Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007825.1 Hibiscus syriacus cultivar Beakdansim tig00110163_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: 2082551
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1162209 original size:15 final size:15
Alignment explanation
Indices: 1162189--1162221 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1162179 CGTAGGACTC
1162189 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
1162204 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
1162219 CTA
1 CTA
1162222 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.15
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:1162349 original size:29 final size:29
Alignment explanation
Indices: 1162317--1162379 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
1162307 CATATACTTC
1162317 TGTCATTTCTCTTGTGATCATGTAGCTCA
1 TGTCATTTCTCTTGTGATCATGTAGCTCA
1162346 TGTCATTTCTCTTGTGATCATGTAGCTCA
1 TGTCATTTCTCTTGTGATCATGTAGCTCA
1162375 TGTCA
1 TGTCA
1162380 CTTCATATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (29 bp):
TGTCATTTCTCTTGTGATCATGTAGCTCA
Found at i:1162412 original size:12 final size:12
Alignment explanation
Indices: 1162395--1162430 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1162385 TATCATGTTC
*
1162395 TCATATTACATG
1 TCATATCACATG
*
1162407 TCATATCACATA
1 TCATATCACATG
1162419 TCATATCACATG
1 TCATATCACATG
1162431 AACATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1162846 original size:64 final size:64
Alignment explanation
Indices: 1162738--1162914 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
1162728 TAATGAAGGT
* * * ** * * **
1162738 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-GTCACTATTAATGGG
* ** *
1162802 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTGTCACTATTAATGGG
1162866 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT
1162915 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
63 1 0.01
64 95 0.99
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1162935 original size:64 final size:64
Alignment explanation
Indices: 1162738--1162963 Score: 217
Period size: 64 Copynumber: 3.5 Consensus size: 64
1162728 TAATGAAGGT
* * * ** * * * ** *
1162738 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCACTATTAATGAG
* ** *
1162802 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGCATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCACTATTAATGAG
* *
1162866 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTCTTTA-TTTTAAAAT-
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCACTATT--AATG
1162929 AG
63 AG
**
1162931 -TGCATCGATGCACTACCAATGCATCGATGCACA
1 ATGCATCGATGCACTACTTATGCATCGATGCACA
1162964 TTCATACAAT
Statistics
Matches: 137, Mismatches: 21, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 129 0.94
65 4 0.03
66 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCACTATTAATGAG
Found at i:1164296 original size:23 final size:23
Alignment explanation
Indices: 1164270--1164333 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1164260 CAGCTCATAT
1164270 AATTGCACC-GAAGTGCCACGTAG
1 AATTGCACCAG-AGTGCCACGTAG
*
1164293 AATTGCACCAGAGTGCCGCGTAG
1 AATTGCACCAGAGTGCCACGTAG
*
1164316 AATTGCACCATAGTGCCA
1 AATTGCACCAGAGTGCCA
1164334 TATAATAATG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 36 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCAGAGTGCCACGTAG
Found at i:1164520 original size:103 final size:103
Alignment explanation
Indices: 1164352--1164566 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
1164342 TGTCCATAAG
* *
1164352 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1164417 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
* *
1164455 GACCACATATCATTTCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
1164520 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
1164558 GACCACATA
1 GACCACATA
1164567 GACCCTCGAC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAT
Found at i:1166447 original size:2 final size:2
Alignment explanation
Indices: 1166440--1166489 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1166430 TATCAAAACG
*
1166440 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1166482 AT AC AT AT
1 AT AT AT AT
1166490 CATTATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1166889 original size:23 final size:23
Alignment explanation
Indices: 1166863--1166928 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1166853 CTCGTATAAA
* *
1166863 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACATAAAAT
*
1166886 TGCACCGAAGTGCCGCATAAAAT
1 TGCACCGAAGTGCCACATAAAAT
* *
1166909 TGCACCGTAGTGCCATATAA
1 TGCACCGAAGTGCCACATAA
1166929 TAATGTCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAAAAT
Found at i:1167067 original size:103 final size:103
Alignment explanation
Indices: 1166942--1167152 Score: 343
Period size: 103 Copynumber: 2.0 Consensus size: 103
1166932 TGTCCATAAG
*
1166942 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTC-CAAAGA
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCAC-AAGA
*
1167006 CCTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
65 CCTCACACATATTCCAAAGAATACATATATGTCCCGAAA
* * *
1167045 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAAGAC
* *
1167110 TTCACACATATTCCAAAGAATACATATATGTCCTGAAA
66 CTCACACATATTCCAAAGAATACATATATGTCCCGAAA
1167148 GACCA
1 GACCA
1167153 TATAGACCCT
Statistics
Matches: 100, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 99 0.99
104 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACAAGAC
CTCACACATATTCCAAAGAATACATATATGTCCCGAAA
Found at i:1167442 original size:15 final size:15
Alignment explanation
Indices: 1167424--1167468 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1167414 TAATCATATA
*
1167424 ATCATATAACTTATT
1 ATCACATAACTTATT
* *
1167439 ATCACATATCTTATA
1 ATCACATAACTTATT
*
1167454 ATCACATACCTTATT
1 ATCACATAACTTATT
1167469 TCAATTCTCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCACATAACTTATT
Found at i:1168617 original size:65 final size:63
Alignment explanation
Indices: 1168481--1168621 Score: 158
Period size: 65 Copynumber: 2.2 Consensus size: 63
1168471 CACCACACCC
* * * *
1168481 TGCATTGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCCTTA
1 TGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGCACTCCATA
* * * *
1168545 TGAATCGATGCATAAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATCGATGCACTGCAT
1 TGCATCGATGCAT-AAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCGATGCACTCCAT
*
1168609 G
63 A
1168610 TGCATCGATGCA
1 TGCATCGATGCA
1168622 CCTTAAACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 11 0.17
65 43 0.67
66 7 0.11
67 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (63 bp):
TGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGCACTCCATA
Found at i:1171842 original size:25 final size:25
Alignment explanation
Indices: 1171792--1171843 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1171782 TATCAAAACG
* * *
1171792 ATATAACATTATATATATATATATT
1 ATATAACATTATACATATACACATT
1171817 ATATAACA-TATACATATCACACATT
1 ATATAACATTATACATAT-ACACATT
1171842 AT
1 AT
1171844 TTTAAATCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (25 bp):
ATATAACATTATACATATACACATT
Found at i:1172246 original size:23 final size:23
Alignment explanation
Indices: 1172216--1172281 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
1172206 CTCGTATAAA
* *
1172216 TGCACCGAAGTGCCATGTAGAAT
1 TGCACCGAAGTGCCATATAAAAT
**
1172239 TGCACCGAAGTGCCGCATAAAAT
1 TGCACCGAAGTGCCATATAAAAT
*
1172262 TGCACCGTAGTGCCATATAA
1 TGCACCGAAGTGCCATATAA
1172282 TAATGTCCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCATATAAAAT
Found at i:1172840 original size:15 final size:15
Alignment explanation
Indices: 1172816--1172850 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1172806 AACCATATAA
* *
1172816 CTTATTATCACATAT
1 CTTATAATCACATAC
1172831 CTTATAATCACATAC
1 CTTATAATCACATAC
1172846 CTTAT
1 CTTAT
1172851 TTCAATTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTATAATCACATAC
Found at i:1173533 original size:23 final size:25
Alignment explanation
Indices: 1173507--1173552 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
1173497 TACCACCTAA
1173507 CATGTAATA-CAAC-TAAGCATATT
1 CATGTAATATCAACATAAGCATATT
*
1173530 CATGTAATATCAACATAATCATA
1 CATGTAATATCAACATAAGCATA
1173553 CAATCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (25 bp):
CATGTAATATCAACATAAGCATATT
Found at i:1173965 original size:64 final size:63
Alignment explanation
Indices: 1173849--1173988 Score: 165
Period size: 64 Copynumber: 2.2 Consensus size: 63
1173839 CACCACACCC
* * * *
1173849 TGCATCGATGCATAAATTCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCCTTA
1 TGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGCACTCCATA
* * * * *
1173913 TGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGTATCGATGCACTGCATG
1 TGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCGATGCACTCCATA
1173977 TGCATCGATGCA
1 TGCATCGATGCA
1173989 CCTTAAACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
64 55 0.85
65 7 0.11
66 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (63 bp):
TGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGCACTCCATA
Found at i:1178739 original size:23 final size:23
Alignment explanation
Indices: 1178713--1178776 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1178703 CATCTCATAT
*
1178713 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
* * *
1178736 AATTACACCGGAGTGCCGCTTAG
1 AATTGCACCGGAGTGCCACGTAG
1178759 AATTGCACCGGAGTGCCA
1 AATTGCACCGGAGTGCCA
1178777 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:1179037 original size:74 final size:74
Alignment explanation
Indices: 1178916--1179064 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
1178906 TCTTTTATAT
1178916 CCTTTTACATATTCATGTAACCATATCATATATTCATATAAGATCATGGTTTTATTCACATATAC
1 CCTTTTACATATTCATGTAACCATATCATATATTCATATAAGATCATGGTTTTATTCACATATAC
1178981 ATGTAATCA
66 ATGTAATCA
1178990 CCTTTTACATATTCATGTAACCATATCATATATTCATATAAGATCATGGTTTTATTCACATATAC
1 CCTTTTACATATTCATGTAACCATATCATATATTCATATAAGATCATGGTTTTATTCACATATAC
1179055 ATGTAATCA
66 ATGTAATCA
1179064 C
1 C
1179065 GTAGTTCATG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.40
Consensus pattern (74 bp):
CCTTTTACATATTCATGTAACCATATCATATATTCATATAAGATCATGGTTTTATTCACATATAC
ATGTAATCA
Found at i:1179786 original size:64 final size:64
Alignment explanation
Indices: 1179653--1179809 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
1179643 TAATGAAGGT
* * * ** *
1179653 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTGTTTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
* *
1179717 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATT-TATT-TTAAA-A
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TTGT-TTATTAAAGA
1179779 G
64 G
* * *
1179780 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
1179810 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
63 2 0.03
64 73 0.92
65 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTGTTTATTAAAGAG
Found at i:1181272 original size:30 final size:29
Alignment explanation
Indices: 1181238--1181308 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1181228 AAATTAAATT
* *
1181238 TTTAGTCCCTAAATTTTACAAAAGTTATAC
1 TTTAGTCCCTAAATTTT-CAAAACTTACAC
* *
1181268 TTTAGTCCTTAAATTTTCAAAACTTACAT
1 TTTAGTCCCTAAATTTTCAAAACTTACAC
*
1181297 TTTAGTCACTAA
1 TTTAGTCCCTAA
1181309 TCAAAATTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 19 0.54
30 16 0.46
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (29 bp):
TTTAGTCCCTAAATTTTCAAAACTTACAC
Found at i:1181300 original size:29 final size:29
Alignment explanation
Indices: 1181219--1181308 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
1181209 TAAAATATAT
*
1181219 AATTTTTAAAAATTAAATTTTTAGTCCCTA
1 AATTTTCAAAAATTAAA-TTTTAGTCCCTA
* * * *
1181249 AATTTTACAAAAGTTATACTTTAGTCCTTA
1 AATTTT-CAAAAATTAAATTTTAGTCCCTA
* * *
1181279 AATTTTCAAAACTTACATTTTAGTCACTA
1 AATTTTCAAAAATTAAATTTTAGTCCCTA
1181308 A
1 A
1181309 TCAAAATTTG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 19 0.39
30 22 0.45
31 8 0.16
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (29 bp):
AATTTTCAAAAATTAAATTTTAGTCCCTA
Found at i:1198040 original size:112 final size:112
Alignment explanation
Indices: 1197897--1198121 Score: 432
Period size: 112 Copynumber: 2.0 Consensus size: 112
1197887 TTATTGAAGT
*
1197897 TGTTTGGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTTATATAGCTTATTTATG
1 TGTTTGGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATG
*
1197962 ATTTATGTATGTTTTTGTCGTATTCGAACAAATTAATTCTAAAGTTG
66 ATTTATGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTG
1198009 TGTTTGGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATG
1 TGTTTGGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATG
1198074 ATTTATGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTG
66 ATTTATGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTG
1198121 T
1 T
1198122 AGGTTATATT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (112 bp):
TGTTTGGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATG
ATTTATGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTG
Found at i:1198149 original size:112 final size:111
Alignment explanation
Indices: 1197903--1198149 Score: 343
Period size: 112 Copynumber: 2.2 Consensus size: 111
1197893 AAGTTGTTTG
* *** *
1197903 GATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTTATATAGCTTATTTATGATTTAT
1 GATTTAAAGAAGATTAAGTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATGATTTAT
* *
1197968 GTATGTTTTTGTCGTATTCGAACAAATTAATTCTAAAGTTGTGTTT
66 GTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTGTGGTT
* ***
1198014 GGATTTCAAGAAGATTGTTTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATGATTTA
1 -GATTTAAAGAAGATTAAGTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATGATTTA
1198079 TGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTGTAGGTT
65 TGTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTGT-GGTT
**
1198127 -ATATTAAAGAATTTTAAGTTGTT
1 GAT-TTAAAGAAGATTAAGTTGTT
1198150 ATTCTTGTTG
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
111 2 0.02
112 119 0.96
113 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.16, T:0.45
Consensus pattern (111 bp):
GATTTAAAGAAGATTAAGTTGTTGAACAAATTAACTTATGCTCATATAGCTTATTTATGATTTAT
GTATGTTTTTGTCGTATTCGAACAAATTAACTCTAAAGTTGTGGTT
Found at i:1198249 original size:27 final size:26
Alignment explanation
Indices: 1198214--1198264 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1198204 TTTTGTGTTG
1198214 TGTTGTTCGTTTATGTTCATTTATTA
1 TGTTGTTCGTTTATGTTCATTTATTA
* *
1198240 TGTTCGTTCGTTTGTGTTCGTTTAT
1 TGTT-GTTCGTTTATGTTCATTTAT
1198265 CATTTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (26 bp):
TGTTGTTCGTTTATGTTCATTTATTA
Found at i:1203414 original size:2 final size:2
Alignment explanation
Indices: 1203407--1203440 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1203397 GTTTTCCGGA
1203407 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
1203441 GCTTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1209800 original size:44 final size:44
Alignment explanation
Indices: 1209745--1209928 Score: 194
Period size: 44 Copynumber: 4.2 Consensus size: 44
1209735 TTTTGAGATT
* * * *
1209745 TAGCAGCGTTTTTAGGGGGGAAACGCCGCTAAAGGTATGGTATA
1 TAGCGGCGTTTTTAGGAGAGAAACGCCGCTAAAGGTCTGGTATA
* * * *
1209789 TAGCGGCGTTTTTAGGATATAAATGCCGTTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGAGAGAAACGCCGCTAAAGGTCTGGTATA
* * *
1209833 TAGTGGCGTTCTTAGG-G-GAAACGTCGCTAAAGGTCTGGTATA
1 TAGCGGCGTTTTTAGGAGAGAAACGCCGCTAAAGGTCTGGTATA
* * * * *
1209875 TAGCAGCGTTTTTAGGATACAAATGCCGCGAAAGGT-TGGTATA
1 TAGCGGCGTTTTTAGGAGAGAAACGCCGCTAAAGGTCTGGTATA
*
1209918 TAGCGCCGTTT
1 TAGCGGCGTTT
1209929 GTAACAATAA
Statistics
Matches: 113, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
42 34 0.30
43 16 0.14
44 63 0.56
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.29
Consensus pattern (44 bp):
TAGCGGCGTTTTTAGGAGAGAAACGCCGCTAAAGGTCTGGTATA
Found at i:1209861 original size:86 final size:85
Alignment explanation
Indices: 1209761--1209920 Score: 257
Period size: 86 Copynumber: 1.9 Consensus size: 85
1209751 CGTTTTTAGG
* * **
1209761 GGGGAAACGCCGCTAAAGGTATGGTATATAGCGGCGTTTTTAGGATATAAATGCCGTTAAAGGTC
1 GGGGAAACGCCGCTAAAGGTATGGTATATAGCAGCGTTTTTAGGATACAAATGCCGCGAAAGGT-
1209826 TGGTATATAGTGGCGTTCTTA
65 TGGTATATAGTGGCGTTCTTA
* *
1209847 GGGGAAACGTCGCTAAAGGTCTGGTATATAGCAGCGTTTTTAGGATACAAATGCCGCGAAAGGTT
1 GGGGAAACGCCGCTAAAGGTATGGTATATAGCAGCGTTTTTAGGATACAAATGCCGCGAAAGGTT
1209912 GGTATATAG
66 GGTATATAG
1209921 CGCCGTTTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 10 0.15
86 58 0.85
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (85 bp):
GGGGAAACGCCGCTAAAGGTATGGTATATAGCAGCGTTTTTAGGATACAAATGCCGCGAAAGGTT
GGTATATAGTGGCGTTCTTA
Found at i:1214461 original size:42 final size:42
Alignment explanation
Indices: 1214393--1214504 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
1214383 CTAAAAATGG
* * * *
1214393 CGCTAAATTACTATTC-ATTACAGCGTTTTAGGTATAAACGC
1 CGCTACATTACCATTCTATTACGGCGTTTTAGATATAAACGC
* *
1214434 CGCTA-ATTTATCATTCTATTACGGCGTTTTCGATATAAACGC
1 CGCTACA-TTACCATTCTATTACGGCGTTTTAGATATAAACGC
* *
1214476 CGCTACATTACCACTATATTACGGCGTTT
1 CGCTACATTACCATTCTATTACGGCGTTT
1214505 GAGCTAAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.02
41 12 0.20
42 46 0.77
43 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (42 bp):
CGCTACATTACCATTCTATTACGGCGTTTTAGATATAAACGC
Found at i:1216983 original size:30 final size:30
Alignment explanation
Indices: 1216947--1217012 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1216937 CAAAATATAC
*
1216947 AACTTTTAAAAA-TTATATTTTTAGTCC-CTA
1 AACTTTTAAAAATTTATA-CTTTAG-CCACTA
*
1216977 AACTTTTATAAATTTATACTTTAGCCACTA
1 AACTTTTAAAAATTTATACTTTAGCCACTA
1217007 AACTTT
1 AACTTT
1217013 CTAAGCTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.06
30 25 0.78
31 5 0.16
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.45
Consensus pattern (30 bp):
AACTTTTAAAAATTTATACTTTAGCCACTA
Found at i:1218474 original size:29 final size:28
Alignment explanation
Indices: 1218432--1218516 Score: 134
Period size: 29 Copynumber: 3.0 Consensus size: 28
1218422 CAGTGACAGC
*
1218432 ATAGGTCGCCATGCACGCCCGACGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCC-T
1218461 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCGTCCT
*
1218489 ATAAGATCGCCATGCACGCCCGGCGTCC
1 AT-AGGTCGCCATGCACGCCCGGCGTCC
1218517 AACATTCTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
28 3 0.06
29 50 0.94
ACGTcount: A:0.18, C:0.39, G:0.26, T:0.18
Consensus pattern (28 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCT
Found at i:1218770 original size:25 final size:26
Alignment explanation
Indices: 1218736--1218802 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 26
1218726 GGTTCTATCA
* *
1218736 TAGGTTGCCATGG-CCGGCGACATGG
1 TAGGTCGCCATGGCCCGACGACATGG
1218761 TAGGTCGCCATGGAGTCCCGACGACATGG
1 TAGGTCGCCAT-G-G-CCCGACGACATGG
*
1218790 TAGATCGCCATGG
1 TAGGTCGCCATGG
1218803 AGTCCCGGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 10 0.29
26 1 0.03
27 2 0.06
28 1 0.03
29 21 0.60
ACGTcount: A:0.19, C:0.25, G:0.36, T:0.19
Consensus pattern (26 bp):
TAGGTCGCCATGGCCCGACGACATGG
Found at i:1218792 original size:29 final size:29
Alignment explanation
Indices: 1218753--1218824 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
1218743 CCATGGCCGG
1218753 CGACATGGTAGGTCGCCATGGAGTCCCGA
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
* *
1218782 CGACATGGTAGATCGCCATGGAGTCCCGG
1 CGACATGGTAGGTCGCCATGGAGTCCCGA
*
1218811 CGACATGGTGGGTC
1 CGACATGGTAGGTC
1218825 CTAAGCCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.26, G:0.36, T:0.18
Consensus pattern (29 bp):
CGACATGGTAGGTCGCCATGGAGTCCCGA
Found at i:1219387 original size:21 final size:21
Alignment explanation
Indices: 1219362--1219405 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1219352 AATCTAGTTA
1219362 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1219383 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1219404 AT
1 AT
1219406 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1220230 original size:26 final size:25
Alignment explanation
Indices: 1220201--1220265 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
1220191 AAATCATATT
*
1220201 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
1220227 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
1220253 ATTATT-AATAATA
1 ATTATTAAATAATA
1220266 TTAGTAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:1223184 original size:60 final size:60
Alignment explanation
Indices: 1223113--1223303 Score: 346
Period size: 60 Copynumber: 3.2 Consensus size: 60
1223103 GTATTTATAA
*
1223113 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
1223173 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
1223233 GATTTAGTAATGATTAGTAATAATAAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1223293 GATTTAGTAAT
1 GATTTAGTAAT
1223304 AATGAAATTA
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 128 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:1223350 original size:120 final size:120
Alignment explanation
Indices: 1223336--1223695 Score: 481
Period size: 120 Copynumber: 3.1 Consensus size: 120
1223326 AATGATTTGA
* *
1223336 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* *
1223400 AT-AAT-GAAAT--T---A---TTATTAATTTTTAATGATTTGATAGTAATGATT
66 ATGAATAGAAATAATGAAATTGTTATTAATATTTAATGATATGATAGTAATGATT
* * *
1223445 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* * *
1223510 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
66 ATGAATAGAAATAATGAAATTGTTATTAATATTTAATGATATGATAGTAATGATT
* *
1223565 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
* * * * * *
1223630 ATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
66 ATGAATAGAAATAATGAAATTGTTATTAATATTTAATGATATGATAGTAATGATT
1223685 TAGTAATGATT
1 TAGTAATGATT
1223696 TGATAGTAAT
Statistics
Matches: 230, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
109 58 0.25
110 7 0.03
111 2 0.01
112 4 0.02
114 1 0.00
117 1 0.00
120 157 0.68
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.46
Consensus pattern (120 bp):
TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
ATGAATAGAAATAATGAAATTGTTATTAATATTTAATGATATGATAGTAATGATT
Found at i:1223630 original size:11 final size:11
Alignment explanation
Indices: 1223614--1223711 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 11
1223604 AATGATTTGA
1223614 TAGTAATGATT
1 TAGTAATGATT
1223625 TAGTAATGA-T
1 TAGTAATGATT
*
1223635 TAGTAAT-AAT
1 TAGTAATGATT
*
1223645 TA--AATTA-T
1 TAGTAATGATT
*
1223653 TATTAAT--TT
1 TAGTAATGATT
1223662 T--TAATGATTT
1 TAGTAATGA-TT
1223672 GATAGTAATGATT
1 --TAGTAATGATT
1223685 TAGTAATGATTT
1 TAGTAATGA-TT
1223697 GATAGTAATGATT
1 --TAGTAATGATT
1223710 TA
1 TA
1223712 TTATAAATAT
Statistics
Matches: 72, Mismatches: 0, Indels: 30
0.71 0.00 0.29
Matches are distributed among these distances:
7 4 0.06
8 6 0.08
9 4 0.06
10 16 0.22
11 20 0.28
12 3 0.04
13 4 0.06
14 15 0.21
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:1223682 original size:14 final size:14
Alignment explanation
Indices: 1223663--1223710 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
1223653 TATTAATTTT
1223663 TAATGATTTGATAG
1 TAATGATTTGATAG
1223677 TAATGA-TT--TAG
1 TAATGATTTGATAG
1223688 TAATGATTTGATAG
1 TAATGATTTGATAG
1223702 TAATGATTT
1 TAATGATTT
1223711 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1223715 original size:60 final size:60
Alignment explanation
Indices: 1223385--1223695 Score: 568
Period size: 60 Copynumber: 5.2 Consensus size: 60
1223375 AATGATTTGA
1223385 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1223445 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* * *
1223505 TAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
* *
1223565 TAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
*
1223625 TAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
1223685 TAGTAATGATT
1 TAGTAATGATT
1223696 TGATAGTAAT
Statistics
Matches: 244, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 244 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT
Found at i:1225867 original size:15 final size:16
Alignment explanation
Indices: 1225847--1225880 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1225837 CGAAAAAATT
1225847 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
1225862 TAATATAATAAACTTA
1 TAATATAATAAACTTA
1225878 TAA
1 TAA
1225881 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:1225967 original size:30 final size:30
Alignment explanation
Indices: 1225933--1226022 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
1225923 TTTCTTTAAA
1225933 CAACTAATAAACTATTCTTTAATATAATTT
1 CAACTAATAAACTATTCTTTAATATAATTT
*
1225963 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAATTT
* * *
1225993 AAACTAATAAAATATTTTTTAATTATAATT
1 CAACTAATAAACTATTCTTTAA-TATAATT
1226023 CACTACTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 48 0.89
31 6 0.11
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAATTT
Found at i:1225985 original size:15 final size:16
Alignment explanation
Indices: 1225937--1225991 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1225927 TTTAAACAAC
1225937 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
1225952 TAATATAA-T-TTCAAC
1 TAATATAACTATTC-TT
1225967 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
1225982 TAATATAACT
1 TAATATAACT
1225992 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:1226196 original size:17 final size:17
Alignment explanation
Indices: 1226174--1226206 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1226164 ATTTTTTACT
1226174 CTAACCCTAAACTAACC
1 CTAACCCTAAACTAACC
1226191 CTAACCCTAAACTAAC
1 CTAACCCTAAACTAAC
1226207 AAACTAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (17 bp):
CTAACCCTAAACTAACC
Found at i:1236603 original size:2 final size:2
Alignment explanation
Indices: 1236592--1236635 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1236582 TGTAACACTT
1236592 TA TA -A 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
1236633 TA T
1 TA T
1236636 GTTGAGTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1238228 original size:14 final size:13
Alignment explanation
Indices: 1238200--1238257 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
1238190 CAAGAGTTAG
*
1238200 TAAAAA-AAGAAA
1 TAAAAATAATAAA
1238212 TAAAAATGAATAAA
1 TAAAAAT-AATAAA
*
1238226 TAAATAATACTAAGA
1 TAAA-AATAATAA-A
1238241 TAAAAATAAT-AA
1 TAAAAATAATAAA
1238253 TAAAA
1 TAAAA
1238258 GGTTAGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 12 0.31
13 1 0.03
14 18 0.46
15 8 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (13 bp):
TAAAAATAATAAA
Found at i:1238762 original size:16 final size:15
Alignment explanation
Indices: 1238736--1238765 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1238726 TGTTGTGGCC
1238736 GGTCATCCCGGGATG
1 GGTCATCCCGGGATG
1238751 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
1238766 CTTCGGCCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.27, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATG
Found at i:1239120 original size:29 final size:28
Alignment explanation
Indices: 1239067--1239127 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1239057 AATTATATAT
*
1239067 TATAGTTTAAAAAATATTTTCAAAATTA
1 TATAGTTTAAAAAATATTTTCAAAACTA
* * *
1239095 TATAGTTTTCAAAAATGTTTTTAAAACTA
1 TATAG-TTTAAAAAATATTTTCAAAACTA
1239124 TATA
1 TATA
1239128 TTACATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (28 bp):
TATAGTTTAAAAAATATTTTCAAAACTA
Found at i:1239157 original size:36 final size:36
Alignment explanation
Indices: 1239091--1239349 Score: 227
Period size: 36 Copynumber: 7.2 Consensus size: 36
1239081 TATTTTCAAA
*
1239091 ATTATAT-AGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTTTC-AAAATGTTTTAAAAACTATAT
* * *
1239127 ATTACATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
** *
1239163 AATATATATGTGTTTTAAAAATGTTTT-AAAA--AT-T
1 -AT-TATATAAGTTTTCAAAATGTTTTAAAAACTATAT
1239197 A-TATAT-A-TTTTCAAAATGTTTTAAAAACTATAT
1 ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
* * *
1239230 GA-TATATATA-TATTTAAAAATATTTTAAAAATTATAT
1 -ATTATATA-AGT-TTTCAAAATGTTTTAAAAACTATAT
*
1239267 ATTATATTTA-TTTTCAAAATGTTTTAAAAACTATAT
1 ATTATA-TAAGTTTTCAAAATGTTTTAAAAACTATAT
*
1239303 -TATATATAAATGTTTTCAAACATGTTTTCAAAACTATAT
1 AT-TATAT-AA-GTTTTCAAA-ATGTTTTAAAAACTATAT
1239342 ATTATATA
1 ATTATATA
1239350 TATACTTTTA
Statistics
Matches: 185, Mismatches: 19, Indels: 36
0.77 0.08 0.15
Matches are distributed among these distances:
29 14 0.08
30 4 0.02
31 5 0.03
32 2 0.01
33 2 0.01
34 7 0.04
35 4 0.02
36 55 0.30
37 41 0.22
38 28 0.15
39 22 0.12
40 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
ATTATATAAGTTTTCAAAATGTTTTAAAAACTATAT
Found at i:1239195 original size:103 final size:102
Alignment explanation
Indices: 1239033--1239307 Score: 289
Period size: 103 Copynumber: 2.7 Consensus size: 102
1239023 AACACATATA
* * * *
1239033 ATATATATTTTAAAAATATTT-TAAAATTATATATTATA---GTTTAAAAAATATTTTCAAAATT
1 ATATATA-TTTAAAAATATTTCAAAAATTATATATTATATGTGTTTTAAAAATGTTTTAAAAATT
* *
1239094 ATATA-GTTTTCAAAAATGTTTTTAAAACTATAT-ATTAC
65 ATATATATTTTC-AAAATGTTTTAAAAACTATATGA-TAC
* *
1239132 ATA-AGT-TTTCAAAATGATTTC-AAAACTATATAATATATATGTGTTTTAAAAATGTTTTAAAA
1 ATATA-TATTTAAAAAT-ATTTCAAAAATTATAT-AT-TATATGTGTTTTAAAAATGTTTTAAAA
*
1239194 ATTATATATATTTTCAAAATGTTTTAAAAACTATATGATAT
62 ATTATATATATTTTCAAAATGTTTTAAAAACTATATGATAC
* * * * *
1239235 ATATATATTTAAAAATATTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAACTA
1 ATATATATTTAAAAATATTTCAAAAATTATATATTATATGTGTTTTAAAAATGTTTTAAAAATTA
1239300 TATTATAT
66 TA-TATAT
1239308 ATAAATGTTT
Statistics
Matches: 147, Mismatches: 15, Indels: 24
0.79 0.08 0.13
Matches are distributed among these distances:
97 8 0.05
98 14 0.10
99 6 0.04
100 4 0.03
102 29 0.20
103 62 0.42
104 24 0.16
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (102 bp):
ATATATATTTAAAAATATTTCAAAAATTATATATTATATGTGTTTTAAAAATGTTTTAAAAATTA
TATATATTTTCAAAATGTTTTAAAAACTATATGATAC
Found at i:1239199 original size:29 final size:29
Alignment explanation
Indices: 1239167--1239230 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1239157 CTATATAATA
* *
1239167 TATATGTGTTTTAAAAATGTTTTAAAAAT
1 TATATGTATTTTAAAAATGTTTTAAAAAC
* *
1239196 TATATATATTTTCAAAATGTTTTAAAAAC
1 TATATGTATTTTAAAAATGTTTTAAAAAC
1239225 TATATG
1 TATATG
1239231 ATATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (29 bp):
TATATGTATTTTAAAAATGTTTTAAAAAC
Found at i:1239281 original size:73 final size:74
Alignment explanation
Indices: 1239093--1239393 Score: 273
Period size: 73 Copynumber: 4.1 Consensus size: 74
1239083 TTTTCAAAAT
* * * * * *
1239093 TATATAGT-TTTCAAAAATGTTTTTAAAACTATATATTACA-TAAGTTTTCAAAATGATTTCAAA
1 TATATA-TATTTCAAAAATATTTTAAAAACTATATATTATATTTA-TTTTCAAAATGTTTTAAAA
1239156 ACTATATAATA
64 ACTATATAATA
* * * *
1239167 TATATGTGTTTTAAAAATGTTTT-AAAA--AT-TA-TATA--TATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTCAAAAATATTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
*
1239225 TATATGATA
66 TATATAATA
*
1239234 TATATATATTT-AAAAATATTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
1 TATATATATTTCAAAAATATTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
*
1239298 TATATTATA
66 TATATAATA
* * * * * *
1239307 TATAAATGTTTTCAAACATGTTTTCAAAACTATATATTATATATATACTTTTAAAAAATGTTTT-
1 TATATAT-ATTTCAAAAATATTTTAAAAACTATATATTATAT-T-TA-TTTT-CAAAATGTTTTA
* *
1239371 CAAACTATACAATA
61 AAAACTATATAATA
1239385 TATATATAT
1 TATATATAT
1239394 ATATATGTAT
Statistics
Matches: 190, Mismatches: 23, Indels: 25
0.80 0.10 0.11
Matches are distributed among these distances:
66 10 0.05
67 40 0.21
68 1 0.01
69 5 0.03
70 4 0.02
71 6 0.03
73 42 0.22
74 22 0.12
75 25 0.13
76 1 0.01
77 3 0.02
78 21 0.11
79 10 0.05
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (74 bp):
TATATATATTTCAAAAATATTTTAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAAC
TATATAATA
Found at i:1239376 original size:39 final size:37
Alignment explanation
Indices: 1239196--1239393 Score: 190
Period size: 39 Copynumber: 5.2 Consensus size: 37
1239186 TTTTAAAAAT
*
1239196 TATATATATTTTCAAAATGTTTTAAAAACTATATGA-TA
1 TATATATATTTTAAAAATGTTTT-AAAACTATAT-ATTA
* *
1239234 TATATATA-TTTAAAAATATTTTAAAAATTATATATTA
1 TATATATATTTTAAAAATGTTTT-AAAACTATATATTA
*
1239271 TAT-T-TATTTTCAAAATGTTTTAAAAACTATAT-TATA
1 TATATATATTTTAAAAATGTTTT-AAAACTATATAT-TA
* * *
1239307 TATAAATGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATATATATTTT-AAAAATGTTTT-AAAACTATATATTA
* * *
1239346 TATATATACTTTTAAAAAATGTTTTCAAACTATACAATA
1 TATATATA-TTTT-AAAAATGTTTTAAAACTATATATTA
1239385 TATATATAT
1 TATATATAT
1239394 ATATATGTAT
Statistics
Matches: 134, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
35 3 0.02
36 29 0.22
37 27 0.20
38 14 0.10
39 46 0.34
40 15 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATATTTTAAAAATGTTTTAAAACTATATATTA
Found at i:1240130 original size:80 final size:80
Alignment explanation
Indices: 1239939--1240284 Score: 512
Period size: 80 Copynumber: 4.3 Consensus size: 80
1239929 CTGAGTGTAA
* * * *
1239939 TCGAACTCGAAGGTCTTCGGTTGACAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T---AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
* * * * *
1240004 GCCCTCGAAGCTGAGTGCAA
62 G-CCTTGGAGCTGAGCGGAG
*
1240024 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
1 TCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
1240089 TGGAGCTGAGCGGAG
66 TGGAGCTGAGCGGAG
1240104 TCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
1 TCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
1240169 TGGAGCTGAGCGGAG
66 TGGAGCTGAGCGGAG
* * *
1240184 TCGAACTTGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
*
1240249 TGGAGCTGAGCGTAG
66 TGGAGCTGAGCGGAG
*
1240264 TCGAACTCAAAGGTCTTTGGT
1 TCGAACTCGAAGGTCTTTGGT
1240285 TGGCAAATAA
Statistics
Matches: 243, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
80 186 0.77
81 38 0.16
85 19 0.08
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (80 bp):
TCGAACTCGAAGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCT
TGGAGCTGAGCGGAG
Found at i:1240636 original size:106 final size:106
Alignment explanation
Indices: 1240450--1241666 Score: 2046
Period size: 106 Copynumber: 11.5 Consensus size: 106
1240440 GCATTGTTTC
* * * * * * *
1240450 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
1240515 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTACGTTGTCTC
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1240556 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* *
1240621 CCAGTGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1240662 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1240727 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1240768 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGCTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1240833 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1240874 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1240939 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1240980 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
* * *
1241045 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1241086 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1241151 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1241192 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1241256 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1241297 GAGTCCAATATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
1241362 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1241403 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAACTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1241467 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1241508 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1241572 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1241613 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1241667 CTCGCTGACA
Statistics
Matches: 1050, Mismatches: 58, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
105 304 0.29
106 746 0.71
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1244337 original size:14 final size:15
Alignment explanation
Indices: 1244318--1244352 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1244308 GCGAATGAAA
*
1244318 AAAAAATGCCA-AAG
1 AAAAAATGCAAGAAG
1244332 AAAAAATGCAAGAAG
1 AAAAAATGCAAGAAG
1244347 AAAAAA
1 AAAAAA
1244353 AAAGTTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.71, C:0.09, G:0.14, T:0.06
Consensus pattern (15 bp):
AAAAAATGCAAGAAG
Found at i:1245532 original size:14 final size:13
Alignment explanation
Indices: 1245504--1245561 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
1245494 CAAGAGTTAG
*
1245504 TAAAAA-AAGAAA
1 TAAAAATAATAAA
1245516 TAAAAATGAATAAA
1 TAAAAAT-AATAAA
*
1245530 TAAATAATACTAAGA
1 TAAA-AATAATAA-A
1245545 TAAAAATAAT-AA
1 TAAAAATAATAAA
1245557 TAAAA
1 TAAAA
1245562 GGTTAGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 12 0.31
13 1 0.03
14 18 0.46
15 8 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (13 bp):
TAAAAATAATAAA
Found at i:1246806 original size:29 final size:28
Alignment explanation
Indices: 1246753--1246813 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1246743 AATTATATAT
*
1246753 TATAGTTTAAAAAATATTTTCAAAATTA
1 TATAGTTTAAAAAATATTTTCAAAACTA
* * *
1246781 TATAGTTTTCAAAAATGTTTTTAAAACTA
1 TATAG-TTTAAAAAATATTTTCAAAACTA
1246810 TATA
1 TATA
1246814 TTACATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (28 bp):
TATAGTTTAAAAAATATTTTCAAAACTA
Found at i:1246843 original size:36 final size:36
Alignment explanation
Indices: 1246777--1247035 Score: 166
Period size: 36 Copynumber: 7.2 Consensus size: 36
1246767 TATTTTCAAA
* *
1246777 ATTATAT-AGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAAGTTTTC-AAAATGATTTAAAAACTATAT
* *
1246813 ATTACATAAGTTTTCAAAATGATTTCAAAACTATAT
1 ATTATATAAGTTTTCAAAATGATTTAAAAACTATAT
* ** * * *
1246849 AATAAATATGTGTTTTAAAAATG-TTTTAAAA--AT-C
1 -AT-TATATAAGTTTTCAAAATGATTTAAAAACTATAT
1246883 A-TATAT-A-TTTTCAAAAT-ATTTTAAAAACTATAT
1 ATTATATAAGTTTTCAAAATGA-TTTAAAAACTATAT
* * *
1246916 GA-TATATATATTTTTAAAAAT-ATTTTAAAAATTATAT
1 -ATTATATA-AGTTTTCAAAATGA-TTTAAAAACTATAT
* *
1246953 ATTATATTTA-TTTTCAAAATGTTTTAAAAACTATAT
1 ATTATA-TAAGTTTTCAAAATGATTTAAAAACTATAT
* *
1246989 -TATATATAAATGTTTTCAAACATGTTTTCAAAACTATAT
1 AT-TATAT-AA-GTTTTCAAA-ATGATTTAAAAACTATAT
1247028 ATTATATA
1 ATTATATA
1247036 TATACTTTTA
Statistics
Matches: 179, Mismatches: 23, Indels: 40
0.74 0.10 0.17
Matches are distributed among these distances:
29 9 0.05
30 7 0.04
31 4 0.02
32 2 0.01
33 1 0.01
34 6 0.03
35 4 0.02
36 54 0.30
37 45 0.25
38 24 0.13
39 22 0.12
40 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATTATATAAGTTTTCAAAATGATTTAAAAACTATAT
Found at i:1246871 original size:38 final size:36
Alignment explanation
Indices: 1246784--1247070 Score: 160
Period size: 36 Copynumber: 7.9 Consensus size: 36
1246774 AAAATTATAT
* * *
1246784 AGTTTTCAAAAATGTTTTTAAAACTATATATTACATA
1 AGTTTT-AAAAATGTTTTAAAAACTATATAATAAATA
* * *
1246821 AGTTTTCAAAATGATTTCAAAACTATATAATAAATA
1 AGTTTTAAAAATGTTTTAAAAACTATATAATAAATA
* *
1246857 TGTGTTTTAAAAATGTTTTAAAAA-T-CAT-AT--AT-
1 --AGTTTTAAAAATGTTTTAAAAACTATATAATAAATA
* * * *
1246889 A-TTTTCAAAATATTTTAAAAACTATATGATATATA
1 AGTTTTAAAAATGTTTTAAAAACTATATAATAAATA
* * * * * *
1246924 TATTTTTAAAAATATTTTAAAAATTATATATTATATTT
1 -AGTTTTAAAAATGTTTTAAAAACTATATAATA-AATA
* * *
1246962 A-TTTTCAAAATGTTTTAAAAACTATATTATATATAA
1 AGTTTTAAAAATGTTTTAAAAACTATATAATAAAT-A
* * *
1246998 ATGTTTTCAAACATGTTTTCAAAACTATATATTATATATA
1 A-GTTTT-AAAAATGTTTTAAAAACTATATA--ATAAATA
* * *
1247038 TACTTTTAAAAAATGTTTT-CAAACTATACAATA
1 -AGTTTT-AAAAATGTTTTAAAAACTATATAATA
1247071 TATATATATA
Statistics
Matches: 194, Mismatches: 38, Indels: 36
0.72 0.14 0.13
Matches are distributed among these distances:
29 18 0.09
30 1 0.01
31 2 0.01
32 2 0.01
33 2 0.01
34 2 0.01
35 3 0.02
36 54 0.28
37 37 0.19
38 23 0.12
39 28 0.14
40 15 0.08
41 7 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
AGTTTTAAAAATGTTTTAAAAACTATATAATAAATA
Found at i:1246881 original size:103 final size:100
Alignment explanation
Indices: 1246721--1246988 Score: 255
Period size: 103 Copynumber: 2.7 Consensus size: 100
1246711 CACATATAAT
* * * * *
1246721 ATATA-TTTTAAAAATATTT-TAAAATTATATAT--TAT-AGTTTAAAAAATATTTTCAAAATTA
1 ATATAGTTTTAAAAATATTTCAAAAATTATATATAATATGTGTTTTAAAAATGTTTTAAAAATTA
* *
1246781 TATAGTTTTCAAAAATGTTTTTAAAACTATAT-ATTAC
66 TATA-TTTTC-AAAATATTTTAAAAACTATATGA-TAC
* *
1246818 ATA-AGTTTTCAAAATGATTTC-AAAACTATATAATAAATATGTGTTTTAAAAATGTTTTAAAAA
1 ATATAGTTTTAAAAAT-ATTTCAAAAATTATAT-AT-AATATGTGTTTTAAAAATGTTTTAAAAA
*
1246881 TCATATATATTTTCAAAATATTTTAAAAACTATATGATAT
63 T--TATATATTTTCAAAATATTTTAAAAACTATATGATAC
* * * * * * *
1246921 ATATATTTTTAAAAATATTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTAAAAACTA
1 ATATAGTTTTAAAAATATTTCAAAAATTATATATAATATGTGTTTTAAAAATGTTTTAAAAATTA
1246986 TAT
66 TAT
1246989 TATATATAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
96 1 0.01
97 12 0.09
98 13 0.09
99 2 0.01
100 5 0.04
102 27 0.19
103 49 0.35
104 25 0.18
105 6 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (100 bp):
ATATAGTTTTAAAAATATTTCAAAAATTATATATAATATGTGTTTTAAAAATGTTTTAAAAATTA
TATATTTTCAAAATATTTTAAAAACTATATGATAC
Found at i:1246909 original size:11 final size:11
Alignment explanation
Indices: 1246887--1246947 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
1246877 AAAATCATAT
*
1246887 ATATTTTCAAA
1 ATATTTTAAAA
1246898 ATATTTTAAAA
1 ATATTTTAAAA
* * *
1246909 ACTATATGATATAT
1 A-TAT-T-TTAAAA
1246923 ATATTTTTAAAA
1 ATA-TTTTAAAA
1246935 ATATTTTAAAA
1 ATATTTTAAAA
1246946 AT
1 AT
1246948 TATATATTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 21 0.54
12 9 0.23
13 4 0.10
14 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (11 bp):
ATATTTTAAAA
Found at i:1246915 original size:29 final size:30
Alignment explanation
Indices: 1246861--1246920 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
1246851 TAAATATGTG
*
1246861 TTTTAAAAATGTTTTAAAAATCATAT-ATA
1 TTTTAAAAATATTTTAAAAATCATATGATA
*
1246890 TTTTCAAAATATTTTAAAAA-CTATATGATA
1 TTTTAAAAATATTTTAAAAATC-ATATGATA
1246920 T
1 T
1246921 ATATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 22 0.81
30 4 0.15
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (30 bp):
TTTTAAAAATATTTTAAAAATCATATGATA
Found at i:1246940 original size:37 final size:37
Alignment explanation
Indices: 1246883--1247079 Score: 193
Period size: 39 Copynumber: 5.2 Consensus size: 37
1246873 TTTAAAAATC
*
1246883 ATATATATTTTCAAAATATTTTAAAAACTATATGATAT
1 ATATATATTTTAAAAATATTTTAAAAACTATAT-ATAT
*
1246921 ATATAT-TTTTAAAAATATTTTAAAAATTATATAT-T
1 ATATATATTTTAAAAATATTTTAAAAACTATATATAT
* * *
1246956 ATATTTATTTTCAAAATGTTTTAAAAACTATATTATAT
1 ATATATATTTTAAAAATATTTTAAAAACTATA-TATAT
* * * * *
1246994 ATAAATGTTTTCAAACATGTTTTCAAAACTATATATTAT
1 ATATATATTTT-AAAAATATTTTAAAAACTATATA-TAT
** *
1247033 ATATATACTTTTAAAAA-ATGTTTTCAAACTATACAATAT
1 ATATATA-TTTTAAAAATAT-TTTAAAAACTATA-TATAT
1247072 ATATATAT
1 ATATATAT
1247080 ATATATATAT
Statistics
Matches: 132, Mismatches: 19, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
35 6 0.05
36 24 0.18
37 27 0.20
38 19 0.14
39 51 0.39
40 5 0.04
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
ATATATATTTTAAAAATATTTTAAAAACTATATATAT
Found at i:1246967 original size:140 final size:140
Alignment explanation
Indices: 1246779--1247030 Score: 330
Period size: 140 Copynumber: 1.8 Consensus size: 140
1246769 TTTTCAAAAT
* * *
1246779 TATATAGTTTTCAAAAATGTTTTTAAAACTATATATTACATAAGTTTTCAAAATGATTTCAAAAC
1 TATATAGTTTTCAAAAATATTTTAAAAACTATATATTACATAAGTTTTCAAAATGATTTAAAAAC
**
1246844 TATATAATAAATATGTGTTTT-AAAAATGTTTTAAAAATCATATATATTTTCAAAATATTTTAAA
66 TATATAATAAATAAATGTTTTCAAAAATGTTTTAAAAA-C-TATATATTTTCAAAATATTTTAAA
1246908 AACTATATGATA
129 AACTATATGATA
* * * * *
1246920 TATATA-TTTTTAAAAATATTTTAAAAATTATATATTATATTTA-TTTTCAAAATGTTTTAAAAA
1 TATATAGTTTTCAAAAATATTTTAAAAACTATATATTACA-TAAGTTTTCAAAATGATTTAAAAA
* * * *
1246983 CTATATTATATATAAATGTTTTCAAACATGTTTTCAAAACTATATATT
65 CTATATAATAAATAAATGTTTTCAAAAATGTTTTAAAAACTATATATT
1247031 ATATATATAC
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
139 8 0.08
140 65 0.68
141 22 0.23
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (140 bp):
TATATAGTTTTCAAAAATATTTTAAAAACTATATATTACATAAGTTTTCAAAATGATTTAAAAAC
TATATAATAAATAAATGTTTTCAAAAATGTTTTAAAAACTATATATTTTCAAAATATTTTAAAAA
CTATATGATA
Found at i:1247075 original size:2 final size:2
Alignment explanation
Indices: 1247068--1247133 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1247058 AAACTATACA
1247068 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
1247110 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
1247134 GTGTGTGTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1247637 original size:8 final size:8
Alignment explanation
Indices: 1247624--1247709 Score: 65
Period size: 8 Copynumber: 11.2 Consensus size: 8
1247614 GTTTTTATAA
1247624 TTTATTAT
1 TTTATTAT
1247632 TTTATT-T
1 TTTATTAT
* **
1247639 ATTAAAATT
1 TTTATTA-T
1247648 TTTATTAT
1 TTTATTAT
* * *
1247656 TTAAGTAA
1 TTTATTAT
*
1247664 TTAATT-T
1 TTTATTAT
1247671 -TTATTAT
1 TTTATTAT
1247678 TTTATTA-
1 TTTATTAT
1247685 TTTATT-T
1 TTTATTAT
1247692 TTTATTAT
1 TTTATTAT
1247700 TTTATTAT
1 TTTATTAT
1247708 TT
1 TT
1247710 AATTGTAAAC
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
6 4 0.07
7 17 0.28
8 34 0.57
9 5 0.08
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (8 bp):
TTTATTAT
Found at i:1247706 original size:22 final size:22
Alignment explanation
Indices: 1247624--1247713 Score: 117
Period size: 22 Copynumber: 4.0 Consensus size: 22
1247614 GTTTTTATAA
*
1247624 TTTATTATTTTATTTATTAAAATT
1 TTTATTATTTTA-TTATT-TAATT
* * *
1247648 TTTATTATTTAAGTAATTAATT
1 TTTATTATTTTATTATTTAATT
*
1247670 TTTATTATTTTATTATTTATTT
1 TTTATTATTTTATTATTTAATT
1247692 TTTATTATTTTATTATTTAATT
1 TTTATTATTTTATTATTTAATT
1247714 GTAAACTTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
22 43 0.75
23 3 0.05
24 11 0.19
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (22 bp):
TTTATTATTTTATTATTTAATT
Found at i:1247710 original size:15 final size:15
Alignment explanation
Indices: 1247616--1247709 Score: 77
Period size: 15 Copynumber: 6.2 Consensus size: 15
1247606 GTATAATTGT
*
1247616 TTTTATAATTTATTA
1 TTTTATTATTTATTA
**
1247631 TTTTATT-TATTAAAA
1 TTTTATTAT-TTATTA
*
1247646 TTTTTATTATTTAAGTA
1 -TTTTATTATTT-ATTA
* *
1247663 ATTAATT-TTTATTA
1 TTTTATTATTTATTA
1247677 TTTTATTATTTATT-
1 TTTTATTATTTATTA
1247691 TTTTATTATTTTATTA
1 TTTTATTA-TTTATTA
1247707 TTT
1 TTT
1247710 AATTGTAAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
14 17 0.27
15 25 0.40
16 17 0.27
17 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (15 bp):
TTTTATTATTTATTA
Found at i:1248624 original size:2 final size:2
Alignment explanation
Indices: 1248617--1248650 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1248607 TTATAGAATG
1248617 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
1248651 TAAACAGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1251616 original size:32 final size:32
Alignment explanation
Indices: 1251544--1251618 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
1251534 TTTCATACGG
1251544 CGTGCCATTCAAGGGAGGTGCGTTCCCTAGGA
1 CGTGCCATTCAAGGGAGGTGCGTTCCCTAGGA
* ** *
1251576 TGCACCATTCGAGGGAGGTGCGTTCCCTAGGA
1 CGTGCCATTCAAGGGAGGTGCGTTCCCTAGGA
1251608 CGTGCCATTCA
1 CGTGCCATTCA
1251619 TAAAACCCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.23
Consensus pattern (32 bp):
CGTGCCATTCAAGGGAGGTGCGTTCCCTAGGA
Found at i:1271745 original size:26 final size:26
Alignment explanation
Indices: 1271709--1271760 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1271699 CCCTAACAAA
1271709 GGCGATAAGAATAAGGAATCGTAGGT
1 GGCGATAAGAATAAGGAATCGTAGGT
1271735 GGCGATAAGAATAAGGAATCGTAGGT
1 GGCGATAAGAATAAGGAATCGTAGGT
1271761 TCACTTACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.35, T:0.19
Consensus pattern (26 bp):
GGCGATAAGAATAAGGAATCGTAGGT
Found at i:1275048 original size:15 final size:16
Alignment explanation
Indices: 1275022--1275053 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1275012 ATTTTTAATA
1275022 ACATATGATATTATGG
1 ACATATGATATTATGG
1275038 ACATA-GATATTATGG
1 ACATATGATATTATGG
1275053 A
1 A
1275054 TATCGCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (16 bp):
ACATATGATATTATGG
Found at i:1276950 original size:25 final size:24
Alignment explanation
Indices: 1276894--1276950 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 24
1276884 TTGAAAAAAC
*
1276894 TATTTTAAAAGCTCGTTTATCGGT
1 TATTTTATAAGCTCGTTTATCGGT
1276918 TCA-TTTATAAGCTCGTTTATTCGGT
1 T-ATTTTATAAGCTCGTTTA-TCGGT
1276943 TATTTTAT
1 TATTTTAT
1276951 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (24 bp):
TATTTTATAAGCTCGTTTATCGGT
Found at i:1305029 original size:14 final size:14
Alignment explanation
Indices: 1305001--1305047 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1304991 CGCTGAGCAT
*
1305001 CCGAGGCCATTCGA
1 CCGAGGCCATCCGA
1305015 CCGAGAG-CATCCGA
1 CCGAG-GCCATCCGA
1305029 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1305043 GCGAG
1 CCGAG
1305048 CTATGCGAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.23, C:0.36, G:0.32, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1305138 original size:29 final size:29
Alignment explanation
Indices: 1305096--1305200 Score: 165
Period size: 29 Copynumber: 3.6 Consensus size: 29
1305086 GGAGCAGGAG
*
1305096 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCC
* *
1305125 GGAGTGCATGGCGACCTACAAGATTGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCC
*
1305154 GGAGTACATGGCGACCTACAAGGTCGCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCC
*
1305183 GGAGGGCATGGCGACCTA
1 GGAGTGCATGGCGACCTA
1305201 TGCTTGGGGA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCC
Found at i:1305600 original size:21 final size:21
Alignment explanation
Indices: 1305574--1305617 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1305564 GTTTCCAGAT
1305574 TCGCAACACGAACTTCGACTA
1 TCGCAACACGAACTTCGACTA
**
1305595 TCGCAATGCGAACTTCGACTA
1 TCGCAACACGAACTTCGACTA
1305616 TC
1 TC
1305618 ACAATGCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (21 bp):
TCGCAACACGAACTTCGACTA
Found at i:1305671 original size:83 final size:83
Alignment explanation
Indices: 1305582--1305775 Score: 325
Period size: 83 Copynumber: 2.3 Consensus size: 83
1305572 ATTCGCAACA
*
1305582 CGAACTTCGACTATCGCAATGCGAACTTCGACTATCACAATGCGAATATGTAAATCGCAATGCGA
1 CGAACTTGGACTATCGCAATGCGAACTTCGACTATCACAATGCGAATATGTAAATCGCAATGCGA
*
1305647 TAGTCAACTAGCGCAATG
66 TAGTCAACTAGCACAATG
* **
1305665 CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGTAATGCGAATATGTAAATCGCAATGCGA
1 CGAACTTGGACTATCGCAATGCGAACTTCGACTATCACAATGCGAATATGTAAATCGCAATGCGA
* *
1305730 TAGTCGACTATCACAATG
66 TAGTCAACTAGCACAATG
1305748 CGAACTTGGACTATCGCAATGCGAACTT
1 CGAACTTGGACTATCGCAATGCGAACTT
1305776 GTAAATCGTA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 103 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (83 bp):
CGAACTTGGACTATCGCAATGCGAACTTCGACTATCACAATGCGAATATGTAAATCGCAATGCGA
TAGTCAACTAGCACAATG
Found at i:1305724 original size:62 final size:62
Alignment explanation
Indices: 1305673--1305794 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 62
1305663 TGCGAACTTG
* *
1305673 GACTATCGCAACGCGAACTTCGACTATCGTAATGCGAA-TATGTAAATCGCAATGCGATAGTC
1 GACTATCACAACGCGAACTTCGACTATCGCAATGCGAACT-TGTAAATCGCAATGCGATAGTC
* * *
1305735 GACTATCACAATGCGAACTTGGACTATCGCAATGCGAACTTGTAAATCGTAATGCGATAG
1 GACTATCACAACGCGAACTTCGACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAG
1305795 CCGAAGTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 53 0.98
63 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (62 bp):
GACTATCACAACGCGAACTTCGACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAGTC
Found at i:1305776 original size:21 final size:21
Alignment explanation
Indices: 1305582--1305775 Score: 170
Period size: 21 Copynumber: 9.3 Consensus size: 21
1305572 ATTCGCAACA
1305582 CGAACTTCGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
*
1305603 CGAACTTCGACTATCACAATG
1 CGAACTTCGACTATCGCAATG
*
1305624 CGAA-TAT-GTA-AATCGCAATG
1 CGAACT-TCG-ACTATCGCAATG
* * *
1305644 CGATA-GTCAACTAGCGCAATG
1 CGA-ACTTCGACTATCGCAATG
* *
1305665 CGAACTTGGACTATCGCAACG
1 CGAACTTCGACTATCGCAATG
*
1305686 CGAACTTCGACTATCGTAATG
1 CGAACTTCGACTATCGCAATG
*
1305707 CGAA-TAT-GTA-AATCGCAATG
1 CGAACT-TCG-ACTATCGCAATG
* *
1305727 CGATA-GTCGACTATCACAATG
1 CGA-ACTTCGACTATCGCAATG
*
1305748 CGAACTTGGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
1305769 CGAACTT
1 CGAACTT
1305776 GTAAATCGTA
Statistics
Matches: 138, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
20 32 0.23
21 106 0.77
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
CGAACTTCGACTATCGCAATG
Found at i:1305789 original size:41 final size:41
Alignment explanation
Indices: 1305582--1305791 Score: 160
Period size: 41 Copynumber: 5.1 Consensus size: 41
1305572 ATTCGCAACA
* **
1305582 CGAACTTCGACTATCGCAATGCGAACTTCGACTATCACAATG
1 CGAACTTGGACTATCGCAATGCGAACTT-GACTATCGTAATG
* * * ** * *
1305624 CGAA-TATGTA-AATCGCAATGCGATAGTCAACTAGCGCAATG
1 CGAACT-TGGACTATCGCAATGCGA-ACTTGACTATCGTAATG
*
1305665 CGAACTTGGACTATCGCAACGCGAACTTCGACTATCGTAATG
1 CGAACTTGGACTATCGCAATGCGAACTT-GACTATCGTAATG
* * * * **
1305707 CGAA-TATGTA-AATCGCAATGCGATAGTCGACTATCACAATG
1 CGAACT-TGGACTATCGCAATGCGA-ACTTGACTATCGTAATG
*
1305748 CGAACTTGGACTATCGCAATGCGAACTTGTA-AATCGTAATG
1 CGAACTTGGACTATCGCAATGCGAACTTG-ACTATCGTAATG
1305789 CGA
1 CGA
1305792 TAGCCGAAGT
Statistics
Matches: 128, Mismatches: 30, Indels: 21
0.72 0.17 0.12
Matches are distributed among these distances:
41 75 0.59
42 53 0.41
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
CGAACTTGGACTATCGCAATGCGAACTTGACTATCGTAATG
Found at i:1305900 original size:41 final size:42
Alignment explanation
Indices: 1305798--1305920 Score: 178
Period size: 41 Copynumber: 3.0 Consensus size: 42
1305788 GCGATAGCCG
* * *
1305798 AAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCC
1 AAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTAC
* *
1305840 AAGTTCGCATTGCGATAGTCGAAGTTCGCGTTACGAT-TTAC
1 AAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTAC
1305881 ATA-TTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGT
1 A-AGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGT
1305921 CCAAAATCGC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
41 36 0.50
42 36 0.50
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (42 bp):
AAGTTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTAC
Found at i:1305930 original size:21 final size:21
Alignment explanation
Indices: 1305787--1305924 Score: 174
Period size: 21 Copynumber: 6.6 Consensus size: 21
1305777 TAAATCGTAA
1305787 TGCGATAG-CCGAAGTTCGCGT
1 TGCGATAGTCC-AAGTTCGCGT
1305808 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
*
1305829 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAAGTTCGCGT
*
1305850 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
* * * *
1305871 TACGAT-TTACATA-TTCGCAT
1 TGCGATAGTCCA-AGTTCGCGT
*
1305891 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCCAAGTTCGCGT
1305912 TGCGATAGTCCAA
1 TGCGATAGTCCAA
1305925 AATCGCAACG
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
20 14 0.14
21 83 0.84
22 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCGCGT
Found at i:1306640 original size:19 final size:19
Alignment explanation
Indices: 1306616--1306732 Score: 108
Period size: 19 Copynumber: 5.7 Consensus size: 19
1306606 CATTGCGATT
1306616 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
1306635 TTGGACTATCACAACGAAT
1 TTGGACTATCGCAACGAAC
*
1306654 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1306677 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
1306696 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
1306719 TTCGACTATCGCAA
1 TTGGACTATCGCAA
1306733 TGCGAATATG
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
19 33 0.42
21 27 0.34
23 19 0.24
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1306687 original size:21 final size:21
Alignment explanation
Indices: 1306663--1306738 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
1306653 TTTGGAATAA
1306663 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
1306684 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTCGACT
1306703 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACT
*
1306726 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1306739 TATGTAAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.22
21 26 0.57
23 10 0.22
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1306729 original size:42 final size:42
Alignment explanation
Indices: 1306623--1306732 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
1306613 ATTTTGGACT
* * *
1306623 ATCGCAA--CGAACTTGGACTATCACAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1306663 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1306705 ATCGCAACGCGAACTTCGACTATCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
1306733 TGCGAATATG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 7 0.11
42 58 0.89
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:1309286 original size:2 final size:2
Alignment explanation
Indices: 1309281--1309310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1309271 ATACACACCC
1309281 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
1309311 GTTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1310270 original size:36 final size:37
Alignment explanation
Indices: 1310229--1310298 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
1310219 CTTAGGATTT
1310229 TATAAAAAATATCAAATTAA-TTTAAAATAAAAATTA
1 TATAAAAAATATCAAATTAATTTTAAAATAAAAATTA
*
1310265 TATAAAAATTATCAAATTAATTTTAAAATAAAAA
1 TATAAAAAATATCAAATTAATTTTAAAATAAAAA
1310299 AATTAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 19 0.59
37 13 0.41
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (37 bp):
TATAAAAAATATCAAATTAATTTTAAAATAAAAATTA
Found at i:1315579 original size:23 final size:23
Alignment explanation
Indices: 1315536--1315580 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1315526 CTATAATAAC
*
1315536 ATAACAAGTAGCGTTTATTTAAT
1 ATAACAAGTAGCGTCTATTTAAT
* *
1315559 ATAATAAGTAGCGTCTGTTTAA
1 ATAACAAGTAGCGTCTATTTAA
1315581 AGCTGACGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (23 bp):
ATAACAAGTAGCGTCTATTTAAT
Found at i:1316507 original size:31 final size:31
Alignment explanation
Indices: 1316469--1316591 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
1316459 CCCGAAGGAC
* *
1316469 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1316500 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1316531 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1316562 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1316592 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1318450 original size:21 final size:21
Alignment explanation
Indices: 1318426--1318530 Score: 70
Period size: 21 Copynumber: 5.1 Consensus size: 21
1318416 GCAAATTCGC
1318426 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** ***
1318447 GTTGAAAATCGCAACGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
1318467 TTTCCATTTTGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1318488 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1318508 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
1318529 GT
1 GT
1318531 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 27, Indels: 4
0.64 0.31 0.05
Matches are distributed among these distances:
20 26 0.47
21 29 0.53
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:1318475 original size:41 final size:41
Alignment explanation
Indices: 1318430--1318530 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
1318420 ATTCGCGTTG
1318430 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
* ***
1318471 CATTTTGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
1318512 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
1318531 CTACAGTTGT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATTTTC
Found at i:1318521 original size:20 final size:20
Alignment explanation
Indices: 1318462--1318527 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1318452 AAATCGCAAC
*
1318462 GCGATTTTCCATTTTGCGTT
1 GCGATTTTCCATTTCGCGTT
* ** **
1318482 GCGATAGTTGAAAATCGCGTT
1 GCGAT-TTTCCATTTCGCGTT
1318503 GCGATTTTCCATTTCGCGTT
1 GCGATTTTCCATTTCGCGTT
1318523 GCGAT
1 GCGAT
1318528 AGTCTACAGT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
GCGATTTTCCATTTCGCGTT
Found at i:1318547 original size:22 final size:22
Alignment explanation
Indices: 1318519--1318571 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1318509 TTCCATTTCG
1318519 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1318541 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1318563 CGTTGCGAT
1 CGTTGCGAT
1318572 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1318972 original size:21 final size:21
Alignment explanation
Indices: 1318946--1319036 Score: 121
Period size: 21 Copynumber: 4.4 Consensus size: 21
1318936 TGGAAAATCT
1318946 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
1318967 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
** ** *
1318988 CAACGCGAAATGGAA-AATCG
1 CAACGCGATTTTCAACTATCG
*
1319008 CAACGTGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
1319029 CAACGCGA
1 CAACGCGA
1319037 ACTGGAAAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 14 0.25
21 43 0.75
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCG
Found at i:1318989 original size:62 final size:62
Alignment explanation
Indices: 1318919--1319036 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
1318909 ACAACTGTAG
*
1318919 ACTATCGCAACGCGAAATGGAAAATCTCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
*
1318981 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCAACTATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGA
1319037 ACTGGAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (62 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCA
Found at i:1319008 original size:41 final size:41
Alignment explanation
Indices: 1318963--1319090 Score: 171
Period size: 41 Copynumber: 3.3 Consensus size: 41
1318953 ATTTTCAACT
1318963 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
1319004 ATCGCAACGTGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
* *
1319045 ATCGCAA--CG-----CAATTATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1319079 ATCGCAACGCGA
1 ATCGCAACGCGA
1319091 AATGAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
34 29 0.37
36 2 0.03
39 1 0.01
41 46 0.59
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.18
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1319009 original size:20 final size:20
Alignment explanation
Indices: 1318922--1319104 Score: 108
Period size: 20 Copynumber: 9.3 Consensus size: 20
1318912 ACTGTAGACT
*
1318922 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
* ** * *
1318942 ATCTCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
** * *
1318963 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
*
1318984 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGCAAA
* ** * *
1319004 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGAAATGCAA-A
* *
1319025 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGCAAA
*
1319045 ATCGCAACGC--AAT----T
1 ATCGCAACGCGAAATGCAAA
*
1319059 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGCAAA
*
1319079 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGCAAA
1319099 ATCGCA
1 ATCGCA
1319105 CGAATTTGCG
Statistics
Matches: 128, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
14 10 0.08
16 3 0.02
18 2 0.02
20 64 0.50
21 49 0.38
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAATGCAAA
Found at i:1319067 original size:34 final size:34
Alignment explanation
Indices: 1319024--1319088 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1319014 GATTTTCAAC
* *
1319024 TATCGCAACGCGAACTGGAAAATCGCAACGCAAT
1 TATCGCAACGCGAAATGAAAAATCGCAACGCAAT
1319058 TATCGCAACGCGAAATGAAAAATCGCAACGC
1 TATCGCAACGCGAAATGAAAAATCGCAACGC
1319089 GAAATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (34 bp):
TATCGCAACGCGAAATGAAAAATCGCAACGCAAT
Found at i:1319463 original size:75 final size:75
Alignment explanation
Indices: 1319302--1319559 Score: 329
Period size: 75 Copynumber: 3.5 Consensus size: 75
1319292 AGAAACAATT
* * * *
1319302 ATTTAACATAATAGATAACGCCTATTTTATTTTACCGTTTACATTA-TATTAACCTTTAAACAAA
1 ATTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
*
1319366 CCGGTAGCTA
66 CCGGTAGATA
* ** * ***
1319376 GTTTAATGTAATAGGTAGCACCTATTTTATTTTACTGTTTACATTATTAGTAGTATTTAAACAAA
1 ATTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
*
1319441 CCGGTAAATA
66 CCGGTAGATA
* ** * *
1319451 ATTTAACTTAATAGGTAGTGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTCAAATAAA
1 ATTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
1319516 CCGGTAGATA
66 CCGGTAGATA
* *
1319526 GTTTAACATAATAGGTAGTACCTATTTTATTTTA
1 ATTTAACATAATAGGTAGCACCTATTTTATTTTA
1319560 ACCAGTTAAG
Statistics
Matches: 155, Mismatches: 28, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
74 39 0.25
75 116 0.75
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (75 bp):
ATTTAACATAATAGGTAGCACCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
CCGGTAGATA
Found at i:1319934 original size:75 final size:75
Alignment explanation
Indices: 1319847--1320112 Score: 338
Period size: 75 Copynumber: 3.5 Consensus size: 75
1319837 TGTAATGCTT
* * *
1319847 ATTTAACATAATATGTAGCACCTATTTTATTTTACCGTTTACATTATTATTAACCTTTAAACAAA
1 ATTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
1319912 -CTGGTAGCTA
66 TC-GGTAGCTA
* * ** *
1319922 ATTTAACGTAATACGTAATGCCTATTTTATTTTACTGTTTACATTATTAGTAACCTTTAAACAAA
1 ATTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
1319987 TCGGTAGAC-A
66 TCGGTAG-CTA
* * * * **
1319997 GTTTAACGTAATAGGTAGTGCCTATTTTATTTTACTGTTTACATTATTAGTAAAATTTAAACAAA
1 ATTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
* *
1320062 TCAGTAGATA
66 TCGGTAGCTA
* *
1320072 TTTTAACATAATAGGTAGCGCCTATTTTATTTTACCATTTA
1 ATTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTA
1320113 TAATTTTTCT
Statistics
Matches: 169, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
75 167 0.99
76 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (75 bp):
ATTTAACATAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAGTAACCTTTAAACAAA
TCGGTAGCTA
Found at i:1320150 original size:22 final size:22
Alignment explanation
Indices: 1320108--1320151 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1320098 TTATTTTACC
*
1320108 ATTTATAATTTTTCTTCATTAT
1 ATTTATAATTTTTCTTAATTAT
1320130 ATTTATAATTTTT-TTGAATTAT
1 ATTTATAATTTTTCTT-AATTAT
1320152 GAACTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTATAATTTTTCTTAATTAT
Found at i:1328095 original size:49 final size:49
Alignment explanation
Indices: 1328035--1328134 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 49
1328025 TCTTCCAACC
*
1328035 ATTCAATCTTTGAAAAAACCTCAAAAATTAATTTAAGAATTCGATTCTA
1 ATTCAACCTTTGAAAAAACCTCAAAAATTAATTTAAGAATTCGATTCTA
* *
1328084 ATTCAACCTTTGAAAAAACCTCAAAAATTAGTTTGAGAATTCGATTCTA
1 ATTCAACCTTTGAAAAAACCTCAAAAATTAATTTAAGAATTCGATTCTA
1328133 AT
1 AT
1328135 AGGATCGTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (49 bp):
ATTCAACCTTTGAAAAAACCTCAAAAATTAATTTAAGAATTCGATTCTA
Found at i:1330820 original size:20 final size:20
Alignment explanation
Indices: 1330797--1330848 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1330787 GTTTCCAAAT
1330797 TCGCAACACAAATCTGTAAA
1 TCGCAACACAAATCTGTAAA
* * *
1330817 TCGCAACGCGAATCTGTAAT
1 TCGCAACACAAATCTGTAAA
1330837 TCGCAACACAAA
1 TCGCAACACAAA
1330849 AGTCAAATTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.19
Consensus pattern (20 bp):
TCGCAACACAAATCTGTAAA
Found at i:1330955 original size:20 final size:19
Alignment explanation
Indices: 1330932--1330981 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
1330922 GATTTTCGAA
1330932 TTCGCAACACGAATTTTAAT
1 TTCGCAACAC-AATTTTAAT
* *
1330952 TTCGCAACA-AGTTTTATT
1 TTCGCAACACAATTTTAAT
1330970 TTCGCAACACAA
1 TTCGCAACACAA
1330982 ATGTTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 9 0.35
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (19 bp):
TTCGCAACACAATTTTAAT
Found at i:1331138 original size:14 final size:15
Alignment explanation
Indices: 1331119--1331156 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1331109 TCCCCATCTC
1331119 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
1331133 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1331149 TAATTTTT
1 TAATTTTT
1331157 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1331754 original size:12 final size:12
Alignment explanation
Indices: 1331733--1331766 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1331723 ACCACATTTC
*
1331733 CAATACCAAACA
1 CAATATCAAACA
1331745 CAATATCAAACA
1 CAATATCAAACA
*
1331757 CAATCTCAAA
1 CAATATCAAA
1331767 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1331906 original size:24 final size:24
Alignment explanation
Indices: 1331878--1331945 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
1331868 GTGAGTACTA
*
1331878 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGAAATTTGATCTTG
*
1331902 GTCAATACTC-AGACTTTGATCTTG
1 GTCAATACTCGA-AATTTGATCTTG
1331926 GTCAATACTCGAAATTTGAT
1 GTCAATACTCGAAATTTGAT
1331946 GATGTTTCAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 1 0.03
24 37 0.95
25 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGAAATTTGATCTTG
Found at i:1334222 original size:18 final size:18
Alignment explanation
Indices: 1334199--1334234 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1334189 AAGCAAAAGG
*
1334199 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1334217 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1334235 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1334518 original size:29 final size:29
Alignment explanation
Indices: 1334476--1334532 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1334466 GCAATTTTTT
*
1334476 GTTGCGATTGTTGCGAAAGTCAAATTCGC
1 GTTGCGATTGTTGCGAAAATCAAATTCGC
1334505 GTTGCGATTGTTGCGAAAATCAAATTCG
1 GTTGCGATTGTTGCGAAAATCAAATTCG
1334533 AAACGTGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (29 bp):
GTTGCGATTGTTGCGAAAATCAAATTCGC
Found at i:1336085 original size:21 final size:21
Alignment explanation
Indices: 1336059--1336177 Score: 136
Period size: 21 Copynumber: 5.7 Consensus size: 21
1336049 GTGAATCAGG
* *
1336059 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
1336080 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
1336101 CTCTTGAACGATTAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
1336122 CTCTTGAATGGTG-GAGGGGTCTC
1 CTCTTGAACGATGAGAGGGG---C
*
1336145 CTCTTGAAAGAT-AG-GGGGC
1 CTCTTGAACGATGAGAGGGGC
1336164 CTCTTGAACGATGA
1 CTCTTGAACGATGA
1336178 TAGGTGAATT
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
19 12 0.14
20 7 0.08
21 49 0.58
22 4 0.05
23 12 0.14
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:1336495 original size:21 final size:21
Alignment explanation
Indices: 1336471--1336529 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
1336461 GTAGAGCGGC
*
1336471 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
1336492 TACCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
* *
1336513 TATCTCACCACATAAAG
1 TACCTCACCACGTAAAG
1336530 CACCATTGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:1336579 original size:21 final size:22
Alignment explanation
Indices: 1336471--1336587 Score: 75
Period size: 21 Copynumber: 5.5 Consensus size: 22
1336461 GTAGAGCGGC
* *
1336471 TACCTCATCACGTAAAGTA-GA
1 TACCTCACCACGTAAAGTACCA
*
1336492 TACCTCACCACGTAAAGTA-GA
1 TACCTCACCACGTAAAGTACCA
* * *
1336513 TATCTCACCACATAAAGCACCA
1 TACCTCACCACGTAAAGTACCA
** * * *
1336535 T-TGTCATCGCGTAAAAT-CTC-
1 TACCTCACCACGTAAAGTAC-CA
1336555 TACCTCACCACGTAAAG-ACCA
1 TACCTCACCACGTAAAGTACCA
*
1336576 TACCTCATCACG
1 TACCTCACCACG
1336588 CCATGCACCA
Statistics
Matches: 74, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
20 3 0.04
21 69 0.93
22 2 0.03
ACGTcount: A:0.35, C:0.32, G:0.11, T:0.22
Consensus pattern (22 bp):
TACCTCACCACGTAAAGTACCA
Found at i:1336628 original size:21 final size:21
Alignment explanation
Indices: 1336604--1336649 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1336594 ACCATTGTCG
* * *
1336604 TCACGTAAAGTACCGACCTCC
1 TCACGCAAAGCACCGACCTCA
*
1336625 TCACGCAAAGCACTGACCTCA
1 TCACGCAAAGCACCGACCTCA
1336646 TCAC
1 TCAC
1336650 ATAACTCCCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.39, G:0.13, T:0.17
Consensus pattern (21 bp):
TCACGCAAAGCACCGACCTCA
Found at i:1336843 original size:42 final size:42
Alignment explanation
Indices: 1336770--1336864 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
1336760 GATGAAATAG
* * * * *
1336770 GTGATGGCTCTCGTTGTGGAGGTATATAATCGGCTCGATCAA
1 GTGATGGCTCTAGGTGTCGAGCTATAGAATCGGCTCGATCAA
* * *
1336812 GTGATGGCTCTAGGTGTCGAGCTGTAGAATCGGCTTGATCAG
1 GTGATGGCTCTAGGTGTCGAGCTATAGAATCGGCTCGATCAA
1336854 GTGATGGCTCT
1 GTGATGGCTCT
1336865 CAAAGTCGGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.19, C:0.17, G:0.34, T:0.31
Consensus pattern (42 bp):
GTGATGGCTCTAGGTGTCGAGCTATAGAATCGGCTCGATCAA
Found at i:1338361 original size:20 final size:20
Alignment explanation
Indices: 1338338--1338403 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
1338328 TATGAAACTT
1338338 AAAATCGCAAAGCGAAAATG
1 AAAATCGCAAAGCGAAAATG
*
1338358 AAAATCGCAACGCG-AAATG
1 AAAATCGCAAAGCGAAAATG
* *
1338377 AAAATCGCAATGCGAAACT-
1 AAAATCGCAAAGCGAAAATG
1338396 AAAATCGC
1 AAAATCGC
1338404 GTTGTGATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 26 0.62
20 16 0.38
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAAAGCGAAAATG
Found at i:1338447 original size:20 final size:20
Alignment explanation
Indices: 1338403--1338441 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1338393 ACTAAAATCG
*
1338403 CGTTGTGATTTTCATTTTCA
1 CGTTGCGATTTTCATTTTCA
1338423 CGTTGCGATTTTCATTTTC
1 CGTTGCGATTTTCATTTTC
1338442 GTGTTGTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.18, G:0.15, T:0.54
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:1339001 original size:20 final size:20
Alignment explanation
Indices: 1338976--1339024 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1338966 TAAACGCGCT
*
1338976 TTGCGAATTTGACTTCTGTA
1 TTGCGAATTTGACTTATGTA
*
1338996 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTA
*
1339016 TTGCAAATT
1 TTGCGAATT
1339025 ACAGATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.20, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTA
Found at i:1339038 original size:20 final size:20
Alignment explanation
Indices: 1339015--1339064 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1339005 TGACTTATGT
1339015 GTTGCAAATTACAGATTCGC
1 GTTGCAAATTACAGATTCGC
* * *
1339035 GTTGCGATTTACATATTCGC
1 GTTGCAAATTACAGATTCGC
*
1339055 ATTGCAAATT
1 GTTGCAAATT
1339065 TGAAAATCGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
GTTGCAAATTACAGATTCGC
Found at i:1339112 original size:21 final size:20
Alignment explanation
Indices: 1339056--1339114 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
1339046 CATATTCGCA
*
1339056 TTGCAAATTTGAAAATCGTG
1 TTGCGAATTTGAAAATCGTG
1339076 TTGCGAATTTGAAAATCGTG
1 TTGCGAATTTGAAAATCGTG
1339096 TTGCGAATTTGGAAAATCG
1 TTGCGAATTT-GAAAATCG
1339115 CAACGCGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCGTG
Done.