA
1746121 TCATCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.18, G:0.00, T:0.13
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAT
Found at i:1748787 original size:12 final size:12
Alignment explanation
Indices: 1748770--1748794 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1748760 TTGAAGGAGG
1748770 TAAGGTCATTTC
1 TAAGGTCATTTC
1748782 TAAGGTCATTTC
1 TAAGGTCATTTC
1748794 T
1 T
1748795 TAGCTTCACA
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (12 bp):
TAAGGTCATTTC
Found at i:1770076 original size:18 final size:19
Alignment explanation
Indices: 1770042--1770078 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1770032 GTTGGGTTAG
*
1770042 GTTTTGGGTTTTGGGTCTT
1 GTTTTGGGTTATGGGTCTT
1770061 GTTTTGGG-TATGGGTCTT
1 GTTTTGGGTTATGGGTCTT
1770079 AAGGCCCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.03, C:0.05, G:0.38, T:0.54
Consensus pattern (19 bp):
GTTTTGGGTTATGGGTCTT
Found at i:1770380 original size:59 final size:59
Alignment explanation
Indices: 1770287--1770405 Score: 148
Period size: 59 Copynumber: 2.0 Consensus size: 59
1770277 CTTTCTTCTA
* * * * **
1770287 GAAATGCTAGTCCCTCGAGTGAGGTGTCGTTGATTTGAAATCTCGTGAATCAAGCAAAG
1 GAAATGCTAATCCCTCAAGTGAGGTATCGCTGATTCAAAATCTCGTGAATCAAGCAAAG
* * * *
1770346 GAAATGTTAATCCCTCAAGTGAGGTATCGCTGATTCAAAATGTTGTGAATCTAGCAAAG
1 GAAATGCTAATCCCTCAAGTGAGGTATCGCTGATTCAAAATCTCGTGAATCAAGCAAAG
1770405 G
1 G
1770406 TTGAACAAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (59 bp):
GAAATGCTAATCCCTCAAGTGAGGTATCGCTGATTCAAAATCTCGTGAATCAAGCAAAG
Found at i:1771014 original size:103 final size:103
Alignment explanation
Indices: 1770763--1771007 Score: 402
Period size: 103 Copynumber: 2.4 Consensus size: 103
1770753 AGATGAAATG
* * *
1770763 TCTCAAGTGATGA-GAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTGTTTCA
1 TCTCAAGCGA-GATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTATTTCA
1770827 AGTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTT
65 AGTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTT
* * *
1770866 TCTTAAGCGATATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTATTTCAT
1 TCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTATTTCAA
1770931 GTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTT
66 GTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTT
* *
1770969 TCTCAAGCGAGATGAAATTTTTTTTAAGAAAAATAATCT
1 TCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCT
1771008 TGAGTGAAAT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
102 1 0.01
103 130 0.99
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (103 bp):
TCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAACTTCTTATTTCAA
GTGAAACAATTTCAAATTTTATATTTCAAGGGAAACTT
Found at i:1771182 original size:38 final size:37
Alignment explanation
Indices: 1770963--1771935 Score: 553
Period size: 36 Copynumber: 25.9 Consensus size: 37
1770953 ATTTCAAGGG
* *
1770963 AAACTTTCTCAAGCGAGATGAAATTTT-TTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
** * * * *
1770999 AAA-TAATCTTGAGTGAAATGAAATTTCTTGTTTTGAATAAA
1 AAACT-ATCTCAAGCGAGAT-AAAATT-TTGTTTT-AA-GAA
* * * *
1771040 AAATTGTCTCAAGCGAGA-CAAAGTTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * *
1771076 AAACAATCTCAAGCGAGATAAATTTTATGTTTTGAGCGA
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAG-AA
* **
1771115 AAATTATCTCAAGCGAGACGAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * ** **
1771151 AAACAATCTCAGGTGAGATAAAATTTATGTTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAGAA
**
1771189 AAACTATCTCAAGCGAGACGAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * **
1771225 AAACAATCTCAAGTGAGATAAAATTTCTGTTTTGAGTG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAGAA
*
1771263 AAACTATCTTAAGCGAGATAAAATTTATGAATCTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGAT-AAA---AT---T-TTGTTTTAAGAA
* * * * ** **
1771308 AAACAATCTCATGTGAGATAAATTTTCTGTTTGGAGTG
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAGAA
* * **
1771346 AAACTATCTCAAGCGAGATGAAATTTT-TTCTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAATTTTGTT-TT-AAGAA
* *
1771384 AAACTATCTCAAGCGAGAT-GAATCTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * * **
1771420 AAA-TAATCTTAAGTGAGAT-AAATTTTCTGTTAAGTG
1 AAACT-ATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* ** **
1771456 AAACTATCTCAAGCGAGATAAAATTTTTGCTTCGAGTG
1 AAACTATCTCAAGCGAGATAAAA-TTTTGTTTTAAGAA
* * *
1771494 AAACTATCTCAAACGAGAT-GAATCTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * * *
1771530 AAACAATCTCAAGTGAGATAAATTTTTGTTTCAAGTGA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAG-AA
* * *
1771568 AAACTGTCTCAAGCGAGAT-GAAGTTTGTTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTG-TTTTAAGAA
* * ** *
1771605 ATACTATCTCAAGTGAGATAAAATTTCTGTTTCGAGTGA
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAG-AA
* * *
1771644 AAATTGTCTTAAGCGAGATAAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * ** *
1771680 AAACAATCTCAAGCGAGATGAATTTTCTGTTTCGAGTGA
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAAG-AA
* * * * *
1771719 AAATTGTCTTAAGTGAGACAAAA-TTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * *
1771755 AAACAATCTCAAGTGAGATAAAATTTCTGTTTCAATTG-A
1 AAACTATCTCAAGCGAGATAAAATTT-TGTTTTAA--GAA
* *
1771794 AAATTATCTCAAGCGAG--AAGA-TTT-TTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * * * **
1771827 AAACAATCTCAAGTGATATAACATTTCTTGTTTCAAGTG
1 AAACTATCTCAAGCGAGATAA-AATT-TTGTTTTAAGAA
* *
1771866 AAACTATCTCAAGCGAGATGAAA-CTTGTTTTAAGAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
* * * *
1771902 AAGCAATCTCAAGTGAGATAAAATTTTGTATTAA
1 AAACTATCTCAAGCGAGATAAAATTTTGTTTTAA
1771936 ATGAGACGGA
Statistics
Matches: 692, Mismatches: 194, Indels: 101
0.70 0.20 0.10
Matches are distributed among these distances:
32 1 0.00
33 14 0.02
34 5 0.01
35 5 0.01
36 209 0.30
37 103 0.15
38 203 0.29
39 104 0.15
40 3 0.00
41 14 0.02
42 3 0.00
44 3 0.00
45 24 0.03
46 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (37 bp):
AAACTATCTCAAGCGAGATAAAATTTTGTTTTAAGAA
Found at i:1771233 original size:74 final size:74
Alignment explanation
Indices: 1770962--1771927 Score: 919
Period size: 75 Copynumber: 12.9 Consensus size: 74
1770952 TATTTCAAGG
* * * ** * *
1770962 GAAACTTTCTCAAGCGAGATGAAATTTTTTTTAAGAAAAATAATCTTGAGTGAAATGAAATTTCT
1 GAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC-
* *
1771027 TGTTTTGAAT
65 TGTTTCGAGT
* * * * * *
1771037 AAAAAATTGTCTCAAGCGAGA-CAAAGTTTGTTTTAAGAAAAACAATCTCAAGCGAGATAAATTT
1 --GAAACTATCTCAAGCGAGATGAAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT
* * *
1771101 TATGTTTTGAGC
63 TCTGTTTCGAGT
* * * *
1771113 GAAAATTATCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAGGTGAGATAAAATTTA
1 G-AAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
1771178 TGTTTCGAGT
65 TGTTTCGAGT
*
1771188 GAAACTATCTCAAGCGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCT
1 GAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCT
*
1771253 GTTTTGAGT
66 GTTTCGAGT
* * *
1771262 GAAACTATCTTAAGCGAGATAAAATTTATGAATCTTGTTTTAAGAAAAACAATCTCATGTGAGAT
1 GAAACTATCTCAAGCGAG-----A-TGA--AAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGAT
* *
1771327 AAATTTTCTGTTTGGAGT
57 AAAATTTCTGTTTCGAGT
* * ** * * * *
1771345 GAAACTATCTCAAGCGAGATGAAATTTTTTCTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCT
1 GAAACTATCTCAAGCGAGATGAAATTTGTT-TT-AAGAAAAACAATCTCAAGTGAGATAAAATTT
**
1771409 -TGTTTTAAG-
64 CTGTTTCGAGT
* * * * ** * *
1771418 AAAAATAATCTTAAGTGAGAT-AAATTT-TCTGTTAAGTGAAACTATCTCAAGCGAGATAAAATT
1 GAAACT-ATCTCAAGCGAGATGAAATTTGT-T-TTAAGAAAAACAATCTCAAGTGAGATAAAATT
* *
1771481 TTTGCTTCGAGT
63 TCTGTTTCGAGT
* *
1771493 GAAACTATCTCAAACGAGATG-AATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT-AAATTTT
1 GAAACTATCTCAAGCGAGATGAAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
*
1771556 TGTTTCAAGT
65 TGTTTCGAGT
* * * *
1771566 GAAAACTGTCTCAAGCGAGATGAAGTTTGTTTTTAAGAAATACTATCTCAAGTGAGATAAAATTT
1 G-AAACTATCTCAAGCGAGATGAAATTTG-TTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
1771631 CTGTTTCGAGT
64 CTGTTTCGAGT
* * * * * * *
1771642 GAAAATTGTCTTAAGCGAGATAAAATTTGTTTTAAGAAAAACAATCTCAAGCGAGATGAATTTTC
1 G-AAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
1771707 TGTTTCGAGT
65 TGTTTCGAGT
* * * * **
1771717 GAAAATTGTCTTAAGTGAGACAAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
1 G-AAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
* *
1771782 TGTTTCAATT
65 TGTTTCGAGT
* * * *
1771792 GAAAATTATCTCAAGCGAGA--AGATTT-TTTTAAGAAAAACAATCTCAAGTGATATAACATTTC
1 G-AAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTC
*
1771854 TTGTTTCAAGT
65 -TGTTTCGAGT
* *
1771865 GAAACTATCTCAAGCGAGATGAAACTTGTTTTAAGAAAAGCAATCTCAAGTGAGATAAAATTT
1 GAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTT
1771928 TGTATTAAAT
Statistics
Matches: 754, Mismatches: 105, Indels: 62
0.82 0.11 0.07
Matches are distributed among these distances:
72 75 0.10
73 48 0.06
74 176 0.23
75 264 0.35
76 73 0.10
77 49 0.06
78 1 0.00
79 1 0.00
80 1 0.00
82 3 0.00
83 63 0.08
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (74 bp):
GAAACTATCTCAAGCGAGATGAAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAAATTTCT
GTTTCGAGT
Done.