Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_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: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1074607 original size:23 final size:23
Alignment explanation
Indices: 1074576--1074639 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
1074566 ATAGGTAAAA
*
1074576 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
1074599 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
1074622 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
1074640 TTATAAAGTA
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:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1075089 original size:23 final size:23
Alignment explanation
Indices: 1075058--1075130 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1075048 ATAAGTAAAA
* *
1075058 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGATT
* *
1075081 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGATT
*
1075104 ATATAATGTAATAGGTAGTGATT
1 ATATAATGTAATAGGTAGCGATT
1075127 ATAT
1 ATAT
1075131 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGATT
Found at i:1075305 original size:490 final size:487
Alignment explanation
Indices: 1074345--1076012 Score: 3058
Period size: 479 Copynumber: 3.4 Consensus size: 487
1074335 CTGTGAAAAT
1074345 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
* *
1074410 CAAAACAATCAAATAATTTTTTGTGTAAATGAAATTATTACATTAATATTGTAGGTGGAAAACAT
66 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
*
1074475 GAAACACTATT-AAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTT
131 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
*
1074539 ATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATA
196 ATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
* *
1074604 ATGTAATATGTATCGTTTATATAATGTAATAGGTA-GT-TA---TAAAGTATCTATCATTTTTAT
261 ATGTAATAGGTATCGTTTATATAATGTAATAGGTAGGTATATTGTAAAGTATCTATCCTTTTTAT
1074664 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
* * *
1074729 AAAATATTAATTTAGTAATTATATGCGACTAATGATTTATTTTTTACGTTACGATATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATT
1074794 ATTAAATTAAAAACAATAAACATATATATTAC
456 ATTAAATTAAAAACAATAAACATATATATTAC
1074826 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1074891 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
66 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
1074956 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
131 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
1075021 ATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
196 ATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
*
1075086 ATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTGATTATATTGTAAAGTGTCTATCCTTTT
261 ATGTAATAGGTATCGTTTATATAATGTAATAGGTAG-G--TATATTGTAAAGTATCTATCCTTTT
1075151 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
323 TATAAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGT
*
1075216 TTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTAAGATATATATT
388 TTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATT
1075281 ATTATTAAATTAAAAACAATAAACATATATATTAC
453 ATTATTAAATTAAAAACAATAAACATATATATTAC
1075316 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
*
1075381 CAAAACAATCAAATAA-TTTTTGTGTAAATGAAATTATT-AATTAATATTGTAGGTGGAAAAC-T
66 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
1075443 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
131 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
*
1075508 ATAAAAAGTATGTACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
196 ATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
1075573 ATGTAATAGGTATCGTTTATATAATGT-A-A--TAGGTAT-TTGTAAAGTATCTATCCTTTTTAT
261 ATGTAATAGGTATCGTTTATATAATGTAATAGGTAGGTATATTGTAAAGTATCTATCCTTTTTAT
*
1075633 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGCTTATCTTTTGAGTGAGTTTT
326 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
1075698 AAGATATTAATTTAGTAATTATAGGCATCTAATGATTTATTTTTTACGTTACGATATATATTATT
391 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATT
*
1075763 ATTAAATTAAAAACAATAAATATATATATTAC
456 ATTAAATTAAAAACAATAAACATATATATTAC
1075795 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1 ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
1075860 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
66 CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
*
1075925 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAATTATCGATCATTTTT
131 GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
1075990 ATAAAAAGTATGGACACTTTCAA
196 ATAAAAAGTATGGACACTTTCAA
1076013 CATATTATAA
Statistics
Matches: 1154, Mismatches: 21, Indels: 23
0.96 0.02 0.02
Matches are distributed among these distances:
479 262 0.23
480 24 0.02
481 162 0.14
482 238 0.21
483 3 0.00
484 1 0.00
485 1 0.00
486 2 0.00
487 159 0.14
488 23 0.02
489 21 0.02
490 258 0.22
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (487 bp):
ATATTTATTATTATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATAT
CAAAACAATCAAATAATTTTTTATGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACAT
GAAACACTATTAAAAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTT
ATAAAAAGTATGGACACTTTCAATATAATAAGTAAAAATATGATGTAATAGGTAGCGCTTATATA
ATGTAATAGGTATCGTTTATATAATGTAATAGGTAGGTATATTGTAAAGTATCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTATT
ATTAAATTAAAAACAATAAACATATATATTAC
Found at i:1075608 original size:23 final size:23
Alignment explanation
Indices: 1075545--1075608 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1075535 ATAAGTAAAA
* *
1075545 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTATCGCTT
*
1075568 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGCTT
1075591 ATATAATGTAATAGGTAT
1 ATATAATGTAATAGGTAT
1075609 TTGTAAAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGCTT
Found at i:1077896 original size:17 final size:16
Alignment explanation
Indices: 1077874--1077915 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 16
1077864 TCATGAGGTG
1077874 AAAATATTATTATTGTA
1 AAAATATTATTATT-TA
*
1077891 AAAATATAATTATTTA
1 AAAATATTATTATTTA
1077907 AATAATATT
1 AA-AATATT
1077916 TAATTTTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
AAAATATTATTATTTA
Found at i:1078573 original size:20 final size:20
Alignment explanation
Indices: 1078548--1078603 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1078538 TGGTTCACGG
1078548 AATGTAAGATTACCAGTGAA
1 AATGTAAGATTACCAGTGAA
* **
1078568 AATGTAAGATTACAAGTGGG
1 AATGTAAGATTACCAGTGAA
*
1078588 AATGTAAGACTACCAG
1 AATGTAAGATTACCAG
1078604 GGAATATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGAA
Found at i:1078835 original size:37 final size:37
Alignment explanation
Indices: 1078761--1078835 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
1078751 GTTGGGAAAT
* *
1078761 ATTTATATATTTTCTTTAAAAAATTTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
* * *
1078798 ATTTATATAATTTTTTTTATAAAATTGAAA-ATCTAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAATATATAAA
1078835 A
1 A
1078836 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
Found at i:1102066 original size:2 final size:2
Alignment explanation
Indices: 1102059--1102090 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1102049 TTTTAAAATA
1102059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1102091 ACATTATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1104240 original size:30 final size:30
Alignment explanation
Indices: 1104204--1104287 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
1104194 CCCGAAGGAC
* * *
1104204 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTCGGCAA
* *
1104234 CTATCCATAGGTCATAAAGATCCTCGGCAA
1 CTATCCATAGGTCACAAAGAACCTCGGCAA
* * *
1104264 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCATAGGTCACAAAGAACCT
1104288 AGGTATACTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTCGGCAA
Found at i:1104301 original size:31 final size:31
Alignment explanation
Indices: 1104263--1104386 Score: 126
Period size: 31 Copynumber: 4.0 Consensus size: 31
1104253 ATCCTCGGCA
* *
1104263 ACTGTCCATAGGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
* **
1104294 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
*
1104325 ACTATCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-A-T
** *
1104358 A-TGTCCATATGTTTCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
1104387 AACCCTCGAC
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
30 1 0.01
31 50 0.66
32 22 0.29
33 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:1104381 original size:63 final size:62
Alignment explanation
Indices: 1104267--1104386 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 62
1104257 TCGGCAACTG
* *
1104267 TCCATAGGTCCCGAAGAACCTAGGTATACTGTCCATATGTTCCTTAGAACATAGGTATACTA
1 TCCATAGGTCCCGAAGAACATAGGTATACTGTCCATATGTTCCGTAGAACATAGGTATACTA
* *
1104329 TCCATATGTCCCGAA-AGACATAGGTAATTA-TGTCCATATGTTTCGTAGAACATAGGTA
1 TCCATAGGTCCCGAAGA-ACATAGGT-A-TACTGTCCATATGTTCCGTAGAACATAGGTA
1104387 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
61 1 0.02
62 21 0.41
63 27 0.53
64 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (62 bp):
TCCATAGGTCCCGAAGAACATAGGTATACTGTCCATATGTTCCGTAGAACATAGGTATACTA
Found at i:1107924 original size:30 final size:30
Alignment explanation
Indices: 1107888--1107971 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
1107878 CCCGAAGGAC
* * *
1107888 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTCGGCAA
* *
1107918 CTATCCATAGGTCATAAAGATCCTCGGCAA
1 CTATCCATAGGTCACAAAGAACCTCGGCAA
* * *
1107948 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCATAGGTCACAAAGAACCT
1107972 AGGTATAATG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTCGGCAA
Found at i:1109137 original size:21 final size:21
Alignment explanation
Indices: 1109113--1109157 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1109103 CCATGTTCGT
* *
1109113 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1109134 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1109155 TTG
1 TTG
1109158 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1114263 original size:14 final size:14
Alignment explanation
Indices: 1114241--1114273 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1114231 CCAATCCATC
1114241 AATCAATTATATGA
1 AATCAATTATATGA
*
1114255 AATCCATTATATGA
1 AATCAATTATATGA
1114269 AATCA
1 AATCA
1114274 CCCCCTGGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (14 bp):
AATCAATTATATGA
Found at i:1124813 original size:2 final size:2
Alignment explanation
Indices: 1124806--1124839 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1124796 ATGATATTTA
1124806 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
1124840 TGTCGGATCA
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:1136616 original size:23 final size:23
Alignment explanation
Indices: 1136589--1136637 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1136579 ACATAATATC
1136589 TGTCTTTATGACACGTTTATCTT
1 TGTCTTTATGACACGTTTATCTT
* * * *
1136612 TGTCTTTGTGGCATGTTTTTCTT
1 TGTCTTTATGACACGTTTATCTT
1136635 TGT
1 TGT
1136638 GTTTTGGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.10, C:0.14, G:0.18, T:0.57
Consensus pattern (23 bp):
TGTCTTTATGACACGTTTATCTT
Found at i:1136680 original size:20 final size:20
Alignment explanation
Indices: 1136657--1136710 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1136647 GCTTACGGTT
*
1136657 TTTTATTGTTGTTTACGATG
1 TTTTGTTGTTGTTTACGATG
1136677 TTTTGTTGTTGTTTACGATG
1 TTTTGTTGTTGTTTACGATG
*
1136697 TTTTGTCGTTGTTT
1 TTTTGTTGTTGTTT
1136711 TTGTTTATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.09, C:0.06, G:0.22, T:0.63
Consensus pattern (20 bp):
TTTTGTTGTTGTTTACGATG
Found at i:1140170 original size:267 final size:265
Alignment explanation
Indices: 1139790--1140277 Score: 689
Period size: 266 Copynumber: 1.8 Consensus size: 265
1139780 CGACCTGATT
* * *
1139790 TGATAGGGTCAGATTTTATTAAAAAGGAGGTAGGACCATAATTCGACCCCATATGATTTAATTTA
1 TGATAGAGTCAGATTTTATTAAAAAGGAGGCAGGACCATAATTCGACCCCATATGATTTAATTCA
* *
1139855 TAGACTAAAATATAGTCGAAGGATAATTTTGTAGCTTTTACTCCATATGA-TTAATCCATAGATT
66 TAGACTAAAATATAGACGAAGGATAATTTTGTAACTTTTACTCCATATGATTTAATCCATAGATT
* *
1139919 AGACCTTAAATAACCGTTTTTATTAAAAA-TGAAATTAGTTAAAAAAATATGAAATGATCAAAAA
131 AGACCTTAAATAACCGCTTTTATTAAAAATTAAAATTAGTT--AAAAA-ATGAAATGAT-AAAAA
1139983 AGTATAAAATTTAAGTATGTGAAAGTAGAGGTGGTAATTTAACCCAATTTGATGGGTTCTGATCC
192 AGTATAAAATTTAAGTATGTGAAAGTAGAGGTGGTAATTTAACCCAATTTGATGGGTTCTGATCC
1140048 AATCCGACC
257 AATCCGACC
* * * * *
1140057 TGATAGAGTCGGATTTT-TTTAAAAGGTGGCAGGACCATTATTTGACCCCATATGATTTAATTCA
1 TGATAGAGTCAGATTTTATTAAAAAGGAGGCAGGACCATAATTCGACCCCATATGATTTAATTCA
* * * *
1140121 TAGATTAAAAATGTAGACGGAA-GATAATTTTGTAACTTTTA-TCCCATATGATTTAATTCATAT
66 TAGACT-AAAATATAGAC-GAAGGATAATTTTGTAACTTTTACT-CCATATGATTTAATCCATAG
** **
1140184 ATTAGACCTTAAATAATGGCTTTTATTAAAAATTAAAATTAGTTAAAAAATGAAATGATAAAAGT
128 ATTAGACCTTAAATAACCGCTTTTATTAAAAATTAAAATTAGTTAAAAAATGAAATGATAAAAAA
*
1140249 GTATAAAATTTAAGTATGTGAAATTAGAG
193 GTATAAAATTTAAGTATGTGAAAGTAGAG
1140278 ATGTCATTTT
Statistics
Matches: 195, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
265 32 0.16
266 57 0.29
267 55 0.28
268 41 0.21
269 10 0.05
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (265 bp):
TGATAGAGTCAGATTTTATTAAAAAGGAGGCAGGACCATAATTCGACCCCATATGATTTAATTCA
TAGACTAAAATATAGACGAAGGATAATTTTGTAACTTTTACTCCATATGATTTAATCCATAGATT
AGACCTTAAATAACCGCTTTTATTAAAAATTAAAATTAGTTAAAAAATGAAATGATAAAAAAGTA
TAAAATTTAAGTATGTGAAAGTAGAGGTGGTAATTTAACCCAATTTGATGGGTTCTGATCCAATC
CGACC
Found at i:1140862 original size:34 final size:32
Alignment explanation
Indices: 1140809--1140879 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
1140799 CCTTACAAAC
* *
1140809 TCCCTAGTTTTTCCGGGCTAAACTATAACATT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
* *
1140841 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
1140875 TCCCT
1 TCCCT
1140880 TTTACAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.34
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:1141704 original size:2 final size:2
Alignment explanation
Indices: 1141697--1141733 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1141687 AATAACTAGA
1141697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1141734 ATTTTTTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1141910 original size:20 final size:21
Alignment explanation
Indices: 1141855--1141911 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1141845 TAGTTAGATT
1141855 ATAAATATTTAATTTAATATC
1 ATAAATATTTAATTTAATATC
*
1141876 ATTCAACT-TTT-ATTTAA-ATC
1 A-T-AAATATTTAATTTAATATC
1141896 ATAAATATTTAATTTA
1 ATAAATATTTAATTTA
1141912 GTTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.10
19 4 0.13
20 9 0.30
21 7 0.23
22 4 0.13
23 3 0.10
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAAATATTTAATTTAATATC
Found at i:1144340 original size:20 final size:21
Alignment explanation
Indices: 1144315--1144366 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1144305 TTTTCCCAAT
*
1144315 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1144335 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1144356 TCGCAATGCGA
1 TCGCAATGCGA
1144367 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1144380 original size:20 final size:20
Alignment explanation
Indices: 1144355--1144468 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
1144345 AATTGGGAAA
*
1144355 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1144375 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
1144395 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
1144416 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1144436 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1144456 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1144469 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1144399 original size:61 final size:61
Alignment explanation
Indices: 1144352--1144468 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1144342 GCGAATTGGG
* * * * *
1144352 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1144413 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1144469 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1145023 original size:18 final size:18
Alignment explanation
Indices: 1144973--1145030 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1144963 ATAGTTTCGA
*
1144973 GAATAAAAATCGCAACAC
1 GAATAAAAATCGCAACGC
**
1144991 GAAATAACTATCGCAACGC
1 G-AATAAAAATCGCAACGC
*
1145010 GAATAAAAAACGCAACGC
1 GAATAAAAATCGCAACGC
1145028 GAA
1 GAA
1145031 ACCAAAATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.52, C:0.22, G:0.16, T:0.10
Consensus pattern (18 bp):
GAATAAAAATCGCAACGC
Found at i:1145042 original size:19 final size:17
Alignment explanation
Indices: 1144977--1145042 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
1144967 TTTCGAGAAT
*
1144977 AAAAATCGCAACACGAA
1 AAAAATCGCAACGCGAA
*
1144994 ATAACTATCGCAACGCGAA
1 A-AA-AATCGCAACGCGAA
*
1145013 TAAAAAACGCAACGCGAA
1 -AAAAATCGCAACGCGAA
1145031 ACCAAAATCGCA
1 A--AAAATCGCA
1145043 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.05
18 14 0.36
19 22 0.56
20 1 0.03
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.09
Consensus pattern (17 bp):
AAAAATCGCAACGCGAA
Found at i:1145098 original size:31 final size:32
Alignment explanation
Indices: 1145043--1145103 Score: 106
Period size: 33 Copynumber: 1.9 Consensus size: 32
1145033 CAAAATCGCA
1145043 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTC-CGTTGCGATTCTCTCG
1145076 TTGCGATTTTCATTT-CGTTGCGATTCTC
1 TTGCGATTTTCATTTCCGTTGCGATTCTC
1145104 ATTATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 13 0.46
33 15 0.54
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (32 bp):
TTGCGATTTTCATTTCCGTTGCGATTCTCTCG
Found at i:1145115 original size:20 final size:19
Alignment explanation
Indices: 1145043--1145126 Score: 92
Period size: 17 Copynumber: 4.7 Consensus size: 19
1145033 CAAAATCGCA
*
1145043 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
1145062 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
1145076 TTGCGATTTTCA-TT-TCG
1 TTGCGATTTTCATTTCTCG
*
1145093 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCTCG
1145113 TTGCGATTTTCATT
1 TTGCGATTTTCATT
1145127 CAACCAAAAG
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
14 10 0.18
16 3 0.05
17 17 0.31
18 2 0.04
19 7 0.13
20 16 0.29
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:1146668 original size:63 final size:61
Alignment explanation
Indices: 1146563--1146688 Score: 225
Period size: 63 Copynumber: 2.0 Consensus size: 61
1146553 TACGTGATGA
1146563 GTCAATGCTTGCGTGAGGAGATCGTACTCTACGCGATAACGATGGTGCATGGCGTGTGGAG
1 GTCAATGCTTGCGTGAGGAGATCGTACTCTACGCGATAACGATGGTGCATGGCGTGTGGAG
*
1146624 GTCAATGCCTTGCGTGAGGAGATCGGTTCTCTACGCGATAACGATGGTGCATGGCGTGTGGAG
1 GTCAATG-CTTGCGTGAGGAGATC-GTACTCTACGCGATAACGATGGTGCATGGCGTGTGGAG
1146687 GT
1 GT
1146689 GTCTACTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
61 7 0.11
62 16 0.26
63 39 0.63
ACGTcount: A:0.20, C:0.18, G:0.37, T:0.25
Consensus pattern (61 bp):
GTCAATGCTTGCGTGAGGAGATCGTACTCTACGCGATAACGATGGTGCATGGCGTGTGGAG
Found at i:1147343 original size:42 final size:42
Alignment explanation
Indices: 1147246--1147447 Score: 194
Period size: 42 Copynumber: 4.8 Consensus size: 42
1147236 GACTCGCCTG
* * * *
1147246 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGA-GCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
1147287 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * * * *
1147329 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
* * *
1147371 TCATTCCTCGAGAGTTCC-CTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAG-TCCACTCCCACCGTTCAAGAGGCCACTA
** * *
1147413 TCATCGTTGAAGAGGT-CACTCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1147448 CCCGATTCAC
Statistics
Matches: 128, Mismatches: 29, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
41 29 0.23
42 95 0.74
43 4 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCACTA
Found at i:1147434 original size:84 final size:83
Alignment explanation
Indices: 1147246--1147417 Score: 308
Period size: 84 Copynumber: 2.1 Consensus size: 83
1147236 GACTCGCCTG
*
1147246 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
1147311 CCGTTCAAGAGGCCACTA
66 CCGTTCAAGAGGCCACTA
*
1147329 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTTCCCTCCC
1 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGA-GCCCCTATCATTCCTCGAGAGTCCCCTCCC
*
1147394 ACCGTTCAAGAGGCCACTG
65 ACCGTTCAAGAGGCCACTA
1147413 TCATC
1 TCATC
1147418 GTTGAAGAGG
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 33 0.39
84 52 0.61
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.24
Consensus pattern (83 bp):
TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGCCCCTATCATTCCTCGAGAGTCCCCTCCCA
CCGTTCAAGAGGCCACTA
Found at i:1147446 original size:21 final size:21
Alignment explanation
Indices: 1147389--1147447 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1147379 CGAGAGTTCC
1147389 CTCCCACCGTTCAAGAGGCCA
1 CTCCCACCGTTCAAGAGGCCA
** * * *
1147410 CTGTCATCGTTGAAGAGGTCA
1 CTCCCACCGTTCAAGAGGCCA
*
1147431 CTCCCACCATTCAAGAG
1 CTCCCACCGTTCAAGAG
1147448 CCCGATTCAC
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (21 bp):
CTCCCACCGTTCAAGAGGCCA
Found at i:1147447 original size:84 final size:84
Alignment explanation
Indices: 1147246--1147447 Score: 273
Period size: 84 Copynumber: 2.4 Consensus size: 84
1147236 GACTCGCCTG
* * * *
1147246 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGA-GCCCCTATCATTCCTCGAGAGTCCCCTCCC
1 TCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
1147310 ACCGTTCAAGAGGCCACTA
66 ACCGTTCAAGAGGCCACTA
* * * *
1147329 TCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTTCCCTCCC
1 TCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
*
1147394 ACCGTTCAAGAGGCCACTG
66 ACCGTTCAAGAGGCCACTA
** *
1147413 TCATCGTTGAAGAGGT-CACTCCCACCATTCAAGAG
1 TCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
1147448 CCCGATTCAC
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
83 33 0.31
84 73 0.68
85 2 0.02
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (84 bp):
TCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCC
ACCGTTCAAGAGGCCACTA
Found at i:1148813 original size:14 final size:14
Alignment explanation
Indices: 1148794--1148829 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1148784 GATTGTTAAT
1148794 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
**
1148808 TGATTTGTAAAATT
1 TGATTTGTAAAAGG
1148822 TGATTTGT
1 TGATTTGT
1148830 TAATTGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1148956 original size:18 final size:18
Alignment explanation
Indices: 1148933--1149003 Score: 87
Period size: 18 Copynumber: 4.1 Consensus size: 18
1148923 AAAAAGTACT
*
1148933 ATCGCAATGCGAAATGAA
1 ATCGCAACGCGAAATGAA
1148951 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATG-AA
1148970 ATCGCAA--CGAAA-G-A
1 ATCGCAACGCGAAATGAA
*
1148984 ATCGCAACGCGAAATTAA
1 ATCGCAACGCGAAATGAA
1149002 AT
1 AT
1149004 TCGCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.17
16 6 0.13
17 5 0.11
18 18 0.39
19 9 0.20
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.14
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:1149057 original size:33 final size:32
Alignment explanation
Indices: 1149007--1149132 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
1148997 ATTAAATTCG
1149007 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1149039 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1149072 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
1149105 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1149133 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
31 3 0.04
32 8 0.09
33 71 0.84
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1149097 original size:66 final size:65
Alignment explanation
Indices: 1149000--1149131 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 65
1148990 ACGCGAAATT
*
1149000 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
*
1149065 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1149130 G
65 G
1149131 A
1 A
1149132 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 14 0.22
66 50 0.78
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:1151400 original size:12 final size:12
Alignment explanation
Indices: 1151383--1151407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1151373 TCTTCGGGGA
1151383 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1151395 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1151407 C
1 C
1151408 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1151615 original size:24 final size:24
Alignment explanation
Indices: 1151581--1151634 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
1151571 CTAAAACATC
*
1151581 ATCAAAATCC-GAGTATTGACCAAT
1 ATCAAAATCCGGA-TATTGACCAAG
*
1151605 ATCAAAGTCCGGATATTGACCAAG
1 ATCAAAATCCGGATATTGACCAAG
1151629 ATCAAA
1 ATCAAA
1151635 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAG
Found at i:1152405 original size:20 final size:20
Alignment explanation
Indices: 1152380--1152430 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1152370 TGTATTATCT
1152380 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1152400 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
1152420 CGTTTCGAAAG
1 CGTTGCGAAAG
1152431 GCAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1152722 original size:14 final size:14
Alignment explanation
Indices: 1152703--1152756 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1152693 GAAAATCGCA
1152703 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1152717 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
1152734 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
1152750 TTGCGAT
1 TTGCGAT
1152757 AATCAGTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1152722 original size:33 final size:33
Alignment explanation
Indices: 1152685--1152755 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
1152675 AAAATCGCAA
*
1152685 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
1152718 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
1152751 TGCGA
1 TGCGA
1152756 TAATCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:1152774 original size:20 final size:20
Alignment explanation
Indices: 1152749--1152787 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1152739 CGATTCTCTC
1152749 GTTGCGATAATCAGTTTTGT
1 GTTGCGATAATCAGTTTTGT
* *
1152769 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAATCAGTTTTG
1152788 CCTTCAACAT
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:0.15, C:0.10, G:0.28, T:0.46
Consensus pattern (20 bp):
GTTGCGATAATCAGTTTTGT
Found at i:1152889 original size:14 final size:14
Alignment explanation
Indices: 1152870--1152906 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1152860 CATCAATTAA
1152870 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1152884 ACAAATCATCTTTT
1 ACAAATCAACATTT
1152898 ACAAATCAA
1 ACAAATCAA
1152907 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1154784 original size:20 final size:20
Alignment explanation
Indices: 1154759--1154812 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1154749 CGAACTTAAA
1154759 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1154779 ATCGCAACGC-AGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
*
1154799 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1154813 TAAAAATCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 28 0.93
21 1 0.03
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1154821 original size:19 final size:19
Alignment explanation
Indices: 1154799--1154874 Score: 65
Period size: 18 Copynumber: 4.3 Consensus size: 19
1154789 AGAAATGGCT
1154799 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
1154818 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATAAAA
*
1154832 ATCGCAATGCGAAAT-GAA
1 ATCGCAATGCGAAATAAAA
* * *
1154850 ATCGCAACGCGAAACACAA
1 ATCGCAATGCGAAATAAAA
1154869 ATCGCA
1 ATCGCA
1154875 TTGTGATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 10 0.22
15 1 0.02
16 2 0.04
17 2 0.04
18 16 0.35
19 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:1154822 original size:39 final size:33
Alignment explanation
Indices: 1154799--1154863 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1154789 AGAAATGGCT
*
1154799 ATCGCAATGCGAAATAAAAATCGCAACG-ACAAA
1 ATCGCAATGCGAAAT-AAAATCGCAACGCAGAAA
*
1154832 ATCGCAATGCGAAATGAAATCGCAACGC-GAAA
1 ATCGCAATGCGAAATAAAATCGCAACGCAGAAA
1154864 CACAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATAAAATCGCAACGCAGAAA
Found at i:1154911 original size:14 final size:14
Alignment explanation
Indices: 1154892--1154949 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1154882 TTTCATTTCG
1154892 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1154906 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1154922 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1154938 CGTTGCGATTTT
1 CGTTGCGATTTT
1154950 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1154956 original size:33 final size:33
Alignment explanation
Indices: 1154879--1154965 Score: 158
Period size: 32 Copynumber: 2.7 Consensus size: 33
1154869 ATCGCATTGT
*
1154879 GATTTTCATTTCGCGTTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
1154912 GA-TTTCATTTCGCATTGCGATTTTGTCGTTGC
1 GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
1154944 GATTTTCATTTCGCATTGCGAT
1 GATTTTCATTTCGCATTGCGAT
1154966 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
32 31 0.60
33 21 0.40
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (33 bp):
GATTTTCATTTCGCATTGCGATTTTGTCGTTGC
Found at i:1154984 original size:20 final size:19
Alignment explanation
Indices: 1154950--1155004 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1154940 TTGCGATTTT
*
1154950 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1154969 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1154989 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1155005 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1155500 original size:18 final size:18
Alignment explanation
Indices: 1155474--1155518 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1155464 GTCGATCAGA
*
1155474 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1155492 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1155510 TGATGGCTC
1 TGATGGCTC
1155519 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1156871 original size:20 final size:20
Alignment explanation
Indices: 1156823--1156882 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1156813 AATAGTTTCT
** *
1156823 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1156843 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1156863 GAATTTGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
1156883 AAACTAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1157149 original size:22 final size:22
Alignment explanation
Indices: 1157122--1157165 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1157112 GATGGAGATA
1157122 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1157144 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1157166 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1157393 original size:41 final size:41
Alignment explanation
Indices: 1157330--1157443 Score: 142
Period size: 41 Copynumber: 2.8 Consensus size: 41
1157320 CGCTTTGAAA
* *
1157330 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
* * * *
1157371 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
*
1157412 ATCGCATTGCGA-TA-GTCAGTATCGCATTGCGA
1 ATCGCATTGCGATTATGT-ATTATCGCATTGCGA
1157444 TTTTCCCAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 2 0.03
40 15 0.24
41 45 0.73
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCATTGCGAAAGTAAGT
Found at i:1157416 original size:20 final size:20
Alignment explanation
Indices: 1157391--1157444 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1157381 GATTTTGTAT
1157391 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1157411 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1157431 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1157445 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1157429 original size:61 final size:62
Alignment explanation
Indices: 1157330--1157447 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
1157320 CGCTTTGAAA
* * * *
1157330 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
*
1157392 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1157448 CCCAATTCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 2 0.04
61 36 0.72
62 12 0.24
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1157463 original size:61 final size:61
Alignment explanation
Indices: 1157330--1157465 Score: 150
Period size: 61 Copynumber: 2.2 Consensus size: 61
1157320 CGCTTTGAAA
* * * * ** *
1157330 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
*
1157392 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
1157454 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
1157466 TTACTTATTC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.03
61 47 0.75
62 14 0.22
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1159306 original size:22 final size:21
Alignment explanation
Indices: 1159281--1159321 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1159271 TTAAAAAATT
*
1159281 TAATAATATAATATAATATTTG
1 TAATAATATAAAAT-ATATTTG
*
1159303 TAATATTATAAAATATATT
1 TAATAATATAAAATATATT
1159322 AAATTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATAATATAAAATATATTTG
Found at i:1159322 original size:49 final size:46
Alignment explanation
Indices: 1159269--1159392 Score: 108
Period size: 49 Copynumber: 2.5 Consensus size: 46
1159259 TTTTTATATT
1159269 TATTAAAAAATTTAATAATATAATATAATATTTGTAATATTATAA-AATA
1 TATTAAAAAATTTAATAATATAATATAATATTT-T--TATT-TAATAATA
* *
1159318 TATTAAATTATATTATAATAATATATGATATTATATTTTTATTTAATAATA
1 TATTAAA--AAATT-TAATAATATA--ATATAATATTTTTATTTAATAATA
*
1159369 T-TTAATAAATATTTAATAAAATAA
1 TATTAA-AAA-ATTTAATAATATAA
1159393 GTTTTATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
47 1 0.02
49 17 0.27
50 10 0.16
51 14 0.22
52 10 0.16
53 1 0.02
54 10 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (46 bp):
TATTAAAAAATTTAATAATATAATATAATATTTTTATTTAATAATA
Found at i:1159350 original size:23 final size:22
Alignment explanation
Indices: 1159305--1159354 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
1159295 AATATTTGTA
*
1159305 ATATTATAAAATATATTAAATT
1 ATATTATAAAATATATGAAATT
*
1159327 ATATTATAATAATATATGATATT
1 ATATTATAA-AATATATGAAATT
1159350 ATATT
1 ATATT
1159355 TTTATTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTATAAAATATATGAAATT
Found at i:1159370 original size:10 final size:10
Alignment explanation
Indices: 1159357--1159387 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1159347 ATTATATTTT
1159357 TATTTAATAA
1 TATTTAATAA
1159367 TATTTAATAAA
1 TATTTAAT-AA
1159378 TATTTAATAA
1 TATTTAATAA
1159388 AATAAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTTAATAA
Found at i:1159379 original size:11 final size:11
Alignment explanation
Indices: 1159357--1159388 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1159347 ATTATATTTT
1159357 TATTTAAT-AA
1 TATTTAATAAA
1159367 TATTTAATAAA
1 TATTTAATAAA
1159378 TATTTAATAAA
1 TATTTAATAAA
1159389 ATAAGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTAATAAA
Found at i:1159496 original size:14 final size:14
Alignment explanation
Indices: 1159470--1159503 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1159460 ATTTTCAAAA
*
1159470 TATAAT-TTTATAT
1 TATAATATTAATAT
1159483 TATAATATTAATAT
1 TATAATATTAATAT
1159497 TATAATA
1 TATAATA
1159504 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATAATATTAATAT
Found at i:1159547 original size:42 final size:42
Alignment explanation
Indices: 1159501--1159583 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
1159491 TAATATTATA
* * *
1159501 ATAATATTTTTATTTTAATAAGTAATTAATATAATTGATAAT
1 ATAATATTCTTATTATAATAAATAATTAATATAATTGATAAT
*
1159543 ATAATATTCTTATTATAATAAATAATTAATATAATTTATAA
1 ATAATATTCTTATTATAATAAATAATTAATATAATTGATAA
1159584 AATTTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (42 bp):
ATAATATTCTTATTATAATAAATAATTAATATAATTGATAAT
Found at i:1159563 original size:17 final size:17
Alignment explanation
Indices: 1159484--1159577 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 17
1159474 ATTTTATATT
*
1159484 ATAATATTAATATTATA
1 ATAATATTATTATTATA
* *
1159501 ATAATATTTTTATTTTA
1 ATAATATTATTATTATA
1159518 ATAAGTAATTAATATAATTGATAA
1 ATAA-T-ATT-AT-T-ATT-AT-A
*
1159542 TATAATATTCTTATTATA
1 -ATAATATTATTATTATA
* *
1159560 ATAA-ATAATTAATATA
1 ATAATATTATTATTATA
1159576 AT
1 AT
1159578 TTATAAAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
16 11 0.18
17 22 0.37
18 2 0.03
19 5 0.08
20 4 0.07
21 2 0.03
22 4 0.07
23 4 0.07
24 2 0.03
25 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAATATTATTATTATA
Found at i:1159792 original size:20 final size:20
Alignment explanation
Indices: 1159769--1159919 Score: 160
Period size: 20 Copynumber: 7.5 Consensus size: 20
1159759 GTTTCCAGAT
*
1159769 TCGCAACGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
1159789 TCGCATTGCGATTTTCCGACTA
1 TCGCAATGCGA--TTCTGACTA
* * *
1159811 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
* * *
1159831 TCACAATGCGAGTATGACTA
1 TCGCAATGCGATTCTGACTA
*
1159851 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
1159871 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
1159891 TCGCAACGCGATTCTGACTG
1 TCGCAATGCGATTCTGACTA
1159911 TCGCAATGC
1 TCGCAATGC
1159920 TGAATTTCAA
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
19 1 0.01
20 90 0.82
21 1 0.01
22 18 0.16
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:1159909 original size:60 final size:61
Alignment explanation
Indices: 1159769--1159919 Score: 180
Period size: 60 Copynumber: 2.5 Consensus size: 61
1159759 GTTTCCAGAT
* *
1159769 TCGCAACGCGATTCTGACTATCGCATTGCGATTTTCCGACTATCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTAT-CGACTATCGCAATGCGAATATGTAAA
* * * * * * *
1159831 TCACAATGCGAGTATGACTATCGCAATGCGATTAT-GACTATCGCAATGCGATTCTG-ACTA
1 TCGCAACGCGATTCTGACTATCGCAATGCGATTATCGACTATCGCAATGCGAATATGTA-AA
*
1159891 TCGCAACGCGATTCTGACTGTCGCAATGC
1 TCGCAACGCGATTCTGACTATCGCAATGC
1159920 TGAATTTCAA
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 44 0.59
62 29 0.39
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (61 bp):
TCGCAACGCGATTCTGACTATCGCAATGCGATTATCGACTATCGCAATGCGAATATGTAAA
Found at i:1162980 original size:18 final size:18
Alignment explanation
Indices: 1162957--1162991 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1162947 AGCAAAAGGC
*
1162957 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1162975 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1162992 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1163194 original size:20 final size:20
Alignment explanation
Indices: 1163169--1163460 Score: 194
Period size: 20 Copynumber: 15.6 Consensus size: 20
1163159 CACATTCATT
1163169 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
1163189 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* * *
1163209 TGAATAGCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
1163226 T-A--ATCGTAATGCGAA-A
1 TGACTATCGCAACGCGAATA
* *
1163242 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
*
1163262 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
1163279 T-A--ATCGCAATGAGAAAA
1 TGACTATCGCAACGCGAATA
*
1163296 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
1163316 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
* * *
1163336 TGACTATCGCAAAGAGAATT
1 TGACTATCGCAACGCGAATA
* *
1163356 TAACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
1163376 TAACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
1163393 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
1163409 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
1163429 TGATTATCGTAACG-GAAATT
1 TGACTATCGCAACGCG-AATA
1163449 TGACTATCGCAA
1 TGACTATCGCAA
1163461 TGAGAAAATC
Statistics
Matches: 219, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
14 21 0.10
15 2 0.01
16 9 0.04
17 9 0.04
18 3 0.01
19 28 0.13
20 147 0.67
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:1163246 original size:53 final size:53
Alignment explanation
Indices: 1163174--1163443 Score: 272
Period size: 53 Copynumber: 4.9 Consensus size: 53
1163164 TCATTTGACT
* * *
1163174 ATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATAGCGCAACGGGATA
1 ATCGCAATGCGAA-ATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
* * *
1163228 ATCGTAATGCGAAATGACTATCGCAATGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
* ** * *
1163281 ATCGCAATGAGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGA
1 ATCGCAATGCG-AAATGACTATCGCAACGCGAATTTGAATATCGCAACG-G--GAT-A
* * * * *
1163339 CTATCGCAAAGAGAATTTAACTATCGCAACGCGAATTT-AACTATCGCAACGAGATA
1 --ATCGCAATGCGAA-ATGACTATCGCAACGCGAATTTGAA-TATCGCAACGGGATA
* * *
1163395 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGTAACGG
1 ATCGCAATGCGAAATGACTATCGCAACGCGAATTTGAATATCGCAACGG
1163444 AAATTTGACT
Statistics
Matches: 179, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
53 74 0.41
54 57 0.32
55 1 0.01
56 1 0.01
57 4 0.02
58 1 0.01
59 3 0.02
60 38 0.21
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (53 bp):
ATCGCAATGCGAAATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
Found at i:1163449 original size:73 final size:73
Alignment explanation
Indices: 1163321--1163506 Score: 221
Period size: 73 Copynumber: 2.5 Consensus size: 73
1163311 GAAAATGACT
* * * *
1163321 ATCGCAACGCGAAAATGACTATCGCAAAGAGAATTTAACTATCGCAACGCGAATTTAACTATCGC
1 ATCGCAACGCG-AAATGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTAACTATCGC
*
1163386 AACGAGATA
65 AACGAGAAA
* *
1163395 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGTAACG-GAAATTTGACTATCGC
1 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAACGCG-AATTTAACTATCGC
*
1163459 AATGAGAAA
65 AACGAGAAA
* * * * *
1163468 ATCGCAAAGTGTATTAGACTATCGCAACGCGAATATGAT
1 ATCGCAACGCGAAAT-GACTATCGCAACGCGAATTTGAT
1163507 GCAGATTGAA
Statistics
Matches: 97, Mismatches: 13, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
72 1 0.01
73 63 0.65
74 33 0.34
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (73 bp):
ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAACGCGAATTTAACTATCGCA
ACGAGAAA
Found at i:1163474 original size:167 final size:164
Alignment explanation
Indices: 1163169--1163505 Score: 378
Period size: 167 Copynumber: 2.0 Consensus size: 164
1163159 CACATTCATT
* * * * * *
1163169 TGACTATCGCAACGCGAATATGACTATCGCAACGTGAATTTGAATAGCGCAACGGGATAATCGTA
1 TGACTATCGCAAAGAGAATATAACTATCGCAACGCGAATTTGAATAGCGCAACGAGATAATCGCA
* * *
1163234 ATGCGAAATGACTATCGCAATGCGAATTTGACTATCGCAACGGGATAATCGCAATGAGAAAATGA
66 ACGCGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGAATAATCGCAATGAG-AAA-GA
*
1163299 CTATCGCAACGCGAAA-ATGACTATCGCAACGCGAAAA
129 C-ATCGCAAAGCGAAATA-GACTATCGCAACGCGAAAA
* *
1163336 TGACTATCGCAAAGAGAATTTAACTATCGCAACGCGAATTT-AACTATCGCAACGAGATAATCGC
1 TGACTATCGCAAAGAGAATATAACTATCGCAACGCGAATTTGAA-TAGCGCAACGAGATAATCGC
* *
1163400 AACGCGAAATGACTATCGCAACGCGAATTTGATTATCGTAACGGAAATTTGACTATCGCAATGAG
65 AACGCGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGG-AA--T-A--ATCGCAATGAG
* * * *
1163465 -AA-A-ATCGCAAAGTGTATTAGACTATCGCAACGCGAATA
124 AAAGACATCGCAAAGCGAAATAGACTATCGCAACGCGAAAA
1163503 TGA
1 TGA
1163506 TGCAGATTGA
Statistics
Matches: 144, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
166 2 0.01
167 124 0.86
168 2 0.01
169 1 0.01
170 1 0.01
171 3 0.02
173 11 0.08
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (164 bp):
TGACTATCGCAAAGAGAATATAACTATCGCAACGCGAATTTGAATAGCGCAACGAGATAATCGCA
ACGCGAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGAATAATCGCAATGAGAAAGACA
TCGCAAAGCGAAATAGACTATCGCAACGCGAAAA
Found at i:1165016 original size:42 final size:42
Alignment explanation
Indices: 1164951--1165042 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1164941 GAATTGGGCA
* * *
1164951 CTAGAATGTTGGGAGGGACCTCTTCAACGATGATAGTGGCCT
1 CTAGAACGGTGGGAGGGACCTCTTCAACGATGATAGGGGCCT
* **
1164993 CTAGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGCCT
1 CTAGAACGGTGGGA-GGGACCTCTTCAACGATGATAGGGGCCT
*
1165035 CTTGAACG
1 CTAGAACG
1165043 ATAGGGGAGG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 38 0.90
43 4 0.10
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (42 bp):
CTAGAACGGTGGGAGGGACCTCTTCAACGATGATAGGGGCCT
Found at i:1165067 original size:42 final size:42
Alignment explanation
Indices: 1164951--1165067 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 42
1164941 GAATTGGGCA
* * * *
1164951 CTAGAATGTTGGGAG-GGACCTCTTCAACGATGATAGTGGCCT
1 CTAGAACGATGGGAGAGGA-CTCTTGAACGATGATAGGGGCCT
* * **
1164993 CTAGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGCCT
1 CTAGAACGATGGGAGAGGACTCTTGAACGATGATAGGGGCCT
* * *
1165035 CTTGAACGATAGGG-GAGGCCTTTTGAACGATGA
1 CTAGAACGAT-GGGAGAGGACTCTTGAACGATGA
1165068 CAGGTGAGTC
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 54 0.90
43 6 0.10
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (42 bp):
CTAGAACGATGGGAGAGGACTCTTGAACGATGATAGGGGCCT
Found at i:1165580 original size:18 final size:19
Alignment explanation
Indices: 1165557--1165601 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
1165547 GAAACTTAAA
1165557 ATCGCAACACGAA-TGACT
1 ATCGCAACACGAATTGACT
1165575 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAA-TTGACT
1165595 ATCGCAA
1 ATCGCAA
1165602 TGCGATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 13 0.52
20 12 0.48
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.20
Consensus pattern (19 bp):
ATCGCAACACGAATTGACT
Found at i:1165657 original size:20 final size:20
Alignment explanation
Indices: 1165632--1165699 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
1165622 GCGATTCTTT
*
1165632 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
*
1165652 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
1165672 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
1165692 CGTTGCGA
1 CGTTGCGA
1165700 AAGTAAACTA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1167670 original size:19 final size:19
Alignment explanation
Indices: 1167582--1167689 Score: 92
Period size: 20 Copynumber: 5.5 Consensus size: 19
1167572 TCTGAAACTT
*
1167582 AAAATCGCAACACGAAAAATG
1 AAAATCGCAACGCG--AAATG
* *
1167603 AAAATCGTAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
1167623 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAA-ATG
**
1167643 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
1167662 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAA-TG
1167681 AAAATCGCA
1 AAAATCGCA
1167690 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
19 28 0.37
20 35 0.46
21 13 0.17
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1168099 original size:22 final size:22
Alignment explanation
Indices: 1168069--1168125 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
1168059 GATAGAGATA
*
1168069 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
* *
1168091 GACTGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
1168113 GACGGATGTCGCC
1 GACGGATTTCGCC
1168126 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.40, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:1168343 original size:20 final size:20
Alignment explanation
Indices: 1168290--1168383 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
1168280 GCGCTTTGAA
*
1168290 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
*
1168310 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
1168330 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
1168350 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
*
1168370 ACTCGCATTGCGAT
1 AATCGCATTGCGAT
1168384 TTACATATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.02
20 60 0.97
21 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:1168356 original size:40 final size:40
Alignment explanation
Indices: 1168312--1168407 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1168302 ACAGTCAGAA
1168312 TCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACATAT
* *
1168352 TCGCGTTGCGATAGTCATACTCGCATTGCGATTTACATAT
1 TCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACATAT
* *
1168392 TTGCATTGCGATAGTC
1 TCGCGTTGCGATAGTC
1168408 GGAAAATCGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (40 bp):
TCGCGTTGCGATAGTCAGAATCGCATTGCGATTTACATAT
Found at i:1168390 original size:20 final size:20
Alignment explanation
Indices: 1168332--1168403 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1168322 ATAGTCAGAA
1168332 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
1168352 TCGCGTTGCGATAGT-CATAC
1 TCGCATTGCGAT-TTACATAT
1168372 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1168392 TTGCATTGCGAT
1 TCGCATTGCGAT
1168404 AGTCGGAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.95
21 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1168653 original size:14 final size:15
Alignment explanation
Indices: 1168635--1168677 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
1168625 AAAATTACAA
**
1168635 AAATAATATTTTAAT
1 AAATAATATTGAAAT
1168650 -AATAATATTGAAAT
1 AAATAATATTGAAAT
1168664 AAATAATATT-AAAT
1 AAATAATATTGAAAT
1168678 TATTTTACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAATAATATTGAAAT
Found at i:1187818 original size:23 final size:23
Alignment explanation
Indices: 1187788--1187837 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1187778 CATGTTCATG
1187788 GTATTGAATTATTAATAGCTATA
1 GTATTGAATTATTAATAGCTATA
*
1187811 GTATTGAATTTTTAATAGCTATA
1 GTATTGAATTATTAATAGCTATA
1187834 GTAT
1 GTAT
1187838 AGATCCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (23 bp):
GTATTGAATTATTAATAGCTATA
Found at i:1193685 original size:2 final size:2
Alignment explanation
Indices: 1193678--1193707 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1193668 ATTATTTAAA
1193678 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
1193708 GAATCAGGTA
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:1194080 original size:4 final size:4
Alignment explanation
Indices: 1194071--1194689 Score: 1141
Period size: 4 Copynumber: 155.0 Consensus size: 4
1194061 ATTATAATAA
1194071 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194119 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194167 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194215 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194263 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * * * * * * * *
1194311 GTAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT GCAT G-AT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194358 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194406 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194454 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194502 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194550 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194598 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194646 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1194690 TTAAAATGCA
Statistics
Matches: 613, Mismatches: 1, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
3 3 0.00
4 610 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:1200003 original size:6 final size:6
Alignment explanation
Indices: 1199992--1200017 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1199982 CTTGACCTGA
1199992 CCTAAC CCTAAC CCTAAC CCTAAC CC
1 CCTAAC CCTAAC CCTAAC CCTAAC CC
1200018 AACAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTAAC
Found at i:1200380 original size:13 final size:13
Alignment explanation
Indices: 1200362--1200390 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1200352 GATACCGTCC
1200362 CCCAAATCAAGAA
1 CCCAAATCAAGAA
1200375 CCCAAATCAAGAA
1 CCCAAATCAAGAA
1200388 CCC
1 CCC
1200391 TATTATCGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.38, G:0.07, T:0.07
Consensus pattern (13 bp):
CCCAAATCAAGAA
Found at i:1202569 original size:2 final size:2
Alignment explanation
Indices: 1202562--1202587 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1202552 TTAAGTTTTA
1202562 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
1202588 TTTTTCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1202808 original size:2 final size:2
Alignment explanation
Indices: 1202801--1202830 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1202791 TTATTTAGTG
1202801 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
1202831 ATTATTTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1204926 original size:25 final size:25
Alignment explanation
Indices: 1204898--1204947 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1204888 ATGCGCATGA
1204898 AAATTTAATTTTAAATAAAT-TATTT
1 AAATTT-ATTTTAAATAAATATATTT
**
1204923 AAATTTATTTTGGATAAATATATTT
1 AAATTTATTTTAAATAAATATATTT
1204948 TTAAGGAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
AAATTTATTTTAAATAAATATATTT
Found at i:1208237 original size:68 final size:68
Alignment explanation
Indices: 1208128--1208278 Score: 293
Period size: 68 Copynumber: 2.2 Consensus size: 68
1208118 ATTGTTGTCG
1208128 AGAACTGATGCCGTTGATGGTTTATCTGTCGCTGTATATCTTGGCTGGTAATGAATGTTTCATTT
1 AGAACTGATGCCGTTGATGGTTTATCTGTCGCTGTATATCTTGGCTGGTAATGAATGTTTCATTT
1208193 GAA
66 GAA
*
1208196 AGAACTGATGCTGTTGATGGTTTATCTGTCGCTGTATATCTTGGCTGGTAATGAATGTTTCATTT
1 AGAACTGATGCCGTTGATGGTTTATCTGTCGCTGTATATCTTGGCTGGTAATGAATGTTTCATTT
1208261 GAA
66 GAA
1208264 AGAACTGATGCCGTT
1 AGAACTGATGCCGTT
1208279 AATGATTCAA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 81 1.00
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (68 bp):
AGAACTGATGCCGTTGATGGTTTATCTGTCGCTGTATATCTTGGCTGGTAATGAATGTTTCATTT
GAA
Found at i:1219049 original size:20 final size:21
Alignment explanation
Indices: 1219026--1219065 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1219016 TTTTTTAAGA
*
1219026 TTTTTAAAAGTTT-TAATTTC
1 TTTTTAAAAATTTATAATTTC
1219046 TTTTTAAAAATTTATAATTT
1 TTTTTAAAAATTTATAATTT
1219066 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTAAAAATTTATAATTTC
Found at i:1219055 original size:21 final size:20
Alignment explanation
Indices: 1219026--1219065 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1219016 TTTTTTAAGA
1219026 TTTTTAAAAGTTT-TAATTTC
1 TTTTTAAAA-TTTATAATTTC
1219046 TTTTTAAAAATTTATAATTT
1 TTTTT-AAAATTTATAATTT
1219066 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTTTAAAATTTATAATTTC
Found at i:1220739 original size:14 final size:15
Alignment explanation
Indices: 1220720--1220748 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1220710 AAAAATCTAC
1220720 ATATAACA-TTGATT
1 ATATAACATTTGATT
1220734 ATATAACATTTGATT
1 ATATAACATTTGATT
1220749 GAAAGACAAC
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:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (15 bp):
ATATAACATTTGATT
Found at i:1221373 original size:16 final size:16
Alignment explanation
Indices: 1221354--1221441 Score: 77
Period size: 16 Copynumber: 5.4 Consensus size: 16
1221344 AATCAAACAT
*
1221354 AACCGAAATCAACCCG
1 AACCGAAAGCAACCCG
* *
1221370 AACCAAAAGCAACTCG
1 AACCGAAAGCAACCCG
* *
1221386 AACCGAAAGAAACCTG
1 AACCGAAAGCAACCCG
* ***
1221402 AATCGAATTTTAACCCG
1 AACCGAA-AGCAACCCG
*
1221419 ATCCGAAAGCAACCCG
1 AACCGAAAGCAACCCG
1221435 AACCGAA
1 AACCGAA
1221442 TTTAACCAAA
Statistics
Matches: 53, Mismatches: 18, Indels: 2
0.73 0.25 0.03
Matches are distributed among these distances:
16 43 0.81
17 10 0.19
ACGTcount: A:0.44, C:0.31, G:0.15, T:0.10
Consensus pattern (16 bp):
AACCGAAAGCAACCCG
Found at i:1226277 original size:17 final size:18
Alignment explanation
Indices: 1226250--1226283 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1226240 GTTTGATTGA
1226250 TATAGAAAAAAGCCATGG
1 TATAGAAAAAAGCCATGG
*
1226268 TATA-AAAAAAGTCATG
1 TATAGAAAAAAGCCATG
1226284 CTAAATTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.21
Consensus pattern (18 bp):
TATAGAAAAAAGCCATGG
Found at i:1231082 original size:17 final size:18
Alignment explanation
Indices: 1231052--1231085 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1231042 AAAAACACAC
*
1231052 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
1231070 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
1231086 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:1231907 original size:142 final size:145
Alignment explanation
Indices: 1231621--1231908 Score: 530
Period size: 142 Copynumber: 2.0 Consensus size: 145
1231611 AAATGAGATA
1231621 CCCAAAAATAATTAGAGAACTAAAATGAAATTATTACAAACATTGGGACCCAAAGTCAAGTATGA
1 CCCAAAAATAATTAGAGAACTAAAATGAAATTATTACAAACATTGGGACCCAAAGTCAAGTATGA
1231686 CTATAATAACATTACATTTAATAGGACTAAAATAAAAATATATAACTGCAGAATACAATGTACAA
66 CTATAATAACATTACA-TTAATAGGACTAAAATAAAAATATATAACTGCAGAATACAATGTACAA
1231751 ATTTATAAAAATTAGC
130 ATTTATAAAAATTAGC
1231767 CCCAAAAAT-A-TAGAGAACTAAAATGAAATTATTACAAACATTGGGA-CCAAAGTCAAGTATGA
1 CCCAAAAATAATTAGAGAACTAAAATGAAATTATTACAAACATTGGGACCCAAAGTCAAGTATGA
1231829 CTATAATAACATTACA-TAATAGGACTAAAATAAAATATATATAACTGCAGAATACAATGTACAA
66 CTATAATAACATTACATTAATAGGACTAAAATAAAA-ATATATAACTGCAGAATACAATGTACAA
1231893 ATTTATAAAAATTAGC
130 ATTTATAAAAATTAGC
1231909 AACAGAGGAT
Statistics
Matches: 141, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
141 19 0.13
142 44 0.31
143 32 0.23
144 36 0.26
145 1 0.01
146 9 0.06
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.26
Consensus pattern (145 bp):
CCCAAAAATAATTAGAGAACTAAAATGAAATTATTACAAACATTGGGACCCAAAGTCAAGTATGA
CTATAATAACATTACATTAATAGGACTAAAATAAAAATATATAACTGCAGAATACAATGTACAAA
TTTATAAAAATTAGC
Found at i:1233312 original size:3 final size:3
Alignment explanation
Indices: 1233306--1233361 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
1233296 AAAAAAAATG
* **
1233306 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1233350 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1233362 AAAAACGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1233343 original size:29 final size:30
Alignment explanation
Indices: 1233311--1233373 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
1233301 AAATGTAATA
* *
1233311 ATAAATAATAATAA-AATAATAAGATAACG
1 ATAAATAATAATAATAATAATAAAAAAACG
1233340 AT-AATAATAATAATAATAATAAAAAAACG
1 ATAAATAATAATAATAATAATAAAAAAACG
1233369 ATAAA
1 ATAAA
1233374 AAAAAACCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 11 0.37
29 17 0.57
30 2 0.07
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (30 bp):
ATAAATAATAATAATAATAATAAAAAAACG
Found at i:1233889 original size:170 final size:170
Alignment explanation
Indices: 1233696--1234330 Score: 980
Period size: 170 Copynumber: 3.7 Consensus size: 170
1233686 TTATCTAGGG
*
1233696 TGACACGACTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
*
1233761 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
66 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTT
1233826 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
131 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
1233866 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
*
1233931 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
66 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTT
1233996 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
131 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
** * * *
1234036 TGACACGGCTCATACGTGATGAAGAGATCTGGTCATCTAAAGG-TGACACGGCTCATACGTGATG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT-GGGGATGACACGGTTCCTACATGATG
* * * * * **
1234100 AAGA-GATCTGG---TCT---GGGGATGACACGGTTCCTACATGATGAGGACGGATGGCCATCTA
62 AGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCT-
* * *
1234158 AAGGTGATAACACGGTTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
125 ATGGT--TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
1234206 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
1234271 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTA
66 CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTA
1234331 GGGATAATGG
Statistics
Matches: 420, Mismatches: 29, Indels: 30
0.88 0.06 0.06
Matches are distributed among these distances:
166 2 0.00
167 65 0.15
168 5 0.01
170 278 0.66
172 2 0.00
173 66 0.16
174 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (170 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGA
CGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTT
GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAA
Found at i:1234108 original size:213 final size:210
Alignment explanation
Indices: 1233569--1234291 Score: 690
Period size: 213 Copynumber: 3.4 Consensus size: 210
1233559 ATCTAAAGGG
* *
1233569 GACACAGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGACTCATACGTGATGAAGA
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGA
* * * * * *
1233633 GTTCTGG-CTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAGGG
65 GATCTGGTC-ATCTAAAGGTG---ACACGGCTCATACGTGATGAAGA-GATCTGG---TCTGGGG
** * * * * * * *
1233696 -TGACACGACTCATACGTGATGAAGA-GATCTGG---TCT---GGGGATGACACGGTTCCTACAT
122 ATGACACGGTTCCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGT
1233753 GATGAGGACGGCTGGCCATCTAAAGGTGAT
186 GATGAGGACGGCTGG--ATCT-AAGGT--T
* * * * * ** * *
1233783 AACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGA
1 GACACGGCTCATACGTGATGAAGA-GATCTGG---TCTGGGGATGACACGGCTCATACGTGATGA
* ***
1233847 GGAGATCTGGTC-TGGGGAA--TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGA
62 AGAGATCTGGTCAT-CTAAAGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGA
1233909 CACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGA
126 CACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGA
*
1233974 GGACGGCTGGTTATCTATGGTT
191 GGACGGCTGG--ATCTAAGGTT
* *
1233996 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGA
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGA
1234061 GATCTGGTCATCTAAAGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACG
65 GATCTGGTCATCTAAAGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACG
*
1234126 GTTCCTACATGATGAGGACGGATGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGA-
130 GTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGAC
* ** *
1234190 GATCTGG-TCTGGGGAAT
195 G-GCTGGATCTAAGG-TT
* * * *
1234207 GACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGAGGAC
1 GACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA-
* *
1234272 G-GCTGGCCATCTAAAGGTGA
65 GATCTGGTCATCTAAAGGTGA
1234292 TAACACGGTT
Statistics
Matches: 428, Mismatches: 57, Indels: 52
0.80 0.11 0.10
Matches are distributed among these distances:
209 6 0.01
210 73 0.17
211 74 0.17
212 27 0.06
213 144 0.34
214 23 0.05
215 7 0.02
216 39 0.09
217 32 0.07
218 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (210 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAG
ATCTGGTCATCTAAAGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGG
TTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
GCTGGATCTAAGGTT
Found at i:1234386 original size:28 final size:28
Alignment explanation
Indices: 1234340--1234393 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1234330 AGGGATAATG
*
1234340 GTTTCAAAGAAGACCAACTCAAAGATGT
1 GTTTCAAAGAAGACAAACTCAAAGATGT
1234368 GTTTCAATAGAA-ACAAACTCAAAGAT
1 GTTTCAA-AGAAGACAAACTCAAAGAT
1234394 TGGATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (28 bp):
GTTTCAAAGAAGACAAACTCAAAGATGT
Found at i:1234698 original size:66 final size:64
Alignment explanation
Indices: 1234523--1234691 Score: 178
Period size: 66 Copynumber: 2.6 Consensus size: 64
1234513 TGTCTCGAGA
* * * ** *
1234523 GAGACAAAATTCATTTCAAAGGAAAC-AACCCAAAGATGGCATTTAAAGGGAATTGTCTCAAGT
1 GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAAAGGGAATTGTCTCAACT
** * * * * * *
1234586 GAGACAAAATTTGTTTTTAAGGGAAACGTTCTCCAAGATCGGTGTTTCATGGGAAATTGTCTTAA
1 GAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GGTGTTTAAAGGG-AATTGTCTCAA
1234651 CT
63 CT
1234653 GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1234692 TTTGTTTGTT
Statistics
Matches: 83, Mismatches: 19, Indels: 6
0.77 0.18 0.06
Matches are distributed among these distances:
63 9 0.11
64 13 0.16
65 8 0.10
66 33 0.40
67 20 0.24
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (64 bp):
GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGGTGTTTAAAGGGAATTGTCTCAACT
Found at i:1235305 original size:4 final size:4
Alignment explanation
Indices: 1235289--1235356 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
1235279 ATGCAAATTT
*
1235289 TATG TAT- TATG TATG TATG TAT- TGATG TATG TATG TAT- TGATA TATG
1 TATG TATG TATG TATG TATG TATG T-ATG TATG TATG TATG T-ATG TATG
*
1235336 TTTG TAT- TGATG TATG TATG T
1 TATG TATG T-ATG TATG TATG T
1235357 TGATTTGTGA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
3 6 0.11
4 45 0.83
5 3 0.06
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (4 bp):
TATG
Found at i:1235318 original size:16 final size:16
Alignment explanation
Indices: 1235289--1235356 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
1235279 ATGCAAATTT
1235289 TATGTATT-ATGTATG
1 TATGTATTGATGTATG
1235304 TATGTATTGATGTATG
1 TATGTATTGATGTATG
*
1235320 TATGTATTGATATATG
1 TATGTATTGATGTATG
*
1235336 TTTGTATTGATGTATG
1 TATGTATTGATGTATG
1235352 TATGT
1 TATGT
1235357 TGATTTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
15 8 0.17
16 40 0.83
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (16 bp):
TATGTATTGATGTATG
Found at i:1240643 original size:17 final size:18
Alignment explanation
Indices: 1240613--1240646 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1240603 AAAAACACAC
*
1240613 ATTACATTATTAAAATAA
1 ATTACATTAGTAAAATAA
1240631 ATTA-ATTAGTAAAATA
1 ATTACATTAGTAAAATA
1240647 TAATCGACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACATTAGTAAAATAA
Found at i:1240840 original size:22 final size:21
Alignment explanation
Indices: 1240811--1240858 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1240801 GTAATTGGAA
1240811 ATAC-AAAATAAAAT-ATTTAC
1 ATACTAAAA-AAAATCATTTAC
*
1240831 ATTACTAAAAAACATCATTTAC
1 A-TACTAAAAAAAATCATTTAC
1240853 ATACTA
1 ATACTA
1240859 CAAACAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (21 bp):
ATACTAAAAAAAATCATTTAC
Found at i:1242943 original size:14 final size:15
Alignment explanation
Indices: 1242925--1243092 Score: 62
Period size: 14 Copynumber: 10.9 Consensus size: 15
1242915 TTAATAAGGT
1242925 ATTTATTTTAAAAT-
1 ATTTATTTTAAAATG
* *
1242939 ATTTATTATAAAATA
1 ATTTATTTTAAAATG
* *
1242954 ATTTACTCTAAAAT-
1 ATTTATTTTAAAATG
* *
1242968 AATTATTATAAATATGGATTG
1 ATTTATT-TTAA-A---A-TG
*
1242989 ATTTATTTTTAAAT-
1 ATTTATTTTAAAATG
*
1243003 ATTTATTTT-AAATA
1 ATTTATTTTAAAATG
* **
1243017 ATTTATTAGTATGGATG
1 ATTTATT-TTA-AAATG
1243034 ATTTATTTTAAAATATG
1 ATTTATTTT-AAA-ATG
1243051 ATTTATTTT--AAT-
1 ATTTATTTTAAAATG
* * *
1243063 ATTTATTAGTATATTG
1 ATTTATT-TTAAAATG
1243079 ATTTATTTTAAAAT
1 ATTTATTTTAAAAT
1243093 ATGGATTGAT
Statistics
Matches: 114, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
12 7 0.06
13 7 0.06
14 35 0.31
15 22 0.19
16 10 0.09
17 22 0.19
19 2 0.02
20 3 0.03
21 6 0.05
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATG
Found at i:1242965 original size:15 final size:15
Alignment explanation
Indices: 1242933--1242971 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1242923 GTATTTATTT
*
1242933 TAAAAT-ATTTATTA
1 TAAAATAATTTACTA
*
1242947 TAAAATAATTTACTC
1 TAAAATAATTTACTA
1242962 TAAAATAATT
1 TAAAATAATT
1242972 ATTATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAAATAATTTACTA
Found at i:1243068 original size:46 final size:47
Alignment explanation
Indices: 1242980--1243134 Score: 182
Period size: 45 Copynumber: 3.4 Consensus size: 47
1242970 TTATTATAAA
*
1242980 TATGGATTGATTTATTTT-TAA-AT-ATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGATTTATTTT-AAT-ATTTATTAG
1243026 TATGGA-TGATTTATTTTAAAATATGATTTATTTTAATATTTATTAG
1 TATGGATTGATTTATTTTAAAATATGATTTATTTTAATATTTATTAG
* *
1243072 TAT--ATTGATTTATTTTAAAATATGGATTGA-TTTATTATTGTAGTT-G
1 TATGGATTGATTTATTTTAAAATAT-GATTTATTTTAATATT-TA-TTAG
1243118 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
1243135 AATAATTTAT
Statistics
Matches: 97, Mismatches: 3, Indels: 16
0.84 0.03 0.14
Matches are distributed among these distances:
44 1 0.01
45 37 0.38
46 31 0.32
47 7 0.07
48 21 0.22
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (47 bp):
TATGGATTGATTTATTTTAAAATATGATTTATTTTAATATTTATTAG
Found at i:1243177 original size:22 final size:24
Alignment explanation
Indices: 1243075--1243220 Score: 111
Period size: 22 Copynumber: 5.8 Consensus size: 24
1243065 TTATTAGTAT
1243075 ATTGATTTATTTTAAA-A-TATGG
1 ATTGATTTATTTTAAATAGTATGG
* * *
1243097 ATTGATTTATTATTGTAGTTGTATGG
1 ATTGATTTATT-TT-AAATAGTATGG
*
1243123 ATTGATTTATTTAATAATTTATTAGTATAG
1 ATTGATTTATTT--TAA---A-TAGTATGG
1243153 ATTGATTTATTTTAAA-A-TATGG
1 ATTGATTTATTTTAAATAGTATGG
*
1243175 ATTGCTTTATTTTAATTTATTAGTATGG
1 ATTGATTTATTTTAA---A-TAGTATGG
1243203 ATTGATTTATTTTAAATA
1 ATTGATTTATTTTAAATA
1243221 ATTTATTTTG
Statistics
Matches: 98, Mismatches: 10, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
22 29 0.30
23 3 0.03
24 3 0.03
25 4 0.04
26 17 0.17
27 2 0.02
28 22 0.22
30 18 0.18
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (24 bp):
ATTGATTTATTTTAAATAGTATGG
Found at i:1243206 original size:50 final size:51
Alignment explanation
Indices: 1243118--1243318 Score: 173
Period size: 50 Copynumber: 3.9 Consensus size: 51
1243108 ATTGTAGTTG
1243118 TATGGATTGATTTATTTAATAATTTATTAGTATAGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTT-ATAATTTATTAGTATAGATTGATTTATTTTAAAA
* *
1243170 TATGGATTGCTTTATTT-TAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTATAATTTATTAGTATAGATTGATTTATTTTAAAA
* * * * * ***
1243219 TA---ATTTATTT-TGTATAGTATTTTTTAAATATGGATTGATTTATTATGTAGTTG
1 TATGGATTGATTTATTTATA--ATTTATT-AGTATAGATTGATTTATT-T-TA-AAA
*
1243272 TATGGATTG-CTTATTTAAATAATTTATTAGTATAGATTGATTTATTT
1 TATGGATTGATTTATTT--ATAATTTATTAGTATAGATTGATTTATTT
1243319 CATGGATTGA
Statistics
Matches: 119, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
45 2 0.02
46 8 0.07
48 6 0.05
49 22 0.18
50 29 0.24
51 1 0.01
52 16 0.13
53 2 0.02
54 1 0.01
55 18 0.15
56 11 0.09
58 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (51 bp):
TATGGATTGATTTATTTATAATTTATTAGTATAGATTGATTTATTTTAAAA
Found at i:1243394 original size:30 final size:31
Alignment explanation
Indices: 1243358--1243417 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1243348 ATTAGTGTAT
* *
1243358 AAATTATTTAAAT-TTAGTATTGTAAAACTA
1 AAATTATTTAAATCTCAGTATTGCAAAACTA
1243388 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAGTATTGCAAAACT
1243418 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AAATTATTTAAATCTCAGTATTGCAAAACTA
Found at i:1246188 original size:18 final size:19
Alignment explanation
Indices: 1246165--1246211 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1246155 TTATCGCATA
1246165 ATCGTAAT-ATTTATAATT
1 ATCGTAATAATTTATAATT
*
1246183 ATCGTAATAACATTTATTATT
1 ATCGTAAT-A-ATTTATAATT
1246204 ATCGTAAT
1 ATCGTAAT
1246212 TATAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
21 17 0.68
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (19 bp):
ATCGTAATAATTTATAATT
Found at i:1249047 original size:23 final size:22
Alignment explanation
Indices: 1249021--1249063 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1249011 ATATTTTATA
1249021 TTTTTTT-AGAAAGTATTTTTCT
1 TTTTTTTCAGAAAGT-TTTTTCT
*
1249043 TTTTTTTCATAAAGTTTTTTC
1 TTTTTTTCAGAAAGTTTTTTC
1249064 ATACGAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.65
Consensus pattern (22 bp):
TTTTTTTCAGAAAGTTTTTTCT
Found at i:1250058 original size:19 final size:19
Alignment explanation
Indices: 1250034--1250070 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1250024 ATGACCAACA
*
1250034 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1250053 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1250071 CAGTATCGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1250363 original size:15 final size:14
Alignment explanation
Indices: 1250343--1250385 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 14
1250333 TATGATAAAC
1250343 TATAAATTTAAATAA
1 TATAAA-TTAAATAA
1250358 TATAAATTAAATAAA
1 TATAAATTAAAT-AA
1250373 TATAAATTAAATA
1 TATAAATTAAATA
1250386 TTTATGATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.26
15 20 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TATAAATTAAATAA
Found at i:1251034 original size:21 final size:21
Alignment explanation
Indices: 1251010--1251049 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1251000 ATTATAAAAT
*
1251010 GTGAACAGTGTTATCGCAACG
1 GTGAACAGTGCTATCGCAACG
1251031 GTGAACAGTGCTATCGCAA
1 GTGAACAGTGCTATCGCAA
1251050 TGATTAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (21 bp):
GTGAACAGTGCTATCGCAACG
Found at i:1251284 original size:14 final size:15
Alignment explanation
Indices: 1251261--1251289 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1251251 CATGATTATT
1251261 TTAAATATTTTATAA
1 TTAAATATTTTATAA
1251276 TTAAA-ATTTTATAA
1 TTAAATATTTTATAA
1251290 AATATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATATTTTATAA
Done.