Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008964.1 Hibiscus syriacus cultivar Beakdansim tig00112305_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: 2156694
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 7 of 11
Found at i:1179479 original size:20 final size:20
Alignment explanation
Indices: 1179456--1179498 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1179446 GTACAACATA
*
1179456 AAAGTTAAATTCGCAACGCG
1 AAAGTTAAATTCACAACGCG
1179476 AAAGTTAAATTCACAACGCG
1 AAAGTTAAATTCACAACGCG
1179496 AAA
1 AAA
1179499 TAAGCATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.19
Consensus pattern (20 bp):
AAAGTTAAATTCACAACGCG
Found at i:1179535 original size:20 final size:20
Alignment explanation
Indices: 1179512--1179550 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1179502 GCATTACGAT
1179512 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCAAA
1179532 AGTCAAATTCGCAACGCAA
1 AGTCAAATTCGCAACGCAA
1179551 TTTTTCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAA
Found at i:1182013 original size:9 final size:9
Alignment explanation
Indices: 1182001--1182025 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1181991 TCTTCGGGGA
1182001 CTTCTTTTT
1 CTTCTTTTT
1182010 CTTCTTTTT
1 CTTCTTTTT
1182019 CTTCTTT
1 CTTCTTT
1182026 AGGTTATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (9 bp):
CTTCTTTTT
Found at i:1182396 original size:12 final size:12
Alignment explanation
Indices: 1182375--1182408 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1182365 GGTTGTGGGT
*
1182375 TTTGAGATTGTG
1 TTTGATATTGTG
1182387 TTTGATATTGTG
1 TTTGATATTGTG
*
1182399 TTTGGTATTG
1 TTTGATATTG
1182409 GAAATGTGGT
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:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1183181 original size:19 final size:19
Alignment explanation
Indices: 1183153--1183224 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
1183143 ACTAAAACCT
*
1183153 GTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
1183172 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
** **
1183193 GTTGCGAATTTGACTTTGT
1 GTTGCGAATTTGAAATTCA
1183212 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1183225 CTATCGCGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 29 0.64
20 1 0.02
21 15 0.33
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:1183203 original size:40 final size:39
Alignment explanation
Indices: 1183153--1183244 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
1183143 ACTAAAACCT
*
1183153 GTTGCAAATTTGAAATTCAGTTGCGAATTTGAA-ATTCCGC
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAATA-T-CGC
** ** *
1183193 GTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGAAATTCAGTTGCGAATTTGAATATCGC
1183232 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1183245 CGTATGTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.36
40 28 0.62
41 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCAGTTGCGAATTTGAATATCGC
Found at i:1183237 original size:20 final size:20
Alignment explanation
Indices: 1183172--1183258 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
1183162 TTGAAATTCA
*
1183172 GTTGCGAATTTGA-AATTCCGC
1 GTTGCGAATTTGACTA-T-CGC
* *
1183193 GTTGCGAATTTGACT-TTGT
1 GTTGCGAATTTGACTATCGC
1183212 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
1183232 GTTGCGAATTTGACGTAT-GT
1 GTTGCGAATTTGAC-TATCGC
1183252 GTTGCGA
1 GTTGCGA
1183259 TTTACAGATT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
19 16 0.28
20 25 0.44
21 16 0.28
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:1183253 original size:40 final size:40
Alignment explanation
Indices: 1183172--1183283 Score: 142
Period size: 40 Copynumber: 2.8 Consensus size: 40
1183162 TTGAAATTCA
*
1183172 GTTGCGAATTTGA-AATTCCGCGTTGCGAATTTGACTTTGT
1 GTTGCGAATTTGACAATT-CGCGTTGCGAATTTGACTATGT
*
1183212 GTTGCGAATTTGACTA-TCGCGTTGCGAATTTGACGTATGT
1 GTTGCGAATTTGACAATTCGCGTTGCGAATTTGAC-TATGT
*
1183252 GTTGCG-ATTT-ACAGATTTGCGTTGCGAATTTG
1 GTTGCGAATTTGACA-ATTCGCGTTGCGAATTTG
1183284 GAAAATCGCA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.03
39 22 0.34
40 39 0.61
41 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (40 bp):
GTTGCGAATTTGACAATTCGCGTTGCGAATTTGACTATGT
Found at i:1183605 original size:31 final size:30
Alignment explanation
Indices: 1183552--1183656 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
1183542 GTTATACGGA
**
1183552 ACATATGGACAGAATTACCTATGTCTTTCGAG
1 ACATATGGACATTA-TACCTATGT-TTTCGAG
* *
1183584 ACATATGGACATTATACCTATGTTTTAAGAA
1 ACATATGGACATTATACCTATGTTTT-CGAG
* *
1183615 ACATATGGACAGTT-TACCTAGGTTATTCGGG
1 ACATATGGACA-TTATACCTATGTT-TTCGAG
*
1183646 ACCTATGGACA
1 ACATATGGACA
1183657 GTTGCCGAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
30 3 0.05
31 42 0.69
32 16 0.26
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
ACATATGGACATTATACCTATGTTTTCGAG
Found at i:1186437 original size:199 final size:199
Alignment explanation
Indices: 1185783--1187146 Score: 1799
Period size: 199 Copynumber: 6.8 Consensus size: 199
1185773 TAGGTAAACA
*
1185783 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * ** * * *
1185848 ATAGGTAAATTTCTAATATAACTGGTAG-GTTAATACCAGTTTAATTAGAAAACATGTCA-ACAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAAT-ATACC-GGTTAATTAGAAAATAGGT-ATACAT
* * * *
1185911 AATGTATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCATAATGAATGCTCAACCGAGGT
128 AATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC-CAAACGAGGT
*
1185976 TCACGCAT
192 GCACGCAT
* * *
1185984 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAACAAATAATTATAATGCA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* ** * * * * * * *
1186049 ATAAGTAAATTTTTAATGAAACCAGTAGATATATATCAGTTTAATTAGAAAATATGTAAACATAA
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATA-CCGGTTAATTAGAAAATAGGTATACATAA
* * * * *
1186114 TGTATTGACACTTTTTAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCTCAACCGAGGTGC
130 TGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC-CAAACGAGGTGC
1186179 ACGCAT
194 ACGCAT
* * * *
1186185 AAAGTGTCAATACATTTATTAAAAGTAGCCATCCCAAAAACATCGAAACAGATAATTACAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* *
1186250 ATAGGTAAATTTCAAATGTAACCAGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
* *
1186315 GTATCGACACTTTTGCAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGGGGTGCAC
131 GTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
*
1186380 ACAT
196 GCAT
* *
1186384 AAAGTGTCGATACATTTATTAAAAGTAGCGATCCCAAAAACATCGAAACAGATAATTACAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* *
1186449 ATATGTAAATTTCAAATGTAACCGATAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
*
1186514 GTATCGACACTTTTGCAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAC-AGGGTGCA
131 GTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGA-GGTGCA
*
1186578 CACAT
195 CGCAT
* * * * *
1186583 TAAGTGTTGATACATTTATTAAAAGTTTCAATCCCAAAAACATCGAAACATATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * * * *
1186648 ATAGGTAAATTTCTAATGTAACCGATAGATATATATCGGTTTAATTAGAAAA-AGGTAAACATAA
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTATACATAA
* *
1186712 TGTATCGACACTTTTGAAA-TTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAACCGAGGTGC
130 TGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGAGGTGC
1186776 ACGCAT
194 ACGCAT
* * * *
1186782 AAAATGTCGATACATTTATTAAAAGTAGCGATCCCAAAAACATTGAAATAGATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
* * *
1186847 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATTGGTCTACATAAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
* * * * *
1186912 GTATCGACACTTTTAAAATTTGTGTCGATACGTTTTGTCCATAATGAATGCCCAACGGGGTGCAC
131 GTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
1186977 GCAT
196 GCAT
* * *
1186981 AAAGTGTCGATACA-TT-TTAAAATGTATCAATCCCAAAAACATCGAAACTGATAATTACAATGT
1 AAAGTGTCGATACATTTATTAAAA-GTATCGATCCCAAAAACATCGAAACAGATAATTATAATGT
* * * * * * * *
1187044 AATAGGTAAA-TTAACAATGTAACCGGTATAAATTTATCGGTTTTATGAGAAAATAGGTTTGCAT
65 AATAGGTAAATTTCA-AATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTATACAT
* * *
1187108 AATGTATCGACACTTTTTAAATTTGTATCGATATTTTTT
128 AATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTT
1187147 TAATTACGTA
Statistics
Matches: 1041, Mismatches: 110, Indels: 26
0.88 0.09 0.02
Matches are distributed among these distances:
197 8 0.01
198 110 0.11
199 543 0.52
200 113 0.11
201 265 0.25
202 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTATAATGTA
ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
GTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
GCAT
Found at i:1186920 original size:597 final size:600
Alignment explanation
Indices: 1185783--1187146 Score: 2012
Period size: 597 Copynumber: 2.3 Consensus size: 600
1185773 TAGGTAAACA
* *
1185783 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTACAATGTA
* * * ** * * *
1185848 ATAGGTAAATTTCTAATATAACTGGTAG-GTTAATACCAGTTTAATTAGAAAACATGTCA-ACAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAAT-ATACC-GGTTAATTAGAAAATAGGT-ATACAT
* *
1185911 AATGTATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCATAATGAATGCTCAACCGAGGT
128 AATGTATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCAGAATGAATGCTCAACAGAGGT
* * * *
1185976 TCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAACAAATAATT
193 GCACACATAAAGTGTCGATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACAAATAATT
* *
1186041 ATAATGCAATAAGTAAATTTTTAATGAAACCAGTAGATATATATCAGTTTAATTAGAAAATATGT
258 ATAATGCAATAAGTAAATTTCTAATGAAACCAGTAGATATATATCAGTTTAATTAGAAAATAGGT
* * *
1186106 AAACATAATGTATTGACACTTTTTAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCTCAAC
323 AAACATAATGTATCGACACTTTTGAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCCAAC
*
1186171 CGAGGTGCACGCATAAAGTGTCAATACATTTATTAAAAGTAGCCATCCCAAAAACATCGAAACAG
388 CGAGGTGCACGCATAAAATGTCAATACATTTATTAAAAGTAGCCATCCCAAAAACATCGAAACAG
1186236 ATAATTACAATGTAATAGGTAAATTTCAAATGTAACCAGTAGAAATATACCGGTTAATTAGAAAA
453 ATAATTACAATGTAATAGGTAAATTTCAAATGTAACCAGTAGAAATATACCGGTTAATTAGAAAA
** *
1186301 TAGGTCTACATAATGTATCGACACTTTTGCAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC
518 TAGGTCTACATAATGTATCGACACTTTTAAAATTTGTGTCGATACGTTTTGTCCAGAATGAATGC
1186366 CAAACGGGGTGCACACAT
583 CAAACGGGGTGCACACAT
*
1186384 AAAGTGTCGATACATTTATTAAAAGTAGCGATCCCAAAAACATCGAAACAGATAATTACAATGTA
1 AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTACAATGTA
* *
1186449 ATATGTAAATTTCAAATGTAACCGATAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
66 ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
** *
1186514 GTATCGACACTTTTGCAATTTGTGTCGATACTTTTTGTCCAGAATGAATGC-CAAACAG-GGTGC
131 GTATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCAGAATGAATGCTC-AACAGAGGTGC
* * * *
1186577 ACACATTAAGTGTTGATACATTTATTAAAAGTTTCAATCCCAAAAACATCGAAACATATAATTAT
195 ACACATAAAGTGTCGATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACAAATAATTAT
* * * *
1186642 AATGTAATAGGTAAATTTCTAATGTAACC-GATAGATATATATCGGTTTAATTAGAAAA-AGGTA
260 AATGCAATAAGTAAATTTCTAATGAAACCAG-TAGATATATATCAGTTTAATTAGAAAATAGGTA
*
1186705 AACATAATGTATCGACACTTTTGAAA-TTGTGTCGATACTTGTT-GTCCAGAATGAATGCCCAAC
324 AACATAATGTATCGACACTTTTGAAATTTATGTCGATACTT-TTGGTCCAGAATGAATGCCCAAC
* * * *
1186768 CGAGGTGCACGCATAAAATGTCGATACATTTATTAAAAGTAGCGATCCCAAAAACATTGAAATAG
388 CGAGGTGCACGCATAAAATGTCAATACATTTATTAAAAGTAGCCATCCCAAAAACATCGAAACAG
* * *
1186833 ATAATTATAATGTAATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAA
453 ATAATTACAATGTAATAGGTAAATTTCAAATGTAACCAGTAGAAATATACCGGTTAATTAGAAAA
* *
1186898 TTGGTCTACATAATGTATCGACACTTTTAAAATTTGTGTCGATACGTTTTGTCCATAATGAATGC
518 TAGGTCTACATAATGTATCGACACTTTTAAAATTTGTGTCGATACGTTTTGTCCAGAATGAATGC
* *
1186963 CCAACGGGGTGCACGCAT
583 CAAACGGGGTGCACACAT
* *
1186981 AAAGTGTCGATACA-TT-TTAAAATGTATCAATCCCAAAAACATCGAAACTGATAATTACAATGT
1 AAAGTGTCGATACATTTATTAAAA-GTATCGATCCCAAAAACATCGAAACAGATAATTACAATGT
* * * * * * * *
1187044 AATAGGTAAA-TTAACAATGTAACCGGTATAAATTTATCGGTTTTATGAGAAAATAGGTTTGCAT
65 AATAGGTAAATTTCA-AATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAATAGGTATACAT
*
1187108 AATGTATCGACACTTTTTAAATTTGTATCGATATTTTTT
128 AATGTATCGACACTTTTTAAATTTGTGTCGATATTTTTT
1187147 TAATTACGTA
Statistics
Matches: 687, Mismatches: 68, Indels: 20
0.89 0.09 0.03
Matches are distributed among these distances:
595 9 0.01
596 69 0.10
597 298 0.43
598 31 0.05
599 115 0.17
600 74 0.11
601 90 0.13
602 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (600 bp):
AAAGTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAGATAATTACAATGTA
ATAGGTAAATTTCAAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATAAT
GTATCGACACTTTTTAAATTTGTGTCGATATTTTTTGTCCAGAATGAATGCTCAACAGAGGTGCA
CACATAAAGTGTCGATACATTTATTAAAAGTATCAATCCCAAAAACATCGAAACAAATAATTATA
ATGCAATAAGTAAATTTCTAATGAAACCAGTAGATATATATCAGTTTAATTAGAAAATAGGTAAA
CATAATGTATCGACACTTTTGAAATTTATGTCGATACTTTTGGTCCAGAATGAATGCCCAACCGA
GGTGCACGCATAAAATGTCAATACATTTATTAAAAGTAGCCATCCCAAAAACATCGAAACAGATA
ATTACAATGTAATAGGTAAATTTCAAATGTAACCAGTAGAAATATACCGGTTAATTAGAAAATAG
GTCTACATAATGTATCGACACTTTTAAAATTTGTGTCGATACGTTTTGTCCAGAATGAATGCCAA
ACGGGGTGCACACAT
Found at i:1187071 original size:20 final size:19
Alignment explanation
Indices: 1187033--1187071 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1187023 CGAAACTGAT
*
1187033 AATTACAATGTAATAGGTA
1 AATTACAATGTAACAGGTA
*
1187052 AATTAACAATGTAACCGGTA
1 AATT-ACAATGTAACAGGTA
1187072 TAAATTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.28
Consensus pattern (19 bp):
AATTACAATGTAACAGGTA
Found at i:1188724 original size:19 final size:19
Alignment explanation
Indices: 1188700--1188747 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1188690 ATGTAGGGGA
1188700 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
1188719 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
1188738 AATTTTGTAT
1 AATTTTGTAT
1188748 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:1191915 original size:198 final size:198
Alignment explanation
Indices: 1191452--1192157 Score: 742
Period size: 198 Copynumber: 3.6 Consensus size: 198
1191442 GTAAACAGAT
* *
1191452 GTGTCGATACATTTTATAAA-AGTATCGACCCCAAAAATATCAAAACCAATAA-T-T-A--TAAT
1 GTGTCGATACA-TTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAAT
* * * * * * *
1191511 AGGTAAAATAACAATATAACCGGTAT-AA-ATACTG-GTTAATTACAAAACATGTCAACATAATG
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAAC-GGTCAACATAATG
* * * * * * *
1191573 TATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATACCCAACCAAGGCGCAT
129 TATCGAAACTTTTTGAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTGCA-
*
1191638 GCATAAA
192 CCATAAA
* * * * *
1191645 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
* *
1191710 AGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAAGCGGCCAACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAA-CGGTCAACATAATGT
* * *
1191775 ATCGAAACTTTTTAAATTTGTGTCGATACTTGTTGTCCAGAATTAATGCCCAAACGAGGTGTACC
130 ATCGAAACTTTTTGAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTGCACC
1191840 AT-AA
194 ATAAA
* *
1191844 GTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAGTA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
** * *
1191908 GGTAAATTTACAATGTAATTGGTATAAATATACCGATTTTATGAGAGAATA-GGTCAACATAATG
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGA-AA-ACGGTCAACATAATG
* * *
1191972 TATC-AACACTTTTTTTGAATTTGTATCGATACTTTTTTTCA-AAGTGAATGCCC-AACGAGGTG
129 TATCGAA-AC--TTTTTGAATTTGTGTCGATACTTTTGTCCAGAA-TGAATGCCCAAACGAGGTG
1192034 CACACATAAA
190 CAC-CATAAA
* * * ** *
1192044 GTGTCAATACATTTA-AAATTGTATCGATTCCAAAAACATTGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
** * * * *
1192108 GGTAAATTTGTAATGTTACCGGTATAAATAAACCTATTTAGTTTAGAAAA
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTA-ATTAGAAAA
1192158 TATGTAATAT
Statistics
Matches: 434, Mismatches: 60, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
192 8 0.02
193 39 0.09
194 1 0.00
195 1 0.00
196 1 0.00
197 2 0.00
198 141 0.32
199 37 0.09
200 124 0.29
201 79 0.18
202 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAACGGTCAACATAATGTA
TCGAAACTTTTTGAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGAGGTGCACCAT
AAA
Found at i:1193010 original size:13 final size:14
Alignment explanation
Indices: 1192984--1193014 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1192974 ATTAATACGA
1192984 AAAAATTATAAAAT
1 AAAAATTATAAAAT
*
1192998 AAAAATTATAAATT
1 AAAAATTATAAAAT
1193012 AAA
1 AAA
1193015 TCTAATACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAAATTATAAAAT
Found at i:1193229 original size:21 final size:21
Alignment explanation
Indices: 1193185--1193242 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
1193175 CGTTGGTTCA
* **
1193185 AAATATAAGATTATTAGT-GG
1 AAATGTAAGATTACCAGTGGG
*
1193205 AAATGTAATATTACCAGTGGG
1 AAATGTAAGATTACCAGTGGG
1193226 AAATGTAAGATTACCAG
1 AAATGTAAGATTACCAG
1193243 GGAATAAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (21 bp):
AAATGTAAGATTACCAGTGGG
Found at i:1193623 original size:21 final size:20
Alignment explanation
Indices: 1193599--1193823 Score: 131
Period size: 21 Copynumber: 10.9 Consensus size: 20
1193589 GATTTACATA
1193599 TTCGCATTGCGATAGTCCAAG
1 TTCGC-TTGCGATAGTCCAAG
*
1193620 TTCGCGTTGCGATAGTCGAAG
1 TTCGC-TTGCGATAGTCCAAG
* *
1193641 TTCGCGTTGCGA-A-TCTGGAAA
1 TTCGC-TTGCGATAGTC--CAAG
* * * *
1193662 CT-GATTTGCAATAGTCGAAG
1 TTCG-CTTGCGATAGTCCAAG
* * *
1193682 TTCGCGTTGCGATTTATTACAAA
1 TTCGC-TTGCGA--TAGTCCAAG
1193705 TTCG-TTGCGATAGTCCAAG
1 TTCGCTTGCGATAGTCCAAG
*
1193724 TTCG-TTGCGATAGTCGAAG
1 TTCGCTTGCGATAGTCCAAG
* * *
1193743 TTCGCGTGCGATTATTCCAAA
1 TTCGCTTGCGA-TAGTCCAAG
*
1193764 TTCG-TTGCGATAGTCGAAG
1 TTCGCTTGCGATAGTCCAAG
* *
1193783 TTCGCGTTGCGATTTATTCCAAA
1 TTCGC-TTGCGA--TAGTCCAAG
1193806 TTCG-TTGCGATAGTCCAA
1 TTCGCTTGCGATAGTCCAA
1193824 AATCGCAACT
Statistics
Matches: 159, Mismatches: 30, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
19 47 0.30
20 21 0.13
21 70 0.44
22 2 0.01
23 19 0.12
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (20 bp):
TTCGCTTGCGATAGTCCAAG
Found at i:1193762 original size:40 final size:41
Alignment explanation
Indices: 1193707--1193820 Score: 187
Period size: 40 Copynumber: 2.8 Consensus size: 41
1193697 ATTACAAATT
* *
1193707 CGTTGCGA-TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1193747 CG-TGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
1193787 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 CGTTGCGA-TTATTCCAAATTCGTTGCGATAGTC
1193821 CAAAATCGCA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
39 5 0.07
40 34 0.49
41 5 0.07
42 25 0.36
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
CGTTGCGATTATTCCAAATTCGTTGCGATAGTCGAAGTTCG
Found at i:1193771 original size:59 final size:62
Alignment explanation
Indices: 1193667--1193795 Score: 201
Period size: 59 Copynumber: 2.1 Consensus size: 62
1193657 GGAAACTGAT
*
1193667 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTT-CG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCCG
* *
1193728 TTGCGATAGTCGAAGTTCGCG-TGCGA-TTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC-CG
1193789 TTGCGAT
1 TTGCGAT
1193796 TTATTCCAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
59 29 0.46
60 5 0.08
61 29 0.46
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (62 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCCG
Found at i:1193791 original size:101 final size:102
Alignment explanation
Indices: 1193605--1193823 Score: 320
Period size: 101 Copynumber: 2.1 Consensus size: 102
1193595 CATATTCGCA
**
1193605 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTGGAAACTGATTTG
1 TTGCGATAGTCCAAGTTC-CGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTCCAAACTGA-TTG
1193670 CAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
64 CAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
*
1193709 TTGCGATAGTCCAAGTT-CGTTGCGATAGTCGAAGTTCGCG-TGCGATTAT-TCCAAATTCG-TT
1 TTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGA--ATCTCCAAACT-GATT
* *
1193770 GCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
63 GCAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
1193810 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
1193824 AATCGCAACT
Statistics
Matches: 107, Mismatches: 5, Indels: 9
0.88 0.04 0.07
Matches are distributed among these distances:
101 59 0.55
102 28 0.26
103 3 0.03
104 17 0.16
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (102 bp):
TTGCGATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGTTGCGAATCTCCAAACTGATTGCA
ATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCG
Found at i:1193824 original size:19 final size:19
Alignment explanation
Indices: 1193701--1193824 Score: 122
Period size: 19 Copynumber: 6.2 Consensus size: 19
1193691 CGATTTATTA
1193701 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
*
1193720 CAAGTTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
* * * *
1193739 GAAGTTCGCGTGCGATTATTC
1 CAAATTCG-TTGCGA-TAGTC
1193760 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
* * *
1193779 GAAGTTCGCGTTGCGATTTATTC
1 CAAATT--CGTTGCGA--TAGTC
1193802 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
1193821 CAAA
1 CAAA
1193825 ATCGCAACTA
Statistics
Matches: 85, Mismatches: 14, Indels: 12
0.77 0.13 0.11
Matches are distributed among these distances:
19 41 0.48
20 10 0.12
21 26 0.31
23 8 0.09
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (19 bp):
CAAATTCGTTGCGATAGTC
Found at i:1193920 original size:6 final size:6
Alignment explanation
Indices: 1193909--1193935 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1193899 AGACACGTAT
1193909 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
1193936 CGAGACGGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1194537 original size:42 final size:42
Alignment explanation
Indices: 1194478--1194741 Score: 294
Period size: 42 Copynumber: 6.3 Consensus size: 42
1194468 TGCGATTTTT
* *
1194478 GACTACCGCAACGAACTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
1194520 GACTATTGCAACGAACTTGGAA-ACTATCGCAA--CGAACTTG
1 GACTATCGCAACGAACTTGGAATA-AATCGCAACGCGAACTTC
* * *
1194560 GAATAAATCGCAACGTGAACTT-CAACT--ATCGCAA--CGAACTTG
1 GACT--ATCGCAAC--GAACTTGGAA-TAAATCGCAACGCGAACTTC
* * *
1194602 GACTATCGCAACGAATTTGGAATAAATCGCAATGTGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
1194644 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1194686 GACTATCGCAACGAACTTGGAATAAATTC-CAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAA-TCGCAACGCGAACTTC
1194728 GACTATCGCAACGA
1 GACTATCGCAACGA
1194742 TTTGGAAAAT
Statistics
Matches: 191, Mismatches: 18, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
38 6 0.03
39 2 0.01
40 24 0.13
41 1 0.01
42 148 0.77
43 4 0.02
44 6 0.03
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:1194639 original size:61 final size:61
Alignment explanation
Indices: 1194478--1194664 Score: 284
Period size: 61 Copynumber: 3.0 Consensus size: 61
1194468 TGCGATTTTT
* ** *
1194478 GACTACCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATTGCAACGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTG
*
1194539 GAAACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCAACTATCGCAACGAACTTG
1 G--ACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTG
* * *
1194602 GACTATCGCAACGAATTTGGAATAAATCGCAATGTGAACTTCGACTATCACAACGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTG
1194663 GA
1 GA
1194665 ATAAATCGCA
Statistics
Matches: 115, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
61 59 0.51
63 56 0.49
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (61 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAACTTG
Found at i:1194718 original size:21 final size:21
Alignment explanation
Indices: 1194484--1194712 Score: 167
Period size: 21 Copynumber: 11.0 Consensus size: 21
1194474 TTTTGACTAC
1194484 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
1194505 CGCAACGCAAACTTCGACT--AT
1 CGCAACG--AACTTGGAATAAAT
* *
1194526 TGCAACGAACTTGGAA-ACTAT
1 CGCAACGAACTTGGAATA-AAT
1194547 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
*
1194568 CGCAACGTGAACTT-CAACT--AT
1 CGCAAC--GAACTTGGAA-TAAAT
*
1194589 CGCAACGAACTTGGACT--AT
1 CGCAACGAACTTGGAATAAAT
*
1194608 CGCAACGAATTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* * *
1194629 CGCAATGTGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
*
1194650 CACAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
1194671 CGCAACGCGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
1194692 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
1194713 TCCAACGCGA
Statistics
Matches: 163, Mismatches: 25, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
19 50 0.31
20 1 0.01
21 76 0.47
22 3 0.02
23 33 0.20
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
CGCAACGAACTTGGAATAAAT
Found at i:1194719 original size:124 final size:123
Alignment explanation
Indices: 1194478--1194755 Score: 295
Period size: 124 Copynumber: 2.3 Consensus size: 123
1194468 TGCGATTTTT
* * **
1194478 GACTACCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATTGCAACGAACTTGGAAA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCACAACGAACTTGGAAA
* * *
1194543 CTATCGCAACGAACTTGGAATAAATCGCAACGTGAACTTCAACTATCGCAA-CGAACTTG
66 CAATCGCAACGAACTTCGAAT-AATCGCAACG-GAACTTCAACTATCGCAACCGAACTTC
* **
1194602 GACTATCGCAACGAATTTGGAATAAATCGCAATGTGAACTTCGACTATCACAACGAACTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCACAACGAACTTGGAA-
* *
1194667 A-AATCGCAACGCGAACTTCGACT-ATCGCAAC-GAACTTGGAA-TAAATTC-CAACGCGAACTT
65 ACAATCGCAA--CGAACTTCGAATAATCGCAACGGAACTT-CAACT--A-TCGCAAC-CGAACTT
1194727 C
123 C
1194728 GACTATCGCAACG-ATTTGG-A-AAATCGCA
1 GACTATCGCAACGAATTTGGAATAAATCGCA
1194756 TTCGATAGTC
Statistics
Matches: 133, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
122 7 0.05
123 10 0.08
124 77 0.58
125 9 0.07
126 30 0.23
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (123 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTCGACTATCACAACGAACTTGGAAA
CAATCGCAACGAACTTCGAATAATCGCAACGGAACTTCAACTATCGCAACCGAACTTC
Found at i:1194782 original size:21 final size:21
Alignment explanation
Indices: 1194758--1194802 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1194748 AAATCGCATT
1194758 CGATAGTCGAAGTTCGCGTTG
1 CGATAGTCGAAGTTCGCGTTG
*
1194779 CGATAGTCGATGTTCGCGTTG
1 CGATAGTCGAAGTTCGCGTTG
1194800 CGA
1 CGA
1194803 ATCTGGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (21 bp):
CGATAGTCGAAGTTCGCGTTG
Found at i:1196177 original size:23 final size:25
Alignment explanation
Indices: 1196124--1196178 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
1196114 TAAAAGGTCT
*
1196124 AAAATTTTTAAAATAATTATAGAAA
1 AAAAATTTTAAAATAATTATAGAAA
*
1196149 CAAAATTTT-AAAT-ATTATA-AAA
1 AAAAATTTTAAAATAATTATAGAAA
1196171 AAGAAATT
1 AA-AAATT
1196179 AAGGCACGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 11 0.42
24 4 0.15
25 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATTTTAAAATAATTATAGAAA
Found at i:1197369 original size:30 final size:29
Alignment explanation
Indices: 1197333--1197399 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
1197323 AATCTGACCT
1197333 GACCCGAACCTAATTTTTTT-AAAAAAATCC
1 GACCCGAACCT-ATTTTTTTAAAAAAAAT-C
** *
1197363 GACCCGATTCTGTTTTTTTAAAAAAAATC
1 GACCCGAACCTATTTTTTTAAAAAAAATC
1197392 GACCCGAA
1 GACCCGAA
1197400 TACCAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (29 bp):
GACCCGAACCTATTTTTTTAAAAAAAATC
Found at i:1199880 original size:46 final size:46
Alignment explanation
Indices: 1199813--1199906 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1199803 CTTGGACATC
1199813 ATGATCTCCAGGAAGATTTTAATATTTGTGACCAATGATGCAATTG
1 ATGATCTCCAGGAAGATTTTAATATTTGTGACCAATGATGCAATTG
1199859 ATGATCTCCAGGAAGATTTTAATATTTGTGACCAATGATGCAATTG
1 ATGATCTCCAGGAAGATTTTAATATTTGTGACCAATGATGCAATTG
1199905 AT
1 AT
1199907 AGCGTTTGCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (46 bp):
ATGATCTCCAGGAAGATTTTAATATTTGTGACCAATGATGCAATTG
Found at i:1202078 original size:18 final size:17
Alignment explanation
Indices: 1202041--1202076 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1202031 TATTTAACCC
1202041 AATCACTCATCTTCAAA
1 AATCACTCATCTTCAAA
1202058 AATCACTCATCTTCAAA
1 AATCACTCATCTTCAAA
1202075 AA
1 AA
1202077 ATAACAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (17 bp):
AATCACTCATCTTCAAA
Found at i:1212515 original size:60 final size:59
Alignment explanation
Indices: 1212422--1212577 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 59
1212412 GTATATGCGT
* *
1212422 ATAGTTTGGGATGAAATTGGAATGTTCAGAAAGTTTG-GAGACTAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGAAATGTTTA-AAAGTTTGAGA-ACTAATTTAGAATGATA-GTC
*
1212482 ATAGTTTGGGGTTGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
* * *
1212542 ATGGTTTAGGAATGAAATTGAAATATTTAAAAGTTT
1 ATAGTTT-GGGATGAAATTGAAATGTTTAAAAGTTT
1212578 AGGGATCAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
60 64 0.75
61 21 0.25
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
Found at i:1212876 original size:2 final size:2
Alignment explanation
Indices: 1212869--1212923 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1212859 TTGGTAATGC
1212869 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
1212911 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1212924 ATAATATTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1213237 original size:60 final size:60
Alignment explanation
Indices: 1213173--1213296 Score: 176
Period size: 60 Copynumber: 2.1 Consensus size: 60
1213163 GTCTCTAACT
* * * ** *
1213173 TATTAAAAGTTACAAAATGGTCCCTCATTTATAGGATGTGGTTTTGTGGAGTCCCTTGAC
1 TATTAAAAGTTACAAAATGGTCACTCAATTATAAGATGTGACTTTGTGGAGTCCCTCGAC
* *
1213233 TATTAAAAGTTACAAAATGGTCACTCAATTATAAGATGTTACTTTGTTGAGTCCCTCGAC
1 TATTAAAAGTTACAAAATGGTCACTCAATTATAAGATGTGACTTTGTGGAGTCCCTCGAC
1213293 TATT
1 TATT
1213297 TAGTATGTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (60 bp):
TATTAAAAGTTACAAAATGGTCACTCAATTATAAGATGTGACTTTGTGGAGTCCCTCGAC
Found at i:1213536 original size:18 final size:18
Alignment explanation
Indices: 1213513--1213551 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1213503 TCATTTCATA
*
1213513 ACTTTTAACACTCAGGGG
1 ACTTTTAACACTCAGGAG
*
1213531 ACTTTTAATACTCAGGAG
1 ACTTTTAACACTCAGGAG
1213549 ACT
1 ACT
1213552 CAACAAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (18 bp):
ACTTTTAACACTCAGGAG
Found at i:1213660 original size:3 final size:3
Alignment explanation
Indices: 1213646--1213767 Score: 235
Period size: 3 Copynumber: 40.7 Consensus size: 3
1213636 AACTTTACCC
*
1213646 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1213694 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1213742 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
1213768 TCCACAAGGT
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 117 1.00
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1217111 original size:17 final size:17
Alignment explanation
Indices: 1217071--1217109 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1217061 TTAATATTTT
1217071 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
*
1217088 GTATTTAATTTCTTTAA
1 GTATTTAATTTATTTAA
1217105 -TATTT
1 GTATTT
1217110 TACTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:1219404 original size:15 final size:14
Alignment explanation
Indices: 1219349--1219396 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
1219339 TATTTAGTAC
*
1219349 TTTTTATTGT-AGT
1 TTTTTATTGTAATT
* *
1219362 TGTTTATTG-AACT
1 TTTTTATTGTAATT
1219375 TTTTTATTGTAATT
1 TTTTTATTGTAATT
1219389 TTTTTATT
1 TTTTTATT
1219397 TATCATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (14 bp):
TTTTTATTGTAATT
Found at i:1219486 original size:34 final size:34
Alignment explanation
Indices: 1219431--1219501 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1219421 CGTTAATATG
1219431 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
*
1219464 GTTGGACTTT-TTGTTAATTTATTTTGCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGCTTAAATTT
1219499 GTT
1 GTT
1219502 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Found at i:1226417 original size:31 final size:31
Alignment explanation
Indices: 1226376--1226434 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1226366 GAAAATGATC
* *
1226376 CCTAATGTTATCGATCCATTTGATTTTATAA
1 CCTAACGTTATCGATCCATTCGATTTTATAA
* *
1226407 CCTAACGTTATCTATCCGTTCGATTTTA
1 CCTAACGTTATCGATCCATTCGATTTTA
1226435 GTCCCTCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (31 bp):
CCTAACGTTATCGATCCATTCGATTTTATAA
Found at i:1227411 original size:16 final size:16
Alignment explanation
Indices: 1227402--1227439 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
1227392 ACCTGATATG
1227402 ATATTTACCTGACTTA
1 ATATTTACCTGACTTA
1227418 ATATTTACCTGACTTA
1 ATATTTACCTGACTTA
1227434 TATATT
1 -ATATT
1227440 ACCATGAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (16 bp):
ATATTTACCTGACTTA
Found at i:1227609 original size:9 final size:9
Alignment explanation
Indices: 1227591--1227620 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1227581 ATAAAATTAT
1227591 TTAATAAAA
1 TTAATAAAA
*
1227600 TTACTAAAA
1 TTAATAAAA
1227609 TTAATAAAA
1 TTAATAAAA
1227618 TTA
1 TTA
1227621 TTTAAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (9 bp):
TTAATAAAA
Found at i:1228260 original size:10 final size:10
Alignment explanation
Indices: 1228245--1228272 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1228235 CGGCAATAGA
1228245 CAGCAGGCTG
1 CAGCAGGCTG
1228255 CAGCAGGCTG
1 CAGCAGGCTG
1228265 CAGCAGGC
1 CAGCAGGC
1228273 AACAACAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.39, T:0.07
Consensus pattern (10 bp):
CAGCAGGCTG
Found at i:1230215 original size:13 final size:13
Alignment explanation
Indices: 1230197--1230222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1230187 TCACATGTAA
1230197 AACAAACACGACT
1 AACAAACACGACT
1230210 AACAAACACGACT
1 AACAAACACGACT
1230223 TGAGACAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (13 bp):
AACAAACACGACT
Found at i:1231182 original size:18 final size:18
Alignment explanation
Indices: 1231156--1231196 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1231146 TTAGGGTCGA
* *
1231156 GTTCAAATTTGGGTTCGT
1 GTTCGAATTTGGGTTCGG
1231174 GTTCGAATTTGGGTTCGG
1 GTTCGAATTTGGGTTCGG
1231192 GTTCG
1 GTTCG
1231197 GGTTCGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.12, G:0.34, T:0.41
Consensus pattern (18 bp):
GTTCGAATTTGGGTTCGG
Found at i:1231199 original size:12 final size:11
Alignment explanation
Indices: 1231184--1231217 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
1231174 GTTCGAATTT
1231184 GGGTTCGGGTTC
1 GGGTTC-GGTTC
1231196 GGGTTCGGTTC
1 GGGTTCGGTTC
1231207 GGGTTCTGGTT
1 GGGTTC-GGTT
1231218 TAGGTTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.47, T:0.38
Consensus pattern (11 bp):
GGGTTCGGTTC
Found at i:1231207 original size:5 final size:6
Alignment explanation
Indices: 1231184--1231217 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1231174 GTTCGAATTT
*
1231184 GGGTTC GGGTTC GGGTTC -GGTTC GGGTTC TGGTT
1 GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTT
1231218 TAGGTTAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.15, G:0.47, T:0.38
Consensus pattern (6 bp):
GGGTTC
Found at i:1231207 original size:17 final size:17
Alignment explanation
Indices: 1231185--1231217 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1231175 TTCGAATTTG
1231185 GGTTCGGGTTCGGGTTC
1 GGTTCGGGTTCGGGTTC
*
1231202 GGTTCGGGTTCTGGTT
1 GGTTCGGGTTCGGGTT
1231218 TAGGTTAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.15, G:0.45, T:0.39
Consensus pattern (17 bp):
GGTTCGGGTTCGGGTTC
Found at i:1231223 original size:6 final size:6
Alignment explanation
Indices: 1231214--1231309 Score: 63
Period size: 6 Copynumber: 15.7 Consensus size: 6
1231204 TTCGGGTTCT
* * * * *
1231214 GGTTTA GGTTAA GGTTAA GGTTAA GG-TCA TGGTTTG GGTTTA GGTTT-
1 GGTTTA GGTTTA GGTTTA GGTTTA GGTTTA -GGTTTA GGTTTA GGTTTA
* *
1231261 GAG-TTC GAGTTTAA GGTTTA GGTTTA GGTTTAA GGTTTA GGTTTG GGTT
1 G-GTTTA G-GTTT-A GGTTTA GGTTTA GGTTT-A GGTTTA GGTTTA GGTT
1231310 ATAGAAGATG
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
5 5 0.07
6 57 0.75
7 13 0.17
8 1 0.01
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (6 bp):
GGTTTA
Found at i:1231291 original size:19 final size:19
Alignment explanation
Indices: 1231269--1231309 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1231259 TTGAGTTCGA
1231269 GTTTAAGGTTTAGGTTTAG
1 GTTTAAGGTTTAGGTTTAG
*
1231288 GTTTAAGGTTTAGGTTTGG
1 GTTTAAGGTTTAGGTTTAG
1231307 GTT
1 GTT
1231310 ATAGAAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.34, T:0.49
Consensus pattern (19 bp):
GTTTAAGGTTTAGGTTTAG
Found at i:1232068 original size:28 final size:27
Alignment explanation
Indices: 1232025--1232093 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
1232015 TAATTTATAT
*
1232025 TAATTAACTATTTATAATTAATATTAAAA
1 TAATTAA-TA-TTATAATTAATATGAAAA
*
1232054 TAATTATATATTATAATTAATATGAATA
1 TAATTA-ATATTATAATTAATATGAAAA
1232082 TAATTAATATTA
1 TAATTAATATTA
1232094 ATATTAGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 6 0.16
28 22 0.59
29 8 0.22
30 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (27 bp):
TAATTAATATTATAATTAATATGAAAA
Found at i:1232112 original size:22 final size:20
Alignment explanation
Indices: 1232084--1232126 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
1232074 TATGAATATA
1232084 ATTAATATTAATATTAGCTTAT
1 ATTAATA-TAATA-TAGCTTAT
*
1232106 ATTAATATAATATAGTTTAT
1 ATTAATATAATATAGCTTAT
1232126 A
1 A
1232127 ATTTGTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTAATATAATATAGCTTAT
Found at i:1232172 original size:31 final size:30
Alignment explanation
Indices: 1232133--1232245 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 30
1232123 TATAATTTGT
1232133 AATTAATATTAATATAAAATATA-GTCTATA
1 AATTAATATTAATATAAAATATATGT-TATA
*
1232163 ACATTAATATTAATATAAACTATATGTTATA
1 A-ATTAATATTAATATAAAATATATGTTATA
* *
1232194 AATTATATAGTATAGTTTATAAACTATA-GTTAATA
1 AATTA-ATA-T-TA--ATATAAAATATATGTT-ATA
1232229 TAATTAATATTAATATA
1 -AATTAATATTAATATA
1232246 GTATAGTTTA
Statistics
Matches: 71, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
30 5 0.07
31 33 0.46
32 3 0.04
33 4 0.06
34 4 0.06
35 17 0.24
36 5 0.07
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAAATATATGTTATA
Found at i:1232185 original size:24 final size:25
Alignment explanation
Indices: 1232140--1232186 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1232130 TGTAATTAAT
**
1232140 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
1232165 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
1232187 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:1232213 original size:14 final size:14
Alignment explanation
Indices: 1232196--1232257 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
1232186 ATGTTATAAA
1232196 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
1232210 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
1232224 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
1232239 TAATATAGTATAGT
1 TTATATAGTATAGT
1232253 TTATA
1 TTATA
1232258 AACGATGTAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:1232291 original size:65 final size:64
Alignment explanation
Indices: 1232104--1232311 Score: 185
Period size: 65 Copynumber: 3.2 Consensus size: 64
1232094 ATATTAGCTT
* *
1232104 ATATTAATATAATATAGTTTAT-AATTTGTAATTAATATTAATATAAAATATAGTCT-ATA-ACA
1 ATATTAATATAATATAGTTTATAAATATGT-ACT-ATATTAATATAAAATATAGT-TAATATA-A
1232166 TTA
62 TTA
* * *
1232169 ATATTAATATAAACTATA-TGTTATAAATTATATAGTATAGTT--TATAAACTATAGTTAATATA
1 ATATTAATAT-AA-TATAGT-TTATAAA-TATGTACTATA-TTAATATAAAATATAGTTAATATA
1232231 ATTA
61 ATTA
* * * *
1232235 ATATTAATATAGTATAGTTTATAAACGATGTACTATATTAATATAAATTATAGTTAAGATAATTA
1 ATATTAATATAATATAGTTTATAAA-TATGTACTATATTAATATAAAATATAGTTAATATAATTA
* *
1232300 ACATTAGTATAA
1 ATATTAATATAA
1232312 ACTATATAGT
Statistics
Matches: 118, Mismatches: 14, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
63 2 0.02
64 19 0.16
65 44 0.37
66 32 0.27
67 12 0.10
68 6 0.05
69 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (64 bp):
ATATTAATATAATATAGTTTATAAATATGTACTATATTAATATAAAATATAGTTAATATAATTA
Found at i:1232361 original size:21 final size:21
Alignment explanation
Indices: 1232329--1232381 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1232319 AGTACATTAA
* * *
1232329 TATAAACAATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
1232350 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
1232371 TATAAACTATA
1 TATAAACTATA
1232382 TAGTACACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:1232518 original size:20 final size:21
Alignment explanation
Indices: 1232421--1232531 Score: 104
Period size: 20 Copynumber: 5.2 Consensus size: 21
1232411 AACTATAAGT
1232421 TACATAT--ATAGTTTATATA
1 TACATATACATAGTTTATATA
* *
1232440 -ACATATAAATAAATTGTATATA
1 TACATATACAT-AGTT-TATATA
1232462 TACATATACTATAGGTTATATATA
1 TACATATAC-ATA-GTT-TATATA
* *
1232486 TATATATATATAGTTTATATA
1 TACATATACATAGTTTATATA
*
1232507 TAC-TATACATAGTTTATACA
1 TACATATACATAGTTTATATA
1232527 TACAT
1 TACAT
1232532 GCACTATAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
18 6 0.08
20 20 0.27
21 12 0.16
22 9 0.12
23 11 0.15
24 17 0.23
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (21 bp):
TACATATACATAGTTTATATA
Found at i:1232552 original size:67 final size:67
Alignment explanation
Indices: 1232424--1232552 Score: 165
Period size: 65 Copynumber: 2.0 Consensus size: 67
1232414 TATAAGTTAC
* * *
1232424 ATATATAGTTTATATAACATATAAATAAATTGTATATATACATATACTATAGGTTATATATATAT
1 ATATATAGTTTATATAACATATAAATAAATTGTATACATACATACACTATAAGTTATATATATAT
1232489 AT
66 AT
* * * *
1232491 ATATATAGTTTATATATAC-TATACAT-AGTT-TATACATACATGCACTATAAGTTACATATATA
1 ATATATAGTTTATATA-ACATATAAATAAATTGTATACATACATACACTATAAGTTATATATATA
1232553 GTTTACATGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 27 0.50
66 3 0.06
67 22 0.41
68 2 0.04
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (67 bp):
ATATATAGTTTATATAACATATAAATAAATTGTATACATACATACACTATAAGTTATATATATAT
AT
Found at i:1232642 original size:21 final size:22
Alignment explanation
Indices: 1232599--1232649 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1232589 ATTAACTATT
1232599 GTTTATG--TATAGTGTTTAGG
1 GTTTATGATTATAGTGTTTAGG
*
1232619 GTTTATGATTATAG-GTTTATG
1 GTTTATGATTATAGTGTTTAGG
*
1232640 GTTTAAGATT
1 GTTTATGATT
1232650 TTTATAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 15 0.56
22 5 0.19
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (22 bp):
GTTTATGATTATAGTGTTTAGG
Found at i:1233109 original size:15 final size:15
Alignment explanation
Indices: 1233091--1233120 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1233081 CTATATATTT
1233091 TATATAGTTTATACA
1 TATATAGTTTATACA
1233106 TATATAGTTTATACA
1 TATATAGTTTATACA
1233121 CACACATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:1233131 original size:2 final size:2
Alignment explanation
Indices: 1233126--1233165 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1233116 ATACACACAC
*
1233126 AT AT AT AT AT AC 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
1233166 TAATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1233171 original size:10 final size:11
Alignment explanation
Indices: 1233124--1233177 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
1233114 TTATACACAC
1233124 ACATATATATAT
1 ACATATATAT-T
1233136 ACATATATA-T
1 ACATATATATT
*
1233146 ATATATATA-T
1 ACATATATATT
*
1233156 ATATATATATT
1 ACATATATATT
*
1233167 A-ATATAAATT
1 ACATATATATT
1233177 A
1 A
1233178 TATTTTATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
10 28 0.72
11 2 0.05
12 9 0.23
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
ACATATATATT
Found at i:1233280 original size:18 final size:19
Alignment explanation
Indices: 1233253--1233305 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
1233243 AATTTATATT
* *
1233253 TATAGCTTATAATAAT-TA
1 TATAGTTTATAATAATAAA
1233271 TATAGTTTATAAT-ATAAA
1 TATAGTTTATAATAATAAA
1233289 TATAGTTTATATATAAT
1 TATAGTTTATA-ATAAT
1233306 CTTATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.80
19 2 0.07
20 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (19 bp):
TATAGTTTATAATAATAAA
Found at i:1235289 original size:36 final size:38
Alignment explanation
Indices: 1235245--1235495 Score: 230
Period size: 39 Copynumber: 6.6 Consensus size: 38
1235235 CGGTTTTGAA
*****
1235245 ATATATAATATATAGTTTTGATTTTTTTTTG-AAA-AT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAACAT
*
1235281 ATATATAATATATAATTTTGAAAACATTTTGAAAACAT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAACAT
* *
1235319 ATATATAATATATAGTTTTTGAAAACATTTTGAATATAT
1 ATATATAATATATAG-TTTTGAAAACATTTTGAAAACAT
* *
1235358 ATATATAATATATAATTTTTGAAAACATTTTGAAAAAATT
1 ATATATAATATAT-AGTTTTGAAAACATTTTGAAAACA-T
** *
1235398 ATATATAATATATAGTTTT-AAAATGTTTTTG-GAA-A-
1 ATATATAATATATAGTTTTGAAAA-CATTTTGAAAACAT
* *
1235433 ATATATAATGTATA-TTTTAGAAAACATGTTGGAAAAC-T
1 ATATATAATATATAGTTTT-GAAAACAT-TTTGAAAACAT
* *
1235471 ATATATAATATTTGGGTTTTGAAAA
1 ATATATAATATAT-AGTTTTGAAAA
1235496 TGTTAGTTTT
Statistics
Matches: 177, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
34 4 0.02
35 14 0.08
36 32 0.18
37 6 0.03
38 33 0.19
39 69 0.39
40 19 0.11
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAACAT
Found at i:1243463 original size:37 final size:37
Alignment explanation
Indices: 1243420--1243766 Score: 386
Period size: 37 Copynumber: 9.7 Consensus size: 37
1243410 TCAGTTTTGG
*
1243420 ATATATATAATATATAGTTTTGAAAGCATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
1243457 ACATATATAATATATAGTTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1243494 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* **
1243531 ACATATATAATATATAGTTTTG--AATTTTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* *
1243566 ATATATATAATATATAATGTTGAAAAC----------
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
1243593 ATATATATAATATATAGTTTTTGAAAATA-TTTTGAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTTGAAA
1243630 ATATATATAATATATAGTTTTTGAAAACA-TTTTGAAA
1 ATATATATAATATATAG-TTTTGAAAACATTTTTGAAA
* * *
1243667 ATATATATAATATGTAGTTTT-AAAATATTTTTGGAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
1243703 A-ATATATAATATGTA-TTTTAGAAAACATGTTGGAAA
1 ATATATATAATATATAGTTTT-GAAAACATTTTTGAAA
* *
1243739 ATTATATATAATATTTGGGTTTTGAAAA
1 A-TATATATAATATAT-AGTTTTGAAAA
1243767 TGTTAGTTTT
Statistics
Matches: 268, Mismatches: 23, Indels: 36
0.82 0.07 0.11
Matches are distributed among these distances:
27 16 0.06
28 8 0.03
34 4 0.01
35 49 0.18
36 24 0.09
37 146 0.54
38 12 0.04
39 5 0.02
40 4 0.01
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:1243611 original size:99 final size:101
Alignment explanation
Indices: 1243494--1243679 Score: 297
Period size: 99 Copynumber: 1.9 Consensus size: 101
1243484 ATTTTTGAAA
*
1243494 ATATATATAATATATAG-TTTTGAAAACATTTTTGAAAACATATATAATATATAG-TTTTG-AAT
1 ATATATATAATATATAGTTTTTGAAAACA-TTTTGAAAACATATATAATATATAGTTTTTGAAAA
**
1243556 TTTTTTGAAAATATATATAATATATAATGTTGAAAAC
65 CATTTTGAAAATATATATAATATATAATGTTGAAAAC
* *
1243593 ATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTTGAAAAC
1243658 ATTTTGAAAATATATATAATAT
66 ATTTTGAAAATATATATAATAT
1243680 GTAGTTTTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
99 41 0.52
100 15 0.19
101 23 0.29
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (101 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAGTTTTTGAAAAC
ATTTTGAAAATATATATAATATATAATGTTGAAAAC
Found at i:1243625 original size:11 final size:11
Alignment explanation
Indices: 1243611--1243670 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
1243601 AATATATAGT
1243611 TTTTGAAAATA
1 TTTTGAAAATA
1243622 TTTTGAAAATA
1 TTTTGAAAATA
*
1243633 TATAT-AATATATA
1 T-TTTGAA-A-ATA
*
1243646 GTTTTTGAAAACA
1 --TTTTGAAAATA
1243659 TTTTGAAAATA
1 TTTTGAAAATA
1243670 T
1 T
1243671 ATATAATATG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 25 0.64
12 3 0.08
13 5 0.13
14 3 0.08
15 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:1243631 original size:64 final size:63
Alignment explanation
Indices: 1243525--1243659 Score: 195
Period size: 64 Copynumber: 2.2 Consensus size: 63
1243515 GAAAACATTT
* *
1243525 TTGAAAAC--ATATATAATATATAGTTTTGAATTTTTTTGAAAATATATATAATATATA-ATG
1 TTGAAAACATATATATAATATATAGTTTTGAAATATTTTGAAAATATATATAATATATAGATG
* *
1243585 TTGAAAACATATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTT
1 TTGAAAACATATATATAATATATAG-TTTTG-AAATATTTTGAAAATATATATAATATATAGATG
1243650 TTGAAAACAT
1 TTGAAAACAT
1243660 TTTGAAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
60 8 0.12
62 15 0.23
63 5 0.08
64 27 0.41
65 11 0.17
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (63 bp):
TTGAAAACATATATATAATATATAGTTTTGAAATATTTTGAAAATATATATAATATATAGATG
Found at i:1243727 original size:136 final size:136
Alignment explanation
Indices: 1243449--1243730 Score: 414
Period size: 136 Copynumber: 2.1 Consensus size: 136
1243439 TTGAAAGCAT
1243449 TTTTGAAAAC--ATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGT
1 TTTTGAAAACATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGT
* *
1243512 TTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTGAATTTTTTTGAAAATATATATAAT
66 TTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTAAATATTTTTGAAAATATATATAAT
1243577 ATATAA
131 ATATAA
* *
1243583 TGTTGAAAACATATATATAATATATAGTTTTTGAAAATA-TTTTGAAAATATATATAATATATAG
1 TTTTGAAAACATATATATAATATATAG-TTTTGAAAACATTTTTGAAAATATATATAATATATAG
* * *
1243647 TTTTTGAAAACA-TTTTGAAAATATATATAATATGTAGTTTTAAAATATTTTTGGAAA-ATATAT
65 -TTTTGAAAACATTTTTGAAAACATATATAATATATAGTTTT-AAATATTTTTGAAAATATATAT
*
1243710 AATATGT-A
128 AATATATAA
1243718 TTTTAGAAAACAT
1 TTTT-GAAAACAT
1243731 GTTGGAAAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
134 9 0.07
135 4 0.03
136 87 0.65
137 33 0.25
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (136 bp):
TTTTGAAAACATATATATAATATATAGTTTTGAAAACATTTTTGAAAATATATATAATATATAGT
TTTGAAAACATTTTTGAAAACATATATAATATATAGTTTTAAATATTTTTGAAAATATATATAAT
ATATAA
Found at i:1243821 original size:20 final size:21
Alignment explanation
Indices: 1243796--1243834 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1243786 TATCGTATAT
1243796 TTATTTTT-TATTATTTTTCC
1 TTATTTTTATATTATTTTTCC
*
1243816 TTATTTTTATTTTATTTTT
1 TTATTTTTATATTATTTTT
1243835 TGTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (21 bp):
TTATTTTTATATTATTTTTCC
Found at i:1243840 original size:12 final size:12
Alignment explanation
Indices: 1243819--1243848 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1243809 TTTTTCCTTA
1243819 TTTTTATTTTAT
1 TTTTTATTTTAT
*
1243831 TTTTTGTTTTAT
1 TTTTTATTTTAT
1243843 TTTTTA
1 TTTTTA
1243849 GGATCTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTATTTTAT
Found at i:1244549 original size:15 final size:15
Alignment explanation
Indices: 1244529--1244560 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1244519 TTCGGCCACC
1244529 AGTGGCGGTGGCCAG
1 AGTGGCGGTGGCCAG
1244544 AGTGGCGGTGGCCAG
1 AGTGGCGGTGGCCAG
1244559 AG
1 AG
1244561 CAGCGGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.53, T:0.12
Consensus pattern (15 bp):
AGTGGCGGTGGCCAG
Found at i:1244566 original size:15 final size:15
Alignment explanation
Indices: 1244533--1244567 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1244523 GCCACCAGTG
**
1244533 GCGGTGGCCAGAGTG
1 GCGGTGGCCAGAGCA
1244548 GCGGTGGCCAGAGCA
1 GCGGTGGCCAGAGCA
1244563 GCGGT
1 GCGGT
1244568 TGGCGGCAGC
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:0.14, C:0.23, G:0.51, T:0.11
Consensus pattern (15 bp):
GCGGTGGCCAGAGCA
Found at i:1245170 original size:23 final size:22
Alignment explanation
Indices: 1245123--1245183 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 22
1245113 TTTTTCTCTA
*
1245123 TTATTTTATCTTTTAACTTGATT
1 TTATTTTATTTTTTAACTT-ATT
1245146 TTATTTTATTTTTTAAACCTT-TT
1 TTATTTTATTTTTT-AA-CTTATT
*
1245169 TTATATATATTTTTT
1 TTAT-TTTATTTTTT
1245184 CTCTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
23 19 0.58
24 11 0.33
25 3 0.09
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTTTATTTTTTAACTTATT
Found at i:1248684 original size:21 final size:21
Alignment explanation
Indices: 1248638--1248684 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1248628 AATATGTAAA
*
1248638 TCGCATTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
1248659 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATTTTCCAAAT
1248680 TCGCG
1 TCGCG
1248685 CGATATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAT
Found at i:1248697 original size:17 final size:17
Alignment explanation
Indices: 1248675--1248740 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 17
1248665 TGCGATTTTC
*
1248675 CAAATTCGCGCGATATT
1 CAAATTCGCGCGATAGT
1248692 CAAATTCGCAACGCGATAGT
1 CAAATTCG---CGCGATAGT
*
1248712 CAAATTCGCAACGCGAAAGT
1 CAAATTCG---CGCGATAGT
1248732 CAAATTCGC
1 CAAATTCGC
1248741 AACTGAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.20
20 35 0.80
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (17 bp):
CAAATTCGCGCGATAGT
Found at i:1248755 original size:19 final size:20
Alignment explanation
Indices: 1248690--1248800 Score: 113
Period size: 19 Copynumber: 5.7 Consensus size: 20
1248680 TCGCGCGATA
1248690 TTCAAATTCGCAACGCG-AT
1 TTCAAATTCGCAACGCGAAT
* *
1248709 AGTCAAATTCGCAACGCGAAA
1 -TTCAAATTCGCAACGCGAAT
* *
1248730 GTCAAATTCGCAAC-TGAAT
1 TTCAAATTCGCAACGCGAAT
* **
1248749 TTCAAATTCGTAA-ATGAAT
1 TTCAAATTCGCAACGCGAAT
1248768 TTCAAATTCGCAACGCGAAT
1 TTCAAATTCGCAACGCGAAT
*
1248788 TT-AATTTCGCAAC
1 TTCAAATTCGCAAC
1248801 AGGTTTTAGT
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
19 41 0.53
20 36 0.46
21 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCAAATTCGCAACGCGAAT
Found at i:1252007 original size:6 final size:6
Alignment explanation
Indices: 1251996--1252030 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1251986 AAGCAAAAGG
* *
1251996 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
1252031 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:1252020 original size:18 final size:18
Alignment explanation
Indices: 1251997--1252037 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1251987 AGCAAAAGGA
*
1251997 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
1252015 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
1252033 AATCA
1 AATCA
1252038 CAACCGGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:1252521 original size:25 final size:25
Alignment explanation
Indices: 1252483--1252532 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1252473 AAATCAATTA
*
1252483 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1252508 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1252533 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1252940 original size:18 final size:18
Alignment explanation
Indices: 1252919--1252955 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1252909 GTAATTGGAG
1252919 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1252937 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1252955 T
1 T
1252956 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1252962 original size:24 final size:24
Alignment explanation
Indices: 1252911--1252963 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1252901 TTTCATATGT
* * *
1252911 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1252935 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1252959 AATTT
1 AATTT
1252964 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1253268 original size:39 final size:39
Alignment explanation
Indices: 1253225--1253311 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1253215 TCCGATGCTC
1253225 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
1253264 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1253303 ATCAAAATC
1 ATCAAAATC
1253312 TATAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:1253568 original size:20 final size:20
Alignment explanation
Indices: 1253529--1253569 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1253519 GTGTTGCGAT
* **
1253529 AGTCAAATTCTCAATGCGAA
1 AGTCAAATTCGCAAACCGAA
1253549 AGTCAAATTCGCAAACCGAA
1 AGTCAAATTCGCAAACCGAA
1253569 A
1 A
1253570 ATCGCGTTGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAAACCGAA
Found at i:1253796 original size:61 final size:63
Alignment explanation
Indices: 1253665--1253805 Score: 171
Period size: 61 Copynumber: 2.2 Consensus size: 63
1253655 TTTTAGAAAC
*
1253665 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
1253730 A
63 A
* * ** *
1253731 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
1253792 AACAAATCAACTTT
1 AACAAATCAACTTT
1253806 CAATGTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.51
62 3 0.04
66 26 0.38
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:1257514 original size:13 final size:13
Alignment explanation
Indices: 1257496--1257527 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1257486 GGGTTTCTTC
1257496 AACAAAAAGACAA
1 AACAAAAAGACAA
*
1257509 AACAAAAAGATAA
1 AACAAAAAGACAA
1257522 AACAAA
1 AACAAA
1257528 GACAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:1257784 original size:42 final size:43
Alignment explanation
Indices: 1257736--1257827 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 43
1257726 ATAGAGAGTG
1257736 AGAGATGGAGATGAGACTGAGTTGTGCTTTAGGG-TTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGTGCTTTAGGGTTTTAGGTT
1257778 AGAGATGGAGATGAGACTGAGTTGTGCTTTAGGGTTTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGTGCTTTAGGGTTTTAGGTT
1257821 AGAGATG
1 AGAGATG
1257828 ATTTGCGATA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.25, C:0.04, G:0.38, T:0.33
Consensus pattern (43 bp):
AGAGATGGAGATGAGACTGAGTTGTGCTTTAGGGTTTTAGGTT
Found at i:1257986 original size:20 final size:20
Alignment explanation
Indices: 1257937--1257995 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
1257927 CGATTTACAT
*
1257937 ATTCGCGTTGCGAAATTAGAA
1 ATTCGCGTTGCGAAATT-GTA
* *
1257958 ACT-GGGTTGCGAAATTGTA
1 ATTCGCGTTGCGAAATTGTA
*
1257977 ATTCGCGTTGCGAATTTGT
1 ATTCGCGTTGCGAAATTGT
1257996 TGGTCATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGTA
Found at i:1261559 original size:3 final size:3
Alignment explanation
Indices: 1261551--1261644 Score: 106
Period size: 3 Copynumber: 32.0 Consensus size: 3
1261541 CCATTTGTTT
* * *
1261551 TTA TTA TTA -TA TTA TTA TTG TTA TTA TTA TT- TTA TTTA TCA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
1261595 TTA TTA TT- TTA TTA TTA -TA TTA TTA TTA TTA TTA TTAA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
1261639 TTA TTA
1 TTA TTA
1261645 CAAACAGACC
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
2 8 0.10
3 63 0.82
4 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1263553 original size:142 final size:143
Alignment explanation
Indices: 1263289--1263554 Score: 344
Period size: 144 Copynumber: 1.9 Consensus size: 143
1263279 TTTTAATATT
* * *
1263289 TATTTATTTTTTAATATTAAGAAATGGTCTGTCTTAAACACCTAGAAGCCTTTTTCTGATATTCT
1 TATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAACACCTAGAAACCATTTTCTGATATTCT
* * * * * * *
1263354 TAAATAAATAAATATCCTATTTTTATAAATTATATATATTAATTTATTTTAATTATTTTTATAGA
66 TAAATAAATAAATATCCTATTTATAAAAATGATATAAAATAATATATATTAATTATTTTTATAGA
1263419 AATGTTTTATTAA
131 AATGTTTTATTAA
*
1263432 TATTT-TTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAAATCATTTTCTGATATT
1 TATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAA-CACCTAG-AAACCATTTTCTGATATT
* *
1263496 -TCTAAGTAAATAAATATCTTATTTATAAAAATGA-A-AAAAT-ATATATATTAATATATTTT
64 CT-TAAATAAATAAATATCCTATTTATAAAAATGATATAAAATAATATATATTAAT-TATTTT
1263555 CTTAAAATTA
Statistics
Matches: 106, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
141 10 0.09
142 40 0.38
143 14 0.13
144 42 0.40
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.47
Consensus pattern (143 bp):
TATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAACACCTAGAAACCATTTTCTGATATTCT
TAAATAAATAAATATCCTATTTATAAAAATGATATAAAATAATATATATTAATTATTTTTATAGA
AATGTTTTATTAA
Found at i:1264053 original size:29 final size:28
Alignment explanation
Indices: 1264021--1264107 Score: 66
Period size: 28 Copynumber: 3.0 Consensus size: 28
1264011 ATATTAAATT
*
1264021 TATAATTCTTTCTTTTCAAAATTTTTATA
1 TATAATT-TTTATTTTCAAAATTTTTATA
* * * *
1264050 TATACTTATTATTTTCATAATATTTATA
1 TATAATTTTTATTTTCAAAATTTTTATA
* * *
1264078 TGTATATTATTTTTTTATCAATATTTTTAT
1 TATA-ATT-TTTATTT-TCAAAATTTTTAT
1264108 TTTATTAAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
28 20 0.47
29 8 0.19
30 5 0.12
31 10 0.23
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (28 bp):
TATAATTTTTATTTTCAAAATTTTTATA
Found at i:1264085 original size:26 final size:27
Alignment explanation
Indices: 1264033--1264090 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1264023 TAATTCTTTC
*
1264033 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
1264061 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
1264087 TTTT
1 TTTT
1264091 TTTATCAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:1264114 original size:28 final size:30
Alignment explanation
Indices: 1264036--1264107 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
1264026 TTCTTTCTTT
*
1264036 TCAAAATTTTTATATATACTTATTATTTTCA
1 TCAATATTTTTATATATA-TTATTATTTTCA
* * *
1264067 T-AATATTTATATGTATATTATT-TTTTTA
1 TCAATATTTTTATATATATTATTATTTTCA
1264095 TCAATATTTTTAT
1 TCAATATTTTTAT
1264108 TTTATTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.17
29 15 0.43
30 13 0.37
31 1 0.03
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (30 bp):
TCAATATTTTTATATATATTATTATTTTCA
Found at i:1273419 original size:21 final size:20
Alignment explanation
Indices: 1273393--1273443 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
1273383 TACATCTACA
1273393 CTCTTCAAAGATGATAAATT
1 CTCTTCAAAGATGATAAATT
*
1273413 CCTCTTCAAAGATGATAGATT
1 -CTCTTCAAAGATGATAAATT
1273434 CTCTTTCAAA
1 CTC-TTCAAA
1273444 TATAAAGGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (20 bp):
CTCTTCAAAGATGATAAATT
Found at i:1274000 original size:113 final size:111
Alignment explanation
Indices: 1273803--1274255 Score: 536
Period size: 113 Copynumber: 4.0 Consensus size: 111
1273793 TAGCAAAGAT
** * * *
1273803 TCGAATCCATCACTTAATGGATCAATA-TGCCAAGTACAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATCCATCACTCGATGGATCAACATTTCCAGGTA-AGTTCATAATGAGAAGAACTCATCTGA
*
1273867 AGAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTTTGC
65 A-AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
1273915 TCGAATCCATCACTCGATGGATCAACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATCCATCACTCGATGGATCAACATTTCCAGGTA-AGTTCATAATGAGAAGAACTCATCTG-
* * *
1273980 AAAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTAAACCTTTTGC
64 AAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
1274028 TTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-
1 TCGAATCCATCACTCGATGGATCAACATTTCCAG-GTAAGTTCATAATGAGAAGAACTCATCTGA
*
1274092 -AA-GAGGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 AAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** *
1274137 TTGACTCTATCACAAAAGGAGATGGATCAGCACCAACATTTCCAGATAACGTTCATAATGAGAAG
1 TCGAATCCATCAC-----TCGATGGAT------CAACATTTCCAGGTAA-GTTCATAATGAGAAG
*
1274202 AACTTATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
54 AACTCATCTGAAAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
1274256 AATTTGATTC
Statistics
Matches: 295, Mismatches: 28, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
109 49 0.17
110 2 0.01
112 24 0.08
113 132 0.45
114 11 0.04
119 2 0.01
120 35 0.12
122 2 0.01
123 38 0.13
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (111 bp):
TCGAATCCATCACTCGATGGATCAACATTTCCAGGTAAGTTCATAATGAGAAGAACTCATCTGAA
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:1274119 original size:17 final size:17
Alignment explanation
Indices: 1274065--1274119 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
1274055 TTTCCAGAGA
1274065 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
*
1274082 AA-CTCATCTGAA-GAGGAAG
1 AAGTTCA--T-AATGA-GAAG
1274101 AAGTTCATAATGAGAAG
1 AAGTTCATAATGAGAAG
1274118 AA
1 AA
1274120 CTTGTTCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
16 3 0.10
17 10 0.33
18 6 0.20
19 8 0.27
20 3 0.10
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (17 bp):
AAGTTCATAATGAGAAG
Found at i:1274249 original size:20 final size:20
Alignment explanation
Indices: 1274187--1274250 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
1274177 TCCAGATAAC
1274187 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * * *
1274207 ATCTGAAAAGGAAGAAGAA---
1 GT-TCATAATG-AGAAGAACTT
1274226 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1274246 GTTCA
1 GTTCA
1274251 ACCTTAATTT
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
19 1 0.03
20 6 0.19
21 5 0.16
22 7 0.23
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1274622 original size:3 final size:3
Alignment explanation
Indices: 1274614--1274682 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
1274604 CCATTTGTTT
* *
1274614 TTA TTA TTA -TA TTA TTA TT- TTA TTTA TCA ATA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
1274657 TTA TTA TTAA TTAA TTA ATA TTA TTA
1 TTA TTA TT-A TT-A TTA TTA TTA TTA
1274683 CAAATAGGCC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
2 6 0.11
3 39 0.71
4 10 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1274653 original size:26 final size:27
Alignment explanation
Indices: 1274618--1274682 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
1274608 TTGTTTTTAT
*
1274618 TATTATATTATTATT-TTATTTATCAA
1 TATTATATTATTATTATTATTAATCAA
*
1274644 TATTATATTATTATTATTATTAATTAA
1 TATTATATTATTATTATTATTAATCAA
*
1274671 T-TAATATTATTA
1 TATTATATTATTA
1274683 CAAATAGGCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
26 25 0.71
27 10 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TATTATATTATTATTATTATTAATCAA
Found at i:1276167 original size:21 final size:18
Alignment explanation
Indices: 1276135--1276193 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
1276125 TTTTATTACT
1276135 TTTTTA-AT-TTTATTTA
1 TTTTTATATGTTTATTTA
1276151 TTTTTAGTCATTGTTTATTTA
1 TTTTTA-T-A-TGTTTATTTA
*
1276172 TATTTTATATGTTTATATA
1 T-TTTTATATGTTTATTTA
1276191 TTT
1 TTT
1276194 AATTATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 6 0.17
18 2 0.06
19 11 0.31
20 2 0.06
21 10 0.28
22 5 0.14
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTTATATGTTTATTTA
Found at i:1276450 original size:153 final size:149
Alignment explanation
Indices: 1276293--1276586 Score: 391
Period size: 149 Copynumber: 1.9 Consensus size: 149
1276283 AAAATATTAT
1276293 TTATAAAT-TTAATTTTATATAAATTACTTTTA-AGAAAAATAATCATATT-TTAATATTTATTT
1 TTATAAATATTAA-TTTATATAAATTACTTTTATAG--AAAT-AT--T-TTATTAATATTTATTT
**
1276355 ATTTTTTAATATTAAGAAATTG-GTTGTCTTAAAGCACCTAGAAGTCATTTTCTGATA-TTCTTA
59 ATTTTTTAATATTAAGAAA-TGACATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTTC-TA
1276418 AATAAATAAATATCCTATTTTTTATAAA
122 AATAAATAAATATCCTATTTTTTATAAA
* * * * *
1276446 TTATATATATTAATTTATTTTAATTATTTTTATAGAAATGTTTTATTAATATTTATTTATTTTTT
1 TTATAAATATTAATTTATATAAATTACTTTTATAGAAATATTTTATTAATATTTATTTATTTTTT
*
1276511 AATATTAAGAAATGACATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTTCTAAGTAAATAA
66 AATATTAAGAAATGACATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTTCTAAATAAATAA
*
1276576 ATATCTTATTT
131 ATATCCTATTT
1276587 ATAAAAATGA
Statistics
Matches: 127, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
148 4 0.03
149 86 0.68
150 3 0.02
151 1 0.01
152 4 0.03
153 23 0.18
154 6 0.05
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (149 bp):
TTATAAATATTAATTTATATAAATTACTTTTATAGAAATATTTTATTAATATTTATTTATTTTTT
AATATTAAGAAATGACATGTCTTAAAGCACCTAGAAGTCATTTTCTGATATTTCTAAATAAATAA
ATATCCTATTTTTTATAAA
Found at i:1283829 original size:90 final size:89
Alignment explanation
Indices: 1283674--1283837 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 89
1283664 TAACACACCC
*
1283674 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
1283739 TAATTAATTGGAATTTAATAATAT
66 TAATTAATTGGAATTTAATAATAT
*
1283763 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
1283828 TTAATTAATT
65 TTAATTAATT
1283838 AAAATTAAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 32 0.44
90 40 0.56
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.48
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAATTGGAATTTAATAATAT
Found at i:1285418 original size:8 final size:8
Alignment explanation
Indices: 1285405--1285429 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1285395 CTTAGTTCTT
1285405 CTTAAGTA
1 CTTAAGTA
1285413 CTTAAGTA
1 CTTAAGTA
1285421 CTTAAGTA
1 CTTAAGTA
1285429 C
1 C
1285430 ATATCATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (8 bp):
CTTAAGTA
Found at i:1286661 original size:16 final size:16
Alignment explanation
Indices: 1286642--1286684 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1286632 TTGATTGAAA
*
1286642 AACATATTAATTAATT
1 AACATATTAATAAATT
*
1286658 AACATATTAACAAATT
1 AACATATTAATAAATT
1286674 AACATATTAAT
1 AACATATTAAT
1286685 CTTTGCGGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
AACATATTAATAAATT
Found at i:1286666 original size:8 final size:8
Alignment explanation
Indices: 1286642--1286683 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1286632 TTGATTGAAA
1286642 AACATATT
1 AACATATT
*
1286650 AA-TTAATT
1 AACAT-ATT
1286658 AACATATT
1 AACATATT
*
1286666 AACAAATT
1 AACATATT
1286674 AACATATT
1 AACATATT
1286682 AA
1 AA
1286684 TCTTTGCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 1 0.04
8 26 0.93
9 1 0.04
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (8 bp):
AACATATT
Found at i:1287296 original size:90 final size:89
Alignment explanation
Indices: 1287139--1287315 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 89
1287129 CCTAACATAC
* *
1287139 CCTTTTATAGTCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATTTATA
1 CCTTTTATAGTCAAGTTACCCAAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
1287204 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
1287228 CCTTTTATA-TCCAAGTTACCCAAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGT-CAAGTTACCCAAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTA
1287292 TATTTAATTAATTGAAATTAAATA
64 TATTTAATTAATTGAAATTAAATA
1287316 TTCAGGATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
88 1 0.01
89 32 0.39
90 49 0.60
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGTCAAGTTACCCAAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:1307649 original size:23 final size:22
Alignment explanation
Indices: 1307619--1307661 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1307609 CATTATGTTT
*
1307619 TATTTTATTTTAATTTATTCAC
1 TATTTTATTCTAATTTATTCAC
*
1307641 TATTATTATTCTGATTTATTC
1 TATT-TTATTCTAATTTATTC
1307662 GAAATTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTTTATTCTAATTTATTCAC
Found at i:1307990 original size:21 final size:21
Alignment explanation
Indices: 1307955--1308002 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1307945 CTTATGTCTA
1307955 TTAA-TTGCCTTTAATTTA-T
1 TTAATTTGCCTTTAATTTAGT
*
1307974 TTGATTTGCCTTTTAATTTAGT
1 TTAATTTGCC-TTTAATTTAGT
1307996 TTAATTT
1 TTAATTT
1308003 CAGTCCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 5 0.21
21 9 0.38
22 7 0.29
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.60
Consensus pattern (21 bp):
TTAATTTGCCTTTAATTTAGT
Found at i:1320127 original size:14 final size:14
Alignment explanation
Indices: 1320108--1320143 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1320098 TTTAATTTAG
*
1320108 TTTAATTTCAATCC
1 TTTAATTTCAATAC
*
1320122 TTTAATTTCATTAC
1 TTTAATTTCAATAC
1320136 TTTAATTT
1 TTTAATTT
1320144 TCTGTCTTTA
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:0.28, C:0.14, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAATAC
Found at i:1320188 original size:14 final size:14
Alignment explanation
Indices: 1320121--1320188 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
1320111 AATTTCAATC
*
1320121 CTTTAATTTCATTA
1 CTTTAATTTTATTA
*
1320135 CTTTAATTTTCTGT-
1 CTTTAATTTTAT-TA
* *
1320149 CTTT-ATTTTTTTT
1 CTTTAATTTTATTA
*
1320162 CTTTCATTTTTTATTA
1 CTTT-A-ATTTTATTA
1320178 CTTTAATTTTA
1 CTTTAATTTTA
1320189 GTCTATTGAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
12 1 0.02
13 10 0.24
14 19 0.45
15 2 0.05
16 10 0.24
ACGTcount: A:0.19, C:0.12, G:0.01, T:0.68
Consensus pattern (14 bp):
CTTTAATTTTATTA
Found at i:1326658 original size:27 final size:27
Alignment explanation
Indices: 1326627--1326759 Score: 147
Period size: 27 Copynumber: 5.1 Consensus size: 27
1326617 TGGTTTTTTT
*
1326627 ACCGGATTAAAAACCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGGTTTTTTTCAA
1326654 ACCGGATAAAAAACCGGTTTTTTT---
1 ACCGGATAAAAAACCGGTTTTTTTCAA
1326678 -CCGGATAAAAAACCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGGTTTTTTTCAA
* *
1326704 ACCAGATAAAAAACTGG-TTTTTT--A
1 ACCGGATAAAAAACCGGTTTTTTTCAA
* *
1326728 TCC-GAAAAAAAATCCGGTTTTTTTACAA
1 ACCGGATAAAAAA-CCGGTTTTTTT-CAA
1326756 ACCG
1 ACCG
1326760 AAACCGGTTA
Statistics
Matches: 89, Mismatches: 7, Indels: 18
0.78 0.06 0.16
Matches are distributed among these distances:
23 31 0.35
24 6 0.07
25 6 0.07
26 6 0.07
27 37 0.42
28 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (27 bp):
ACCGGATAAAAAACCGGTTTTTTTCAA
Found at i:1326682 original size:50 final size:50
Alignment explanation
Indices: 1326618--1326759 Score: 205
Period size: 50 Copynumber: 2.8 Consensus size: 50
1326608 TTGAACGACT
*
1326618 GGTTTTTTTACCGGATTAAAAACCGGTTTTTTTCAAACCGGATAAAAAACC
1 GGTTTTTTT-CCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACC
* *
1326669 GGTTTTTTTCCGGATAAAAAACCGGTTTTTTTCAAACCAGATAAAAAACT
1 GGTTTTTTTCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACC
*
1326719 GGTTTTTTATCC-GAAAAAAAATCCGGTTTTTTTACAAACCG
1 GGTTTTTT-TCCGGATAAAAAA-CCGGTTTTTTT-CAAACCG
1326760 AAACCGGTTA
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
50 54 0.65
51 23 0.28
52 6 0.07
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (50 bp):
GGTTTTTTTCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACC
Found at i:1326886 original size:21 final size:21
Alignment explanation
Indices: 1326862--1326903 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1326852 CGGTTTTTAT
1326862 CCGATCCGGATTGGATTGAAA
1 CCGATCCGGATTGGATTGAAA
1326883 CCGATCCGGATTGGATTGAAA
1 CCGATCCGGATTGGATTGAAA
1326904 TCCGGCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (21 bp):
CCGATCCGGATTGGATTGAAA
Found at i:1329357 original size:60 final size:61
Alignment explanation
Indices: 1329293--1329460 Score: 148
Period size: 60 Copynumber: 2.8 Consensus size: 61
1329283 AACTATAACC
* * * * * *
1329293 CTCATTTTAAATTGA-TGCTTAAACTTTTAAATATTCTAATTTTATCCTTAAACTATGGCT
1 CTCATTTTAAATTGAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTAAGACT
** * **
1329353 CTCA-TCCAAATTTAGTCCTTAAACTTTTGGACATTCTAATTTCATCCCTAAACTAAGACT
1 CTCATTTTAAATTGAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTAAGACT
** * *
1329413 CTC-TTTCTAAATT-AGTCCCCAAACTTTCT-AATATTCCAATTTCATCCC
1 CTCATTT-TAAATTGAGTCCTTAAACTTT-TAAACATTCTAATTTCATCCC
1329461 CAAAATCATC
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
59 7 0.08
60 73 0.85
61 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.41
Consensus pattern (61 bp):
CTCATTTTAAATTGAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCTAAACTAAGACT
Found at i:1330210 original size:21 final size:21
Alignment explanation
Indices: 1330169--1330210 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1330159 TAATGTTAAT
*
1330169 AATAAGACACATGTTTAATAA
1 AATAAGACACATGTATAATAA
*
1330190 AATATAGA-ACATGTATCATAA
1 AATA-AGACACATGTATAATAA
1330211 TAAGAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
AATAAGACACATGTATAATAA
Found at i:1330621 original size:24 final size:24
Alignment explanation
Indices: 1330594--1330669 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
1330584 TTCCTTAATG
*
1330594 CACAAACAATGTCACGTAGAATTA
1 CACAAACAATGCCACGTAGAATTA
* * * *
1330618 CACATATAGTGCCACGTAGAATTG
1 CACAAACAATGCCACGTAGAATTA
* * * *
1330642 CACATATAGTGCCACATAGAATGTA
1 CACAAACAATGCCACGTAGAAT-TA
1330667 CAC
1 CAC
1330670 GAATGTACCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 40 0.91
25 4 0.09
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (24 bp):
CACAAACAATGCCACGTAGAATTA
Found at i:1331500 original size:31 final size:31
Alignment explanation
Indices: 1331460--1331579 Score: 111
Period size: 31 Copynumber: 3.9 Consensus size: 31
1331450 CTTAGGGAGC
* *
1331460 ATCTTGGGGCCTGAGAGCCTACCCAAGGAAG
1 ATCTCGGGGCCTGAGAGCCTACCCAAGAAAG
* * * *
1331491 TTCTCGGGGCCACGAG-GCTTACCTAAGAAAG
1 ATCTCGGGGCC-TGAGAGCCTACCCAAGAAAG
*
1331522 ATCTCGGGGCC-GCAGGGCCTACCCAAGAAAG
1 ATCTCGGGGCCTG-AGAGCCTACCCAAGAAAG
* *
1331553 ATCTCGAGG-CTATAGAGCCTACCCAAG
1 ATCTCGGGGCCT-GAGAGCCTACCCAAG
1331580 GGTCGCCTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
29 1 0.01
30 3 0.04
31 65 0.90
32 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.16
Consensus pattern (31 bp):
ATCTCGGGGCCTGAGAGCCTACCCAAGAAAG
Found at i:1332318 original size:22 final size:22
Alignment explanation
Indices: 1332292--1332362 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
1332282 CACGGTCAAA
*
1332292 GTCAAAGTCAATGATCAAACCG
1 GTCAAAGTCAATGATCAGACCG
* * *
1332314 GTCAAAGTTAATGGTCTGACCG
1 GTCAAAGTCAATGATCAGACCG
* * * *
1332336 ATCAAGGTCAACGATCAGACTG
1 GTCAAAGTCAATGATCAGACCG
1332358 GTCAA
1 GTCAA
1332363 CGGTTTGGGT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (22 bp):
GTCAAAGTCAATGATCAGACCG
Found at i:1335253 original size:45 final size:45
Alignment explanation
Indices: 1335202--1335592 Score: 611
Period size: 45 Copynumber: 8.7 Consensus size: 45
1335192 TTCATTAGTG
* *
1335202 TCATTTATGGCATCATTTAATGCCTTTAATGCACCGTTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
* ** *
1335247 TTATTTATGGCATCCTTTCATGCCTGCAATGCACCATTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
1335292 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
* * ****
1335337 TTATTTATGGCATCCTTTAATGCCTTTAATGCTTAATTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
* *
1335382 TCATTTATGACATCCTTTCATGCCTTTAATGCACCTTTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
*
1335427 TTATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
1335472 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
* * *
1335517 TCATTTATGGTATCCTTTCATGCCTTTAATGCACCATTATGTATT
1 TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
*
1335562 TCATTTATGTCATCCTTTCATGCCTTTAATG
1 TCATTTATGGCATCCTTTCATGCCTTTAATG
1335593 TTCTATTTAT
Statistics
Matches: 314, Mismatches: 32, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 314 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATT
Done.