Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001465.1 Hibiscus syriacus cultivar Beakdansim tig00002840_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: 11160956
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 55
Found at i:5737488 original size:9 final size:9
Alignment explanation
Indices: 5737466--5737499 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
5737456 TAAATTATCA
5737466 AAATAAAAT
1 AAATAAAAT
5737475 AAAATAAAAT
1 -AAATAAAAT
5737485 AAATAAAAT
1 AAATAAAAT
5737494 AAATAA
1 AAATAA
5737500 CATTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5739002 original size:84 final size:84
Alignment explanation
Indices: 5738857--5739024 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
5738847 GGTTTTAATC
5738857 TTAAAGGAGAATTTAACTCATTTAATTAACTGCTAATTGTGTTGTTTCCCTACAGGCTCTTCTCT
1 TTAAAGGAGAATTTAACTCATTTAATTAACTGCTAATTGTGTTGTTTCCCTACAGGCTCTTCTCT
5738922 CGATTTTAGATAGCCCGGT
66 CGATTTTAGATAGCCCGGT
*
5738941 TTAAAGGAGAATTTAACTCATTTAATTAACTGCTAATTGTGTTGTTTCCCTACAGGTTCTTCTCT
1 TTAAAGGAGAATTTAACTCATTTAATTAACTGCTAATTGTGTTGTTTCCCTACAGGCTCTTCTCT
5739006 CGATTTTAGATAGCCCGGT
66 CGATTTTAGATAGCCCGGT
5739025 CAATAAGGCT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (84 bp):
TTAAAGGAGAATTTAACTCATTTAATTAACTGCTAATTGTGTTGTTTCCCTACAGGCTCTTCTCT
CGATTTTAGATAGCCCGGT
Found at i:5744317 original size:275 final size:273
Alignment explanation
Indices: 5743826--5744514 Score: 864
Period size: 275 Copynumber: 2.5 Consensus size: 273
5743816 ATCTTCAATC
* *
5743826 TTTCAGCTACTTTTCAGAGGCCATTTATTGCAGCAACAATGCACCGTTTCAATTACTTTTCAGAG
1 TTTCAGCTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCA-CGTTTCAATTAC-TTTCAGAG
*
5743891 GTCATTTAATGCAGAATTCAAGCAACTATTAAGAAAACGGGTGAAAATAGTGTTGCATTATCATC
64 GTCATTTAATGCAGAATTCAAGCAACTATTAAGAAAACGGGTGAAAATAGTGATGCATTATCATC
* * ** * *
5743956 TTCTGCAACTTCTTAGTGATATGTCAACTCAAATCAAAAAAACTTTTCAATGTTGAATTGCCACT
129 TTCTGCAACTTCTCAGTGATATATCAACTCAAATCAAAAAAACAATTCAATGTTGAATTACCAAT
* ** * *
5744021 TCAAATCAAAAAACGTGTATTTTAACCAAGCCAAATTATTCATTGCTTCAGTTACTTTTTTG-TT
194 TCAAATCAAAAAACGTGTATTTTAACCAAGCCAAATTATTCAATGCTTCAACTAC-TTTTCGATG
* **
5744085 CTCAATTAATTCACTG
258 CTCAATTAATGCACCA
* * * * * *
5744101 TTTCAGCTATTTTTCATAGGTCATTTATTGTAACAATAATGCATCGTTTTAGTTACTTTGCAGAG
1 TTTCAGCTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCA-CGTTTCAATTACTTT-CAGAG
* * * * *
5744166 GCCATTTAATGGAGAATTCAAGCAACTATTCAGAAAACGGGTGAAAATGGTGATGCATTTTCATC
64 GTCATTTAATGCAGAATTCAAGCAACTATTAAGAAAACGGGTGAAAATAGTGATGCATTATCATC
* *
5744231 TTCTGCAACTTCTCAGTGATATATCAACTCAAAT-AAAAAAA-AATTCAGTGTTGAATTATCAAT
129 TTCTGCAACTTCTCAGTGATATATCAACTCAAATCAAAAAAACAATTCAATGTTGAATTACCAAT
* * *
5744294 TCAAATCACAAAAAACGTGTATTTTAACGAGGCCAAATTATTCAATGTTTCAACTACTTTTCGAT
194 TCAAAT--CAAAAAACGTGTATTTTAACCAAGCCAAATTATTCAATGCTTCAACTACTTTTCGAT
5744359 GCTCAATTAATGCACCA
257 GCTCAATTAATGCACCA
* * * * *
5744376 TTTCAGATACTTTTCGGAGGTCATTTATTGCAGCAATAATGCACTGTTTCAACTACTTTTAAAGG
1 TTTCAGCTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCAC-GTTTCAATTACTTTCAGAGG
* * * * * *
5744441 TCATTTAATGTAGAATTCAAGCAACTATTTAGAAAATGGGTG-AAATAATGGTGCATTAACATTC
65 TCATTTAATGCAGAATTCAAGCAACTATTAAGAAAACGGGTGAAAATAGTGATGCATTATCA-TC
*
5744505 TTCAGCAACT
129 TTCTGCAACT
5744515 ATTAATATTT
Statistics
Matches: 353, Mismatches: 55, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
273 36 0.10
274 69 0.20
275 248 0.70
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (273 bp):
TTTCAGCTACTTTTCAGAGGTCATTTATTGCAGCAATAATGCACGTTTCAATTACTTTCAGAGGT
CATTTAATGCAGAATTCAAGCAACTATTAAGAAAACGGGTGAAAATAGTGATGCATTATCATCTT
CTGCAACTTCTCAGTGATATATCAACTCAAATCAAAAAAACAATTCAATGTTGAATTACCAATTC
AAATCAAAAAACGTGTATTTTAACCAAGCCAAATTATTCAATGCTTCAACTACTTTTCGATGCTC
AATTAATGCACCA
Found at i:5745953 original size:31 final size:31
Alignment explanation
Indices: 5745915--5745974 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5745905 AGGGAACATG
5745915 GTCACTAACACCATTGGTCCGTCCGATTTAA
1 GTCACTAACACCATTGGTCCGTCCGATTTAA
***
5745946 GTCACTAACGTTATTGGTCCGTCCGATTT
1 GTCACTAACACCATTGGTCCGTCCGATTT
5745975 CAATCCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (31 bp):
GTCACTAACACCATTGGTCCGTCCGATTTAA
Found at i:5751616 original size:28 final size:29
Alignment explanation
Indices: 5751567--5751632 Score: 98
Period size: 28 Copynumber: 2.3 Consensus size: 29
5751557 ATTGAAAATC
* *
5751567 AGTTCACCCTCTAGAATTTTATAACTTTA
1 AGTTCACCCTCAAGAATTTTATAACTTCA
*
5751596 AGTTCACCCT-AAGAATTTTATAAGTTCA
1 AGTTCACCCTCAAGAATTTTATAACTTCA
5751624 AGTTCACCC
1 AGTTCACCC
5751633 CAAACATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 24 0.71
29 10 0.29
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (29 bp):
AGTTCACCCTCAAGAATTTTATAACTTCA
Found at i:5751831 original size:23 final size:23
Alignment explanation
Indices: 5751805--5751848 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5751795 ATAAACAACT
* * *
5751805 TATTTACTTTACATATTCGTTAA
1 TATTTACATTAAATACTCGTTAA
5751828 TATTTACATTAAATACTCGTT
1 TATTTACATTAAATACTCGTT
5751849 CATGTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.50
Consensus pattern (23 bp):
TATTTACATTAAATACTCGTTAA
Found at i:5753908 original size:2 final size:2
Alignment explanation
Indices: 5753901--5753928 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5753891 ACATACATAC
5753901 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
5753929 GAAGAAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5768087 original size:66 final size:66
Alignment explanation
Indices: 5767893--5768146 Score: 262
Period size: 67 Copynumber: 3.8 Consensus size: 66
5767883 AAGAAATTTG
* * *
5767893 TTTCAAGAGAAGTTATCTCAGGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTTAAATGTTTA
1 TTTCAAGAGAA-TTATCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
5767958 TA
65 TA
** * * *
5767960 TTTCAAGAGAAATTGCCTCAAACT-AGATAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTT
1 TTTCAAGAG-AATTATCTC-AAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTT
*
5768024 ATC
64 ATA
* * * * *
5768027 TTTCAAGAGAATCTGTCTCAAGTGAGGCAAAA-TTTGTTTCAAGAAAAACAATATCAAAGG-TTA
1 TTTCAAGAGAAT-TATCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTA
*
5768090 TG
65 TA
* * * * *
5768092 TTTCAAGAGAAACTATCTCAAGCGATAAAAAACTTTGTTTCGAGATAAACAATCT
1 TTTCAAGAG-AATTATCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCT
5768147 TAAATGAGAT
Statistics
Matches: 154, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
65 27 0.18
66 51 0.33
67 72 0.47
68 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (66 bp):
TTTCAAGAGAATTATCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTAT
A
Found at i:5768128 original size:132 final size:134
Alignment explanation
Indices: 5767893--5768146 Score: 316
Period size: 132 Copynumber: 1.9 Consensus size: 134
5767883 AAGAAATTTG
* * * * * *
5767893 TTTCAAGAGAAGTTATCTCAGGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTTAAATGTTTA
1 TTTCAAGAGAAGTTATCTCAAGTGAGACAAAACTTTGTTTCAAGAAAAACAATATCAAATGGTTA
* * * * *
5767958 TATTTCAAGAGAAATTGCCTCAAACTAGATAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTT
66 TATTTCAAGAGAAACTACCTCAAACGAGAAAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
5768023 TATC
131 TATC
* *
5768027 TTTCAAGAGAA-TCTGTCTCAAGTGAGGCAAAA-TTTGTTTCAAGAAAAACAATATCAAA-GGTT
1 TTTCAAGAGAAGT-TATCTCAAGTGAGACAAAACTTTGTTTCAAGAAAAACAATATCAAATGGTT
* * * * *
5768089 ATGTTTCAAGAGAAACTATCTCAAGCGATAAAAAACTTTGTTTCGAGATAAACAATCT
65 ATATTTCAAGAGAAACTACCTCAAACGAGAAAAAACTTTGTTTCGAGAGAAACAATCT
5768147 TAAATGAGAT
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
132 51 0.50
133 23 0.23
134 27 0.27
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (134 bp):
TTTCAAGAGAAGTTATCTCAAGTGAGACAAAACTTTGTTTCAAGAAAAACAATATCAAATGGTTA
TATTTCAAGAGAAACTACCTCAAACGAGAAAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
TATC
Found at i:5768350 original size:103 final size:103
Alignment explanation
Indices: 5768129--5768354 Score: 246
Period size: 104 Copynumber: 2.2 Consensus size: 103
5768119 AAAAACTTTG
* * ** * *
5768129 TTTCGAGATAAACAATCTTAAATGAGATCAATTTTGTTTCAAGAGACACAATTTTAAAATTTGTG
1 TTTCGAGA-AAACAATCTCAAATGAGATCAATTTTGTTTCAAGAGAAACAACATCAAAATTTGGG
* * *
5768194 TTTTAAGGGAAAATTGTCTCAAGTGAGACAGAATTTGTT
65 CTTAAAGGGAAAATTGTCTAAAGTGAGACAGAATTTGTT
* * *
5768233 TTTAG-GAAAACAATCTCAAATGAGATCAATTTCTTGTTTCTAGTGAAACAACATCAAAATTTGG
1 TTTCGAGAAAACAATCTCAAATGAGATCAA-TT-TTGTTTCAAGAGAAACAACATCAAAATTTGG
*
5768297 GCTTAAATGG-AAATTGTCTTAAAG-GAGACA-AATTT-TT
64 GCTTAAAGGGAAAATTGTC-TAAAGTGAGACAGAATTTGTT
*
5768334 TTTCGAAAGAAACAATCTCAA
1 TTTCGAGA-AAACAATCTCAA
5768355 GCGAGATAGA
Statistics
Matches: 102, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
101 6 0.06
102 27 0.26
103 30 0.29
104 39 0.38
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (103 bp):
TTTCGAGAAAACAATCTCAAATGAGATCAATTTTGTTTCAAGAGAAACAACATCAAAATTTGGGC
TTAAAGGGAAAATTGTCTAAAGTGAGACAGAATTTGTT
Found at i:5777112 original size:16 final size:15
Alignment explanation
Indices: 5777091--5777127 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
5777081 ATATTAATTA
5777091 TTTTTATTCTAATAT
1 TTTTTATTCTAATAT
*
5777106 CTTTTTATTTTAATAT
1 -TTTTTATTCTAATAT
5777122 TTTTTA
1 TTTTTA
5777128 AAGTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATTCTAATAT
Found at i:5788570 original size:14 final size:14
Alignment explanation
Indices: 5788551--5788577 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5788541 GATCGAAACT
5788551 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
5788565 TCAAGATTCCAGA
1 TCAAGATTCCAGA
5788578 CAGATTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:5789154 original size:106 final size:107
Alignment explanation
Indices: 5788819--5789252 Score: 559
Period size: 106 Copynumber: 4.0 Consensus size: 107
5788809 ATATCGCGCC
* ** * * * *
5788819 ACTCGAGACAACACAAGTTCAACTTCATGACGAAGGGACGACTGGTTGTCAATAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
* *
5788883 CAGTTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 CA-ATT--TT-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
5788929 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGAACGACAGGTTGTCAACAAAACAACTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
***
5788994 CAATTTTAGAGCCAATTTCAACTTCACAGTAAAGGATATTGG
66 CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* ** *
5789036 ACTCAAGACAACACAAGTTCAACTTCAAAACGAAGGGACGGTTGGTTGTCAA-AAAATAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
*
5789100 CAATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
5789142 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
* ** * *
5789206 CAGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
5789248 ACTCA
1 ACTCA
5789253 GAATAGTACA
Statistics
Matches: 285, Mismatches: 37, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
106 147 0.52
107 79 0.28
108 2 0.01
110 55 0.19
111 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.24
Consensus pattern (107 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
CAATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:5789195 original size:213 final size:215
Alignment explanation
Indices: 5788819--5789232 Score: 584
Period size: 213 Copynumber: 1.9 Consensus size: 215
5788809 ATATCGCGCC
* ** * * *
5788819 ACTCGAGACAACACAAGTTCAACTTCATGACGAAGGGACGACTGGTTGTCAATAAACCACTTTTC
1 ACTCAAGACAACACAAGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAATAAAACAATTTCC
* *
5788884 AGTTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTC
66 AGATT-ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTC
* **
5788949 AACTTCACAATGAAGGAACGACAGGTTGTCAACAAAACAACTTCCCAATTTTAGAGCCAATTTCA
130 AACTTCACAACGAAGGAACGACAGGTTGTCAAC-AAACAACTTCCCAATTCCAGAGCCAATTTCA
5789014 ACTTCACAGTAAAGGATATTGG
194 ACTTCACAGTAAAGGATATTGG
** *
5789036 ACTCAAGACAACACAAGTTCAACTTCAAAACGAAGGGACGGTTGGTTGTCAA-AAAATAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAATAAAACAATTT-C
* *
5789100 CA-ATT-TT-AGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCGAGACAACACAAGTTC
65 CAGATTATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTC
* * * * *
5789162 AACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAA
130 AACTTCACAACGAAGGAACGACAGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAA
5789227 CTTCAC
195 CTTCAC
5789233 GACGGAGGAT
Statistics
Matches: 175, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
212 34 0.19
213 81 0.46
214 2 0.01
216 9 0.05
217 49 0.28
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (215 bp):
ACTCAAGACAACACAAGTTCAACTTCAAAACGAAGGGACGACTGGTTGTCAATAAAACAATTTCC
AGATTATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGTTCA
ACTTCACAACGAAGGAACGACAGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAAC
TTCACAGTAAAGGATATTGG
Found at i:5790662 original size:16 final size:15
Alignment explanation
Indices: 5790641--5790677 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
5790631 ATATTAATTA
5790641 TTTTTATTCTAATAT
1 TTTTTATTCTAATAT
*
5790656 CTTTTTATTTTAATAT
1 -TTTTTATTCTAATAT
5790672 TTTTTA
1 TTTTTA
5790678 AAGTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTATTCTAATAT
Found at i:5790690 original size:2 final size:2
Alignment explanation
Indices: 5790685--5790728 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5790675 TTAAAGTTAT
5790685 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5790727 TA
1 TA
5790729 ACTATTATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5795276 original size:31 final size:32
Alignment explanation
Indices: 5795241--5795300 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
5795231 TGTCGTCGGC
* *
5795241 TTCTCCTTTT-TGCTGTGGTGGAGTCATTAGA
1 TTCTCCTTTTGGGCTGTGGAGGAGTCATTAGA
5795272 TTCTCCTTTTGGGCTGTGGAGGAGTCATT
1 TTCTCCTTTTGGGCTGTGGAGGAGTCATT
5795301 TCAATCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.12, C:0.17, G:0.28, T:0.43
Consensus pattern (32 bp):
TTCTCCTTTTGGGCTGTGGAGGAGTCATTAGA
Found at i:5798506 original size:43 final size:41
Alignment explanation
Indices: 5798459--5798812 Score: 281
Period size: 42 Copynumber: 8.5 Consensus size: 41
5798449 TAGTTTTATA
* *
5798459 TTTTACCTTTATAATTGGGGCCTTTAATTTTTTCAATTACACT
1 TTTTACCTTTATAATTGAGGCC-CTAATTTTTTCAATT-CACT
*
5798502 TTTTACCTTTATAATTGA-GCCTCTGATTTTTTCAATCTCACT
1 TTTTACCTTTATAATTGAGGCC-CTAATTTTTTCAAT-TCACT
* * * * *
5798544 TTCTACCTTTATAATTGAGATCCATGATTTTTT-AATCCCACT
1 TTTTACCTTTATAATTGAG-GCCCTAATTTTTTCAAT-TCACT
* * *
5798586 TTTTACGTTTATAACTAAGGCCCTTAATTTTTTCAATCTCACT
1 TTTTACCTTTATAATTGAGGCCC-TAATTTTTTCAAT-TCACT
* * *
5798629 TTCTACCTTTGTAATTGAGGCCCCTAATTTTATC---TCACT
1 TTTTACCTTTATAATTGAGG-CCCTAATTTTTTCAATTCACT
* ** * *
5798668 TTTTACATTTATAATTGAATCCCTAA-TTTTTCAATCCCACC
1 TTTTACCTTTATAATTGAGGCCCTAATTTTTTCAAT-TCACT
* ** ** *
5798709 TTTTACATTTATAATTGAGGTCATTGGTTTTTTCAA-TAACAT
1 TTTTACCTTTATAATTGAGG-CCCTAATTTTTTCAATTCAC-T
* *
5798751 TTTTACCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACT
1 TTTTACCTTTATAATTGAGGCCCTAA-TTTTTTCAAT-TCACT
*
5798794 TTCTACCTTTATAATTGAG
1 TTTTACCTTTATAATTGAG
5798813 ACTCCTTTTT
Statistics
Matches: 247, Mismatches: 48, Indels: 32
0.76 0.15 0.10
Matches are distributed among these distances:
37 5 0.02
38 6 0.02
39 20 0.08
41 27 0.11
42 96 0.39
43 85 0.34
44 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.48
Consensus pattern (41 bp):
TTTTACCTTTATAATTGAGGCCCTAATTTTTTCAATTCACT
Found at i:5798574 original size:85 final size:84
Alignment explanation
Indices: 5798485--5798813 Score: 343
Period size: 85 Copynumber: 3.9 Consensus size: 84
5798475 GGGGCCTTTA
*
5798485 ATTTTTTCAATTACACTTTTTACCTTTATAATTGAGCCTCTGATTTTTTCAATCTCACTTTCTAC
1 ATTTTTTCAATTACACTTTTTACCTTTATAATTGAGCC-CTAATTTTTTCAATCTCACTTTCTAC
5798550 CTTTATAATTGAGATCCATG
65 CTTTATAATTGAGATCCATG
** * * *
5798570 ATTTTTT-AATCCCACTTTTTACGTTTATAACTAAGGCCCTTAATTTTTTCAATCTCACTTTCTA
1 ATTTTTTCAATTACACTTTTTACCTTTATAATTGA-GCCC-TAATTTTTTCAATCTCACTTTCTA
* ** * *
5798634 CCTTTGTAATTGAGGCCCCTA
64 CCTTTATAATTGAGATCCATG
* * * *
5798655 ATTTTATC---T-CACTTTTTACATTTATAATTGAATCCCTAA-TTTTTCAATCCCACCTTT-TA
1 ATTTTTTCAATTACACTTTTTACCTTTATAATTG-AGCCCTAATTTTTTCAATCTCA-CTTTCTA
* *
5798714 CATTTATAATTGAGGT-CATTG
64 CCTTTATAATTGAGATCCA-TG
* * *
5798735 GTTTTTTCAATAACA-TTTTTACCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTA
1 ATTTTTTCAATTACACTTTTTACCTTTATAATTGAG-CCCTAA-TTTTTTCAATCTCACTTTCTA
5798799 CCTTTATAATTGAGA
64 CCTTTATAATTGAGA
5798814 CTCCTTTTTA
Statistics
Matches: 198, Mismatches: 32, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
79 1 0.01
80 34 0.17
81 7 0.04
82 22 0.11
83 23 0.12
84 29 0.15
85 82 0.41
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (84 bp):
ATTTTTTCAATTACACTTTTTACCTTTATAATTGAGCCCTAATTTTTTCAATCTCACTTTCTACC
TTTATAATTGAGATCCATG
Found at i:5798865 original size:60 final size:60
Alignment explanation
Indices: 5798756--5798872 Score: 164
Period size: 60 Copynumber: 1.9 Consensus size: 60
5798746 AACATTTTTA
*
5798756 CCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTATAATTGAGACT
1 CCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTATAACTGAGACT
* * * **
5798816 CCTTTTTAATTGAGGTCCCTAGTTTTTTT-AATCTCACTTTTTATGTTTATAACTGAG
1 CCTTTGTAATTGA-GTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTATAACTGAG
5798873 TCTCTTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 36 0.72
61 14 0.28
ACGTcount: A:0.22, C:0.19, G:0.10, T:0.49
Consensus pattern (60 bp):
CCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTATAACTGAGACT
Found at i:5798927 original size:43 final size:42
Alignment explanation
Indices: 5798822--5799484 Score: 359
Period size: 43 Copynumber: 15.5 Consensus size: 42
5798812 GACTCCTTTT
* * * **
5798822 TAATTGAGGTCCCTAGTTTTTTTAATCTCACTTTTTATGTTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
* * * * * * *
5798865 TAACTGAGTCTCTTAAATTTTTTCAATATCATTTTCTACCTTTG
1 TAATTGAGGCCCCT-AATTTTTTCAATCTCATTTT-TACATTTA
*
5798909 TAATTGAGGCCCCTAA-TTTTT-AATCTCAATTTTTGCATTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTC-ATTTTTACATTTA
* * **
5798950 TTATTCA-TACCCTAATTTTTTCAATCT--TTTTTACATTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCATTTTTACATTTA
* * ** ** * *
5798989 TAATTAAGGTCATTGGTTTTTTCAATCACACTTTTTACCTTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
* *
5799032 TAATTGA-GCCTCTAATTTTTTTCAATCTCACTTTCTACATTTA
1 TAATTGAGGCCCCTAA-TTTTTTCAATCTCA-TTTTTACATTTA
** * * * *
5799075 TAATTGAGATCCCTGATTTTTTTTTAATCCCACTTTTTACGTTTA
1 TAATTGAGGCCCCT-A-ATTTTTTCAATCTCA-TTTTTACATTTA
** * * * *
5799120 TAACCGAGGCCCCTAATGTTTTTCAATCTCAATATCTACCTTTG
1 TAATTGAGGCCCCTAAT-TTTTTCAATCTC-ATTTTTACATTTA
*
5799164 TAATTGAGACCCCTAA--TTTT-AA-CTCACTTTTTACATTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
**
5799203 TAATTGA-ATCCCTAATTTTTTTCAATC-CAACTTTTTACATTTA
1 TAATTGAGGCCCCTAA-TTTTTTCAATCTC-A-TTTTTACATTTA
* ** ** * *
5799246 TAATTGAGGTCATTGGTTTTTTCAATCACACTTTTTACCTTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
* * *
5799289 TAATTGA-GTCCCTAATTTTTTCAATCTCACTTTCTACCTTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
* * *
5799331 TAATTGAGACCCCT--TTTTAATTGATGTCTCTGATTTTTTTAATCCATTTA
1 TAATTGAGGCCCCTAATTTT--TTCA-ATCTC--A--TTTTT-A--CATTTA
* *
5799381 TAACTGAGGCCCCTAA-TTTTTGAATCTCACTTTTTACATTTA
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
* ** * * * *
5799423 TTATTGAAACCCCTATTTTTTTCAATCTTATTTTTTACTTTTG
1 TAATTGAGGCCCCTAATTTTTTCAATCTCA-TTTTTACATTTA
*
5799466 TAATTGAGGCTCCTAATTT
1 TAATTGAGGCCCCTAATTT
5799485 AATATTTTTT
Statistics
Matches: 475, Mismatches: 108, Indels: 74
0.72 0.16 0.11
Matches are distributed among these distances:
38 8 0.02
39 34 0.07
40 21 0.04
41 32 0.07
42 74 0.16
43 159 0.33
44 72 0.15
45 40 0.08
46 2 0.00
47 4 0.01
48 5 0.01
49 4 0.01
50 17 0.04
51 3 0.01
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.49
Consensus pattern (42 bp):
TAATTGAGGCCCCTAATTTTTTCAATCTCATTTTTACATTTA
Found at i:5799206 original size:171 final size:167
Alignment explanation
Indices: 5799017--5799344 Score: 444
Period size: 171 Copynumber: 1.9 Consensus size: 167
5799007 TTTTCAATCA
*
5799017 CACTTTTTACCTTTATAATTG-AGCCTCTAATTTTTTTCAATCTC-ACTTTCTACATTTATAATT
1 CACTTTTTACATTTATAATTGAAGCC-CTAATTTTTTTCAATC-CAACTTTCTACATTTATAATT
* * * * *
5799080 GAGATCCCTGATTTTTTTTTAATCCCACTTTTTACGTTTATAACCGAGGCCCCTAATGTTTTTCA
64 GAGATCACTG--GTTTTTTCAATCACACTTTTTACCTTTATAACCGA-GCCCCTAAT-TTTTTCA
*
5799145 ATCTCAATATCTACCTTTGTAATTGAGACCCCTAATTTTAACT
125 ATCTCAATATCTACCTTTATAATTGAGACCCCTAATTTTAACT
* *
5799188 CACTTTTTACATTTATAATTGAATCCCTAATTTTTTTCAATCCAACTTTTTACATTTATAATTGA
1 CACTTTTTACATTTATAATTGAAGCCCTAATTTTTTTCAATCCAACTTTCTACATTTATAATTGA
* * ** *
5799253 GGTCATTGGTTTTTTCAATCACACTTTTTACCTTTATAATTGAGTCCCTAATTTTTTCAATCTCA
66 GATCACTGGTTTTTTCAATCACACTTTTTACCTTTATAACCGAGCCCCTAATTTTTTCAATCTCA
* *
5799318 CTTTCTACCTTTATAATTGAGACCCCT
131 ATATCTACCTTTATAATTGAGACCCCT
5799345 TTTTAATTGA
Statistics
Matches: 139, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
167 37 0.27
168 8 0.06
169 29 0.21
170 1 0.01
171 61 0.44
172 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (167 bp):
CACTTTTTACATTTATAATTGAAGCCCTAATTTTTTTCAATCCAACTTTCTACATTTATAATTGA
GATCACTGGTTTTTTCAATCACACTTTTTACCTTTATAACCGAGCCCCTAATTTTTTCAATCTCA
ATATCTACCTTTATAATTGAGACCCCTAATTTTAACT
Found at i:5799548 original size:526 final size:512
Alignment explanation
Indices: 5798482--5799504 Score: 1361
Period size: 526 Copynumber: 2.0 Consensus size: 512
5798472 ATTGGGGCCT
* *
5798482 TTAATTTTTTCAAT-TACACTTTTTACCTTTATAATTGAGCCTCTGATTTTTTCAATCTCACTTT
1 TTAATTTATTCAATCTACACTTTTTACCTTTATAATTGAGCCTCTAATTTTTTCAATCTCACTTT
* * *
5798546 CTACCTTTATAATTGAGATCCATGATTTTTTAATCCCACTTTTTACGTTTATAACTAAGGCCCTT
66 CTACATTTATAATTGAGATCCATGATTTTTTAATCCCACTTTTTACGTTTATAACCAAGGCCCCT
* * * *
5798611 AATTTTTTCAATCTCACTTTCTACCTTTGTAATTGAGGCCCCTAATTTTATCTCACTTTTTACAT
131 AATTTTTTCAATCTCAATATCTACCTTTGTAATTGAGACCCCTAATTTTAACTCACTTTTTACAT
*
5798676 TTATAATTGAATCCCTAATTTTTCAATCCCACCTTTTACATTTATAATTGAGGTCATTGGTTTTT
196 TTATAATTGAATCCCTAATTTTTCAATCCAACCTTTTACATTTATAATTGAGGTCATTGGTTTTT
*
5798741 TCAATAACATTTTTACCTTTGTAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTAT
261 TCAATAACATTTTTACCTTTATAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTAT
*
5798806 AATTGAGACTCCTTTTTAATTGAGGTCCCTAGTTTTTTTAATCTCACTTTTTATGTTTATAACTG
326 AATTGAGACCCCTTTTTAATTGAGGTCCCTAGTTTTTTTAA-CTCAC----TA-GTTTATAACTG
* * * * * **
5798871 AGTCTCTTAAATTTTTTCAATATCATTTTCTACCTTTGTAATTGAGGCCCCTAATTTTTAATCTC
385 AGGCCCCTAAATTTTTTCAATATCATTTTCTACATTTATAATTGAAACCCCTAATTTTTAATCTC
* * * **
5798936 AATTTTTGCATTTATTATTCATACCCTAATTTTTTCAATCTTTTTTACATTTATAATTAAGGTCA
450 AATTTTTACATTTATAATTCAGACCCTAATTTAAT-AATCTTTTTTACATTTATAATTAA-GTCA
** *
5799001 TTGGTTTTTTCAATC-ACACTTTTTACCTTTATAATTGAGCCTCTAATTTTTTTCAATCTCACTT
1 TTAATTTATTCAATCTACACTTTTTACCTTTATAATTGAGCCTCTAA-TTTTTTCAATCTCACTT
* *
5799065 TCTACATTTATAATTGAGATCCCTGATTTTTTTTTAATCCCACTTTTTACGTTTATAACCGAGGC
65 TCTACATTTATAATTGAGATCCATGA---TTTTTTAATCCCACTTTTTACGTTTATAACCAAGGC
5799130 CCCTAATGTTTTTCAATCTCAATATCTACCTTTGTAATTGAGACCCCTAATTTTAACTCACTTTT
127 CCCTAAT-TTTTTCAATCTCAATATCTACCTTTGTAATTGAGACCCCTAATTTTAACTCACTTTT
*
5799195 TACATTTATAATTGAATCCCTAATTTTTTTCAATCCAACTTTTTACATTTATAATTGAGGTCATT
191 TACATTTATAATTGAATCCCTAA--TTTTTCAATCCAACCTTTTACATTTATAATTGAGGTCATT
*
5799260 GGTTTTTTCAATCACACTTTTTACCTTTATAATTGAGTCCCTAA-TTTTTTCAATCTCACTTTCT
254 GGTTTTTTCAATAACA-TTTTTACCTTTATAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCT
* *
5799324 ACCTTTATAATTGAGACCCCTTTTTAATTGATGTCTCT-GATTTTTTTAA-TC-C-A-TTTATAA
318 ACCTTTATAATTGAGACCCCTTTTTAATTGAGGTCCCTAG-TTTTTTTAACTCACTAGTTTATAA
* * * *
5799384 CTGAGGCCCCT-AA-TTTTTGAATCTCACTTTT-TACATTTATTATTGAAACCCCTATTTTTTTC
382 CTGAGGCCCCTAAATTTTTTCAATATCA-TTTTCTACATTTATAATTGAAACCCCTA-ATTTTT-
* * * * * * *
5799446 AATCTTATTTTTTACTTTTGTAATTGAGGCTCCTAATTTAAT-AT-TTTTTTCCAATTTAT
444 AATCTCAATTTTTACATTTATAATTCAGAC-CCTAATTTAATAATCTTTTTTAC-ATTTAT
5799505 TAATATAATA
Statistics
Matches: 447, Mismatches: 42, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
514 36 0.08
515 19 0.04
516 36 0.08
517 9 0.02
518 1 0.00
519 42 0.09
520 41 0.09
523 41 0.09
524 78 0.17
525 1 0.00
526 117 0.26
527 26 0.06
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.49
Consensus pattern (512 bp):
TTAATTTATTCAATCTACACTTTTTACCTTTATAATTGAGCCTCTAATTTTTTCAATCTCACTTT
CTACATTTATAATTGAGATCCATGATTTTTTAATCCCACTTTTTACGTTTATAACCAAGGCCCCT
AATTTTTTCAATCTCAATATCTACCTTTGTAATTGAGACCCCTAATTTTAACTCACTTTTTACAT
TTATAATTGAATCCCTAATTTTTCAATCCAACCTTTTACATTTATAATTGAGGTCATTGGTTTTT
TCAATAACATTTTTACCTTTATAATTGAGTCCCTAATTTTTTTCAATCTCACTTTCTACCTTTAT
AATTGAGACCCCTTTTTAATTGAGGTCCCTAGTTTTTTTAACTCACTAGTTTATAACTGAGGCCC
CTAAATTTTTTCAATATCATTTTCTACATTTATAATTGAAACCCCTAATTTTTAATCTCAATTTT
TACATTTATAATTCAGACCCTAATTTAATAATCTTTTTTACATTTATAATTAAGTCA
Found at i:5811754 original size:37 final size:37
Alignment explanation
Indices: 5811705--5811779 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5811695 TGTAAGATTG
5811705 ATTATTAGCAACACAACTTGTAGCTTGTGAATCACAT
1 ATTATTAGCAACACAACTTGTAGCTTGTGAATCACAT
*
5811742 ATTATTAGCAACACAGCTTGTAGCTTGTGAATCACAT
1 ATTATTAGCAACACAACTTGTAGCTTGTGAATCACAT
5811779 A
1 A
5811780 ATAATGACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (37 bp):
ATTATTAGCAACACAACTTGTAGCTTGTGAATCACAT
Found at i:5815628 original size:4 final size:4
Alignment explanation
Indices: 5815619--5815648 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
5815609 ATGACTAGTG
5815619 AAAT AAAT AAAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT A
5815649 TTAAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:5815641 original size:17 final size:19
Alignment explanation
Indices: 5815619--5815656 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
5815609 ATGACTAGTG
5815619 AAATAAATAAA-A-TAAAT
1 AAATAAATAAATATTAAAT
5815636 AAATAAATAAATATTAAAT
1 AAATAAATAAATATTAAAT
5815655 AA
1 AA
5815657 TATTATCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAATAAATATTAAAT
Found at i:5819915 original size:25 final size:25
Alignment explanation
Indices: 5819887--5819937 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5819877 GGTTTGTTCA
5819887 TGTTATATGATATTATTTATGATTT
1 TGTTATATGATATTATTTATGATTT
* *
5819912 TGTTATCTTATATTATTTATGATTT
1 TGTTATATGATATTATTTATGATTT
5819937 T
1 T
5819938 TATAAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (25 bp):
TGTTATATGATATTATTTATGATTT
Found at i:5823929 original size:2 final size:2
Alignment explanation
Indices: 5823922--5823949 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5823912 ACAAACTTTA
5823922 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
5823950 CCAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5824074 original size:18 final size:15
Alignment explanation
Indices: 5824036--5824066 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5824026 TGTGTTTCAT
5824036 ATTG-ATTTAAAAAA
1 ATTGAATTTAAAAAA
5824050 ATTGAATTTAAAAAA
1 ATTGAATTTAAAAAA
5824065 AT
1 AT
5824067 ATATGAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
ATTGAATTTAAAAAA
Found at i:5829614 original size:24 final size:24
Alignment explanation
Indices: 5829587--5829635 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5829577 ATGTTCATTT
*
5829587 ATTTATGTTTGTTCATTTATATTC
1 ATTTATGTTCGTTCATTTATATTC
*
5829611 ATTTATGTTCGTTCGTTTATATTC
1 ATTTATGTTCGTTCATTTATATTC
5829635 A
1 A
5829636 AGTCAATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.59
Consensus pattern (24 bp):
ATTTATGTTCGTTCATTTATATTC
Found at i:5831392 original size:37 final size:37
Alignment explanation
Indices: 5831257--5831490 Score: 250
Period size: 36 Copynumber: 6.4 Consensus size: 37
5831247 TTTTGAAATG
* * *
5831257 TATATATTATAT-GGTTTTTAAAATATTTTGAAAA-T
1 TATATATTATATAGTTTTTTAAAACATTTTGAAAACA
* *
5831292 TATATAATATATAGTTTTTAAAAAACATTTTG-AAA-A
1 TATATATTATATAGTTTTT-TAAAACATTTTGAAAACA
* * *
5831328 TATATAATATAT-GGTTTTTAAAACATTTTAAAAACA
1 TATATATTATATAGTTTTTTAAAACATTTTGAAAACA
*
5831364 TATATATTATATAGTTTTTTAAAACATTTTTAAAACA
1 TATATATTATATAGTTTTTTAAAACATTTTGAAAACA
*
5831401 TATATATAATATATA-ATTTTT-AAAC-TTTTGAAAACA
1 TATATAT--TATATAGTTTTTTAAAACATTTTGAAAACA
*
5831437 TATATATGTTATATAGTTTTTAAAAAACATTTTGAAAACA
1 TATATA--TTATATAGTTTTT-TAAAACATTTTGAAAACA
5831477 TATATATATATATA
1 TATATAT-TATATA
5831491 TATATATATA
Statistics
Matches: 170, Mismatches: 15, Indels: 24
0.81 0.07 0.11
Matches are distributed among these distances:
34 10 0.06
35 19 0.11
36 54 0.32
37 47 0.28
38 7 0.04
39 16 0.09
40 17 0.10
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
TATATATTATATAGTTTTTTAAAACATTTTGAAAACA
Found at i:5831481 original size:2 final size:2
Alignment explanation
Indices: 5831476--5831510 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5831466 TTTTGAAAAC
5831476 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 A
5831511 GTTTTAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5831536 original size:96 final size:91
Alignment explanation
Indices: 5831400--5831582 Score: 249
Period size: 95 Copynumber: 2.0 Consensus size: 91
5831390 TTTTTAAAAC
* * *
5831400 ATATATATAATATATAATTTTTAAACTTTTGAAAACATATATATGTTATATAGTTTTTAAAAAAC
1 ATATATATAATATATAATTTTAAAACTTTTGAAAAAATATATATATTATATAGTTTTT-AAAAAC
5831465 ATTTTGAAAACATATATATATATATATAT
65 ATTTTGAAAA-ATATATA-ATATATATAT
* * *
5831494 ATATATATATATATATAGTTTTAAAACATTTTGAAAAAATATATATATTATTTAGTTTTTGAAAA
1 ATATATATA-ATATATAATTTTAAAAC-TTTTGAAAAAATATATATATTATATAGTTTTTAAAAA
* *
5831559 TATTTTGAAAATTATATAATATAT
64 CATTTTGAAAAATATATAATATAT
5831583 GATTTTTTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
93 6 0.08
94 15 0.19
95 29 0.37
96 29 0.37
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (91 bp):
ATATATATAATATATAATTTTAAAACTTTTGAAAAAATATATATATTATATAGTTTTTAAAAACA
TTTTGAAAAATATATAATATATATAT
Found at i:5831569 original size:39 final size:40
Alignment explanation
Indices: 5831494--5831620 Score: 122
Period size: 38 Copynumber: 3.2 Consensus size: 40
5831484 ATATATATAT
*
5831494 ATATATATATATATATAG-TTTT-AAAACATTTTGAAAA-A
1 ATATATATAT-TATTTAGTTTTTGAAAACATTTTGAAAATA
* *
5831532 ATATATATATTATTTAGTTTTTGAAAATATTTTGAAAATT
1 ATATATATATTATTTAGTTTTTGAAAACATTTTGAAAATA
* **
5831572 ATATAATATATGA-TT--TTTTTGAAAACATTTTTTAAATA
1 ATAT-ATATATTATTTAGTTTTTGAAAACATTTTGAAAATA
5831610 TATAATATATA
1 -AT-ATATATA
5831621 GTTTTAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
37 6 0.08
38 33 0.44
39 21 0.28
40 8 0.11
41 7 0.09
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (40 bp):
ATATATATATTATTTAGTTTTTGAAAACATTTTGAAAATA
Found at i:5831575 original size:38 final size:38
Alignment explanation
Indices: 5831494--5831658 Score: 121
Period size: 38 Copynumber: 4.4 Consensus size: 38
5831484 ATATATATAT
5831494 ATATATATATATATATAGTTTTAAAACATTTTGAAAAA
1 ATATATATATATATATAGTTTTAAAACATTTTGAAAAA
* *
5831532 ATATATATAT-TATTTAGTTTTTGAAAATATTTTG-AAAA
1 ATATATATATATATATAG-TTTT-AAAACATTTTGAAAAA
* ** **
5831570 TTATATA-ATATATGATTTTTTTGAAAACATTTT---TTA
1 ATATATATATATAT-ATAGTTTT-AAAACATTTTGAAAAA
* ***
5831606 A-ATATATA-ATATATAGTTTTAAAATATTTTTTGAAA
1 ATATATATATATATATAGTTTTAAAACATTTTGAAAAA
* *
5831642 ATATTTTTATATATATA
1 ATATATATATATATATA
5831659 ATATATATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
33 9 0.09
34 6 0.06
35 9 0.09
36 4 0.04
37 13 0.13
38 48 0.48
39 11 0.11
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (38 bp):
ATATATATATATATATAGTTTTAAAACATTTTGAAAAA
Found at i:5831582 original size:132 final size:132
Alignment explanation
Indices: 5831363--5831620 Score: 301
Period size: 132 Copynumber: 1.9 Consensus size: 132
5831353 TTTTAAAAAC
* * *
5831363 ATATATATTATATAGTTTTTTAAAACATTTTTAAAACATATATATAATATATAATTTTTAAACTT
1 ATATATATTATATAG-TTTTTAAAACATTTTGAAAAAATATATATAATATATAATTTTTAAAATT
**
5831428 TTGAAAACATATATATGTTATAT-AGTTTTTAAAAAACATTTTGAAAACATATATATATATATAT
65 TTGAAAACATATATATAATATATGAGTTTTTAAAAAACATTTTGAAAACATATA-ATATATATAT
5831492 ATAT
129 ATAT
* * *
5831496 ATATATATATATATAG-TTTTAAAACATTTTGAAAAAATATATATATTATTTAGTTTTTGAAAAT
1 ATATATAT-TATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAATTTTT--AAA-
* ** ** *
5831560 ATTTTG-AAA-AT-TATATAATATATGATTTTTTTGAAAACATTTTTTAAATATATAATATATA
62 ATTTTGAAAACATATATATAATATATGAGTTTTTAAAAAACATTTTGAAAACATATAATATATA
5831621 GTTTTAAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
132 54 0.51
133 34 0.32
134 13 0.12
135 5 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (132 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAATTTTTAAAATTT
TGAAAACATATATATAATATATGAGTTTTTAAAAAACATTTTGAAAACATATAATATATATATAT
AT
Found at i:5831674 original size:3 final size:3
Alignment explanation
Indices: 5831666--5831711 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
5831656 ATAATATATA
*
5831666 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT ATAT TTT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT -TAT TAT TAT TA
5831712 ATTCTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5832906 original size:25 final size:25
Alignment explanation
Indices: 5832878--5832949 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
5832868 TTTGTTTTGT
5832878 TTTGTTTTATTTCATTTTTTATTTC
1 TTTGTTTTATTTCATTTTTTATTTC
*
5832903 TTTGATTTCTTTTTC-TTTTTT-TTTC
1 TTTG-TTT-TATTTCATTTTTTATTTC
* *
5832928 TTATTTTTTATTT-ATTCTTTAT
1 TT-TGTTTTATTTCATTTTTTAT
5832950 CTTATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
24 9 0.24
25 14 0.37
26 10 0.26
27 5 0.13
ACGTcount: A:0.11, C:0.08, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTGTTTTATTTCATTTTTTATTTC
Found at i:5832934 original size:11 final size:11
Alignment explanation
Indices: 5832912--5832959 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
5832902 CTTTGATTTC
5832912 TTTTTCTT-TT
1 TTTTTCTTATT
5832922 TTTTTCTTATT
1 TTTTTCTTATT
5832933 TTTTAT-TTATT
1 TTTT-TCTTATT
*
5832944 CTTTATCTTATT
1 -TTTTTCTTATT
5832956 TTTT
1 TTTT
5832960 CCCCTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
10 8 0.25
11 15 0.47
12 9 0.28
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:5836912 original size:95 final size:95
Alignment explanation
Indices: 5836724--5836924 Score: 235
Period size: 95 Copynumber: 2.1 Consensus size: 95
5836714 AGATTATAAT
* * *
5836724 ATTATATATATACAATAAAACTTGAACTATCCCTCTAAAGTAATTGGTTAAATGCCCCAACTTTA
1 ATTATA-ATATACAATAAAACTTGAACTATCCCTCTAAAGCAAATGGTTAAATGCCACAACTTTA
* * * *
5836789 TTGATAAGATTTAACTAGACCGATAAAGGTG
65 TGGATAAGATTCAACTAGACCAACAAAGGTG
* * ***
5836820 ATTATAATATACAATAAAACTT-AAGTTGTCCCTCTAAAGCAAATGGTTAAATGCCACGGGTTTA
1 ATTATAATATACAATAAAACTTGAA-CTATCCCTCTAAAGCAAATGGTTAAATGCCACAACTTTA
* *
5836884 TGGATAAGATTCAGCTAG-CTTAACAAAGGTG
65 TGGATAAGATTCAACTAGAC-CAACAAAGGTG
5836915 ATTATAATAT
1 ATTATAATAT
5836925 TGAGCTATCC
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
94 3 0.03
95 80 0.90
96 6 0.07
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (95 bp):
ATTATAATATACAATAAAACTTGAACTATCCCTCTAAAGCAAATGGTTAAATGCCACAACTTTAT
GGATAAGATTCAACTAGACCAACAAAGGTG
Found at i:5838193 original size:85 final size:85
Alignment explanation
Indices: 5838045--5838739 Score: 914
Period size: 85 Copynumber: 8.2 Consensus size: 85
5838035 CTATTCGCAA
* * *
5838045 CATAACTCAAGGCGAGAAGGGTTATCTTTCAAACAAGACCTTCGAGTTTGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
5838110 AATGCATATCAAATTTGCAG
66 AAGGCATATCAAATTTACAG
* * * *
5838130 CATAGCTCAAGGCGAGAAGGGCTATATGTCAACCAAGACCTTCGAGTTCGATTCCATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
***
5838195 AAGGCATATCAAATTCGTAG
66 AAGGCATATCAAATTTACAG
* * * *
5838215 CATAATTCAAGGCGAGAAGGGTTATATGCCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTC
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTCGATTACATTCAGCTC
*
5838280 AAAGGCATATCAAATTTATAG
65 AAAGGCATATCAAATTTACAG
* * *
5838301 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGGGTTCGATTCCATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
5838366 AAGGCATGTCAAATTTACAA
66 AAGGCATATCAAATTTACAG
* * *
5838386 CATAACTCAAGGCGAGAAGGGTTATCTTTCAGCAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
*
5838451 AAGGCATGTCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* * * *
5838471 CATAACTCAAGGCGAGAAGGGTTATCTGTCAGCAAATACCTTCGAGTTCGATTACTTTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
5838536 AAGGCATGTCAAATTTATAG
66 AAGGCATATCAAATTTACAG
* * *
5838556 CATAACTCAAAGCGAGAAGGGTTATCTGTCCACAAAGACCTTCGAGTTCGATTACATTCAGCTC-
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
5838620 AAGGACATATTAAATTTACAA
66 AAGG-CATATCAAATTTACAG
* * * * * *
5838641 CATAACTCAAGGCAAGAAGGGTTATCTGT----CAATATCTTTGAGTTCGATTCCAATCAGCTCA
1 CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
* *
5838702 AGGGCATGTCAAATTTACAG
66 AAGGCATATCAAATTTACAG
* *
5838722 CATAACTTAAGTCGAGAA
1 CATAACTCAAGGCGAGAA
5838740 AAACTATATG
Statistics
Matches: 544, Mismatches: 63, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
81 53 0.10
82 3 0.01
84 4 0.01
85 407 0.75
86 77 0.14
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (85 bp):
CATAACTCAAGGCGAGAAGGGTTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAGCTCA
AAGGCATATCAAATTTACAG
Found at i:5839212 original size:42 final size:38
Alignment explanation
Indices: 5839137--5839230 Score: 116
Period size: 42 Copynumber: 2.3 Consensus size: 38
5839127 AAGTTTTCTT
*
5839137 TATATATATATATTATAGTTTGCAAATGATTTTTGAAA
1 TATATATATATATTATAGTTTGAAAATGATTTTTGAAA
*
5839175 TATATATATAATATATATAGTTTTGAAAATGATTTTTTTAAA
1 TATATATAT-ATAT-TATAG-TTTGAAAATGA-TTTTTGAAA
*
5839217 TGTATATATTATAT
1 TATATATA-TATAT
5839231 GGTTTTTGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
38 9 0.19
39 4 0.08
40 5 0.10
41 10 0.21
42 19 0.40
43 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (38 bp):
TATATATATATATTATAGTTTGAAAATGATTTTTGAAA
Found at i:5839280 original size:37 final size:37
Alignment explanation
Indices: 5839167--5839608 Score: 308
Period size: 39 Copynumber: 11.6 Consensus size: 37
5839157 TGCAAATGAT
* **
5839167 TTTTGAAATATATATATAATATATATAGTTTTGAAAATGA
1 TTTTGAAA-ATATATAT-A-ATATATAGTTTTTAAAAACA
** * * * *
5839207 TTTTTTTAAATGTATATATTATATGGTTTTT-GAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
5839244 TTTTGAAAAT-TATATAATATATAGTTTTTAAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTT-AAAAACA
* *
5839281 TTTTG-AAA-ATATATAGTATATGGTTTTT-AAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
* * * *
5839315 TTTTGAAAACATATATATTATATAGTTTTTTAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
*
5839352 TTTTTAAAACATATATATAATATATAGTTTTTAAAAACA
1 -TTTTGAAA-ATATATATAATATATAGTTTTTAAAAACA
** *
5839391 TTTTGAAAACATATATATGTTATACAGTTTTTAAAAAAACA
1 TTTTG-AAA-ATATATATAATATATAGTTTTT--AAAAACA
* * *
5839432 TTTTAAAAACATATATATAATATATAATTTTTAAAATA-T
1 TTTT-GAAA-ATATATATAATATATAGTTTTTAAAA-ACA
* * *
5839471 TTTTGAAAAAATATATATATTATTTAGTTTTTGAAAACA
1 TTTTG--AAAATATATATAATATATAGTTTTTAAAAACA
* * * *
5839510 TTTTGAAAAT-GATATAATATATGATTTTTTTAAAACGT
1 TTTTGAAAATATATATAATATAT-AGTTTTTAAAAAC-A
*** * * **
5839548 TTTTTTTAA-ATATATAAGATATAG-TTTCAAAATATT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAA-ACA
*
5839584 TTTTGAAAAAATATATATATATATA
1 TTTTGAAAATATATATA-ATATATA
5839609 TAATATATTA
Statistics
Matches: 320, Mismatches: 59, Indels: 47
0.75 0.14 0.11
Matches are distributed among these distances:
34 11 0.03
35 20 0.06
36 68 0.21
37 43 0.13
38 44 0.14
39 84 0.26
40 11 0.03
41 39 0.12
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACA
Found at i:5839649 original size:27 final size:27
Alignment explanation
Indices: 5839611--5839664 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
5839601 TATATATATA
5839611 ATATATTATTATT-ATTATTTGTTTATT
1 ATATATTATTATTAATTATTT-TTTATT
* *
5839638 ATATATTTTTATTAATTCTTTTTTATT
1 ATATATTATTATTAATTATTTTTTATT
5839665 TTCTTTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
ATATATTATTATTAATTATTTTTTATT
Found at i:5839668 original size:12 final size:13
Alignment explanation
Indices: 5839619--5839673 Score: 51
Period size: 14 Copynumber: 4.2 Consensus size: 13
5839609 TAATATATTA
*
5839619 TTATTATTATTTGT
1 TTATTATTCTTT-T
*
5839633 TTATTATAT-ATTT
1 TTATTAT-TCTTTT
5839646 TTATTAATTCTTTT
1 TTATT-ATTCTTTT
5839660 TTATT-TTCTTTT
1 TTATTATTCTTTT
5839672 TT
1 TT
5839674 GTCAATTCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
12 9 0.25
13 7 0.19
14 19 0.53
15 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (13 bp):
TTATTATTCTTTT
Found at i:5840900 original size:23 final size:21
Alignment explanation
Indices: 5840874--5840933 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 21
5840864 TCTTTTATTA
*
5840874 TCTTTTTTTATCTTTACATTTTT
1 TCTTTTTTTA--TTTAAATTTTT
5840897 TCTTTTGATTTATTTAAATTTTT
1 TCTTTT--TTTATTTAAATTTTT
*
5840920 TATTTTTTTTATTT
1 T-CTTTTTTTATTT
5840934 TTTCCCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 7 0.22
23 17 0.53
24 4 0.12
25 4 0.12
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (21 bp):
TCTTTTTTTATTTAAATTTTT
Found at i:5845314 original size:5 final size:5
Alignment explanation
Indices: 5845304--5845329 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5845294 ATGTGAGATG
5845304 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
5845330 TATTTAGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:5845392 original size:27 final size:27
Alignment explanation
Indices: 5845354--5845421 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
5845344 ATCAATTAAT
5845354 AATAAACGTTCATATTTTTTATAAAAA
1 AATAAACGTTCATATTTTTTATAAAAA
5845381 AATAAACGTTCATATTTTTTATAAAAA
1 AATAAACGTTCATATTTTTTATAAAAA
5845408 AATAAACGTTCATA
1 AATAAACGTTCATA
5845422 CTTCTTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (27 bp):
AATAAACGTTCATATTTTTTATAAAAA
Found at i:5846113 original size:20 final size:20
Alignment explanation
Indices: 5846090--5846160 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
5846080 GGTTCCAAAT
5846090 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*** *
5846110 TCGCAACAATAATAGGTAAA
1 TCGCAACGCGAATATGTAAA
* *
5846130 TTGCAACGTGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
5846150 TCGCAACGCGA
1 TCGCAACGCGA
5846161 TTTTCCAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:5846114 original size:40 final size:40
Alignment explanation
Indices: 5846070--5846181 Score: 97
Period size: 40 Copynumber: 2.8 Consensus size: 40
5846060 AACTCCAATT
5846070 TCGCAACACAGGTTCCAAATTCGCAACGCGAATATGTAAA
1 TCGCAACACAGGTTCCAAATTCGCAACGCGAATATGTAAA
* *
5846110 TCGCAACAATAATAGG-T--AAATT-GCAACGTGAATATGTAAA
1 TCGCAAC----ACAGGTTCCAAATTCGCAACGCGAATATGTAAA
* ** *
5846150 TCGCAACGCGATTTTCCAAATTCGCAATGCGA
1 TCGCAACAC-AGGTTCCAAATTCGCAACGCGA
5846182 TTTTCAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
40 36 0.65
41 12 0.22
43 1 0.02
44 4 0.07
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (40 bp):
TCGCAACACAGGTTCCAAATTCGCAACGCGAATATGTAAA
Found at i:5846170 original size:20 final size:20
Alignment explanation
Indices: 5846150--5846199 Score: 82
Period size: 21 Copynumber: 2.5 Consensus size: 20
5846140 AATATGTAAA
5846150 TCGCAACGCGATTTTCCAAAT
1 TCGCAACGCGATTTT-CAAAT
*
5846171 TCGCAATGCGATTTTCAAAT
1 TCGCAACGCGATTTTCAAAT
5846191 TCGCAACGC
1 TCGCAACGC
5846200 CAATTACCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTTTCAAAT
Found at i:5846239 original size:57 final size:57
Alignment explanation
Indices: 5846171--5846398 Score: 375
Period size: 57 Copynumber: 4.0 Consensus size: 57
5846161 TTTTCCAAAT
*
5846171 TCGCAATGCGATTTTCAAATTCGCAACGCCAATTACCGATATAGGTAAACAGTACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* *
5846228 TCGCAACGCGATTTTCAAATTCGCAACGCTAATTGCCGATATAGGTAAACAGTACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
5846285 TCGCAATGCGATTTTAAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* * * * *
5846342 TCGTAATGCGATTTTCAAATTTGTAACGCTAATTATCGATATAGGTAAACAATACTA
1 TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
5846399 AAATTCGCGT
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 159 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (57 bp):
TCGCAATGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:5847112 original size:17 final size:17
Alignment explanation
Indices: 5847086--5847119 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5847076 TCTTTCGCCA
* *
5847086 TTTATCTTTTATTTATT
1 TTTATATTTTAATTATT
5847103 TTTATATTTTAATTATT
1 TTTATATTTTAATTATT
5847120 GACAACAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATATTTTAATTATT
Found at i:5852636 original size:18 final size:18
Alignment explanation
Indices: 5852613--5852752 Score: 246
Period size: 18 Copynumber: 7.8 Consensus size: 18
5852603 GGGTCTACGC
5852613 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
5852631 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
*
5852649 GGTCCTTCGGGGCACAGT
1 GGTCCTTCGGGACACAGT
5852667 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
5852685 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
*
5852703 GGTCCTTCGGGATACAGT
1 GGTCCTTCGGGACACAGT
5852721 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACACAGT
5852739 GGT-CTTACGGGACA
1 GGTCCTT-CGGGACA
5852753 AATTCTACGC
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
17 3 0.03
18 114 0.97
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.23
Consensus pattern (18 bp):
GGTCCTTCGGGACACAGT
Found at i:5855100 original size:2 final size:2
Alignment explanation
Indices: 5855093--5855144 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5855083 TGAATAAGAA
5855093 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
5855135 AT AT AT AT AT
1 AT AT AT AT AT
5855145 TGAGTATCGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5856971 original size:18 final size:18
Alignment explanation
Indices: 5856948--5857015 Score: 109
Period size: 18 Copynumber: 3.8 Consensus size: 18
5856938 GGGTCTACGC
*
5856948 GGTCCTTCGGGATATAGT
1 GGTCCTTCGGGACATAGT
*
5856966 GGTCCTTCGAGACATAGT
1 GGTCCTTCGGGACATAGT
*
5856984 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACATAGT
5857002 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
5857016 AATTCTACGC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:5858962 original size:20 final size:19
Alignment explanation
Indices: 5858917--5858966 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5858907 AAATAACCAA
* * *
5858917 CAAAATCGCAACGCGATTT
1 CAAATTCGCAACACAATTT
5858936 CAAATTCGCAACACAATTT
1 CAAATTCGCAACACAATTT
5858955 CTAAATTCGCAA
1 C-AAATTCGCAA
5858967 TTCGAACATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.40, C:0.26, G:0.10, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAACACAATTT
Found at i:5859565 original size:20 final size:20
Alignment explanation
Indices: 5859528--5859567 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5859518 ATTTGATTTG
* *
5859528 CGAAATTCGTGTTTCGAAAA
1 CGAAATTCGCGTTGCGAAAA
*
5859548 CGAAATTTGCGTTGCGAAAA
1 CGAAATTCGCGTTGCGAAAA
5859568 TTTTTATGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
CGAAATTCGCGTTGCGAAAA
Found at i:5860534 original size:17 final size:17
Alignment explanation
Indices: 5860512--5860550 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
5860502 ATTTATGATA
5860512 AAATCGCACGAA-TTTCT
1 AAATCGCACGAACTTT-T
5860529 AAATCGCACGAACTTTT
1 AAATCGCACGAACTTTT
5860546 AAATC
1 AAATC
5860551 AAATATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (17 bp):
AAATCGCACGAACTTTT
Found at i:5864208 original size:50 final size:50
Alignment explanation
Indices: 5864162--5864271 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 50
5864152 TCCCCTGCAT
* * * * *
5864162 CGCGTTATATGCTGATTTGATGTCACGTGGGTATAGAGCGCCCCCTGTCC
1 CGCGATATACGCTGATCTGACGTCACGTGAGTATAGAGCGCCCCCTGTCC
* * *
5864212 CGCGATATACGGTGATCTGGCGTCACGTGAGTATAGCGCGCCCCCTGAT-C
1 CGCGATATACGCTGATCTGACGTCACGTGAGTATAGAGCGCCCCCTG-TCC
*
5864262 CGCGCTATAC
1 CGCGATATAC
5864272 CTGGATATCT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.17, C:0.29, G:0.28, T:0.25
Consensus pattern (50 bp):
CGCGATATACGCTGATCTGACGTCACGTGAGTATAGAGCGCCCCCTGTCC
Found at i:5864434 original size:12 final size:10
Alignment explanation
Indices: 5864393--5864433 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
5864383 TTTATCACAC
5864393 CAAATTCTCT
1 CAAATTCTCT
5864403 CAAATTCTCT
1 CAAATTCTCT
5864413 -AAATTTCTCT
1 CAAA-TTCTCT
*
5864423 CAAATACTCT
1 CAAATTCTCT
5864433 C
1 C
5864434 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:5864756 original size:111 final size:111
Alignment explanation
Indices: 5864557--5864778 Score: 376
Period size: 111 Copynumber: 2.0 Consensus size: 111
5864547 TGGAAATCAT
5864557 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
5864622 TATTTAGTTGATTTATTATATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTATATGCATGATTATTAAATTAAGAATTAA
*
5864668 ATATCT-TGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCT-ACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
5864732 ATAATTAGTTGATTCATT-TAATGCATGATTATTAAATTAAGAATTAA
65 ATAATTAGTTGATTCATTAT-ATGCATGATTATTAAATTAAGAATTAA
5864779 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
110 2 0.02
111 103 0.98
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.45
Consensus pattern (111 bp):
ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTATATGCATGATTATTAAATTAAGAATTAA
Found at i:5866649 original size:3 final size:3
Alignment explanation
Indices: 5866641--5866693 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
5866631 ACCTGCTCAG
* * * * **
5866641 GAC GAC GAC GAT GAC GAC GAT GAC GAC GAT GAC GAT GGT GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
5866689 GAC GA
1 GAC GA
5866694 TGATAACAGT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.32, C:0.23, G:0.36, T:0.09
Consensus pattern (3 bp):
GAC
Found at i:5866658 original size:9 final size:9
Alignment explanation
Indices: 5866644--5866693 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
5866634 TGCTCAGGAC
5866644 GACGACGAT
1 GACGACGAT
5866653 GACGACGAT
1 GACGACGAT
5866662 GACGACGAT
1 GACGACGAT
* *
5866671 GACGATGGT
1 GACGACGAT
*
5866680 GACGACGAC
1 GACGACGAT
5866689 GACGA
1 GACGA
5866694 TGATAACAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.32, C:0.22, G:0.36, T:0.10
Consensus pattern (9 bp):
GACGACGAT
Found at i:5866694 original size:18 final size:18
Alignment explanation
Indices: 5866644--5866697 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
5866634 TGCTCAGGAC
*
5866644 GACGACGATGACGACGAT
1 GACGACGATGACGATGAT
*
5866662 GACGACGATGACGATGGT
1 GACGACGATGACGATGAT
*
5866680 GACGACGACGACGATGAT
1 GACGACGATGACGATGAT
5866698 AACAGTGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.31, C:0.20, G:0.35, T:0.13
Consensus pattern (18 bp):
GACGACGATGACGATGAT
Found at i:5870533 original size:50 final size:50
Alignment explanation
Indices: 5870475--5870584 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
5870465 AGCGGATCAA
* * * * *
5870475 GGGGCGCGCTATACCCACGTGGCGCTAGATCACCGTATATCGCGGGGCAG
1 GGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCACGGGGCAG
* *
5870525 GGGGCGCGCTATACCCACGTGGCGCCAAATCAGCATATAGCACGGTGCAG
1 GGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCACGGGGCAG
5870575 GGGGCGCGCT
1 GGGGCGCGCT
5870585 TTTCTACTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.19, C:0.30, G:0.36, T:0.15
Consensus pattern (50 bp):
GGGGCGCGCTATACCCACGTGGCGCCAAATCACCATATAGCACGGGGCAG
Found at i:5871582 original size:27 final size:27
Alignment explanation
Indices: 5871531--5871582 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5871521 TTGAAATTGG
*
5871531 AGTTTTTCAAAATTTTGAGTTTTTTTA
1 AGTTTTTCAAAATTTTGAGTATTTTTA
*
5871558 AGTTTTTTAAAATTTT-ATGTATTTT
1 AGTTTTTCAAAATTTTGA-GTATTTT
5871583 GAAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.62
Consensus pattern (27 bp):
AGTTTTTCAAAATTTTGAGTATTTTTA
Found at i:5878522 original size:16 final size:18
Alignment explanation
Indices: 5878498--5878541 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
5878488 TAATATGGTG
*
5878498 ATTTTAAAAT-TTATT-T
1 ATTTAAAAATATTATTAT
5878514 ATTTAAAAATATTATTAT
1 ATTTAAAAATATTATTAT
5878532 ATTTATAAAA
1 ATTTA-AAAA
5878542 GAACCCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 9 0.38
17 5 0.21
18 6 0.25
19 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTAAAAATATTATTAT
Found at i:5879269 original size:23 final size:23
Alignment explanation
Indices: 5879243--5879291 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
5879233 CTCCATCATC
5879243 ATCTAGAGTGGATTTGCATCAAT
1 ATCTAGAGTGGATTTGCATCAAT
5879266 ATCTAGAGTGGATTTGCATCAAT
1 ATCTAGAGTGGATTTGCATCAAT
5879289 ATC
1 ATC
5879292 ATCACTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (23 bp):
ATCTAGAGTGGATTTGCATCAAT
Found at i:5880223 original size:18 final size:18
Alignment explanation
Indices: 5880202--5880244 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5880192 GTTGTTTTTA
* *
5880202 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAAAT
*
5880220 AAATAAAAGAAAATAAAT
1 AAATAAAAGAAAAGAAAT
5880238 AAATAAA
1 AAATAAA
5880245 TTAAAGAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAAGAAAT
Found at i:5880501 original size:19 final size:19
Alignment explanation
Indices: 5880477--5880522 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5880467 AAGTTGAATA
5880477 TACTTCAATAAACAAATCC
1 TACTTCAATAAACAAATCC
*
5880496 TACTTCAATAAGCAAATCC
1 TACTTCAATAAACAAATCC
*
5880515 TTCTTCAA
1 TACTTCAA
5880523 ACGTTAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.30
Consensus pattern (19 bp):
TACTTCAATAAACAAATCC
Found at i:5881512 original size:30 final size:31
Alignment explanation
Indices: 5881478--5881538 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
5881468 TGTTCTGAAG
5881478 AACATAGGTAA-ATGTCCACATGTCCCGAAC
1 AACATAGGTAACATGTCCACATGTCCCGAAC
* *
5881508 AACATAGGTAATCCTGTCCATATGTCCCGAA
1 AACATAGGTAA-CATGTCCACATGTCCCGAA
5881539 GGACATAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
32 16 0.59
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (31 bp):
AACATAGGTAACATGTCCACATGTCCCGAAC
Found at i:5881545 original size:32 final size:30
Alignment explanation
Indices: 5881462--5881546 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
5881452 GAAGGACCTA
* *
5881462 TCCATATGTTCTGAAGAACATAGGTAAATG
1 TCCATATGTCCCGAAGAACATAGGTAAATG
* * *
5881492 TCCACATGTCCCGAACAACATAGGTAATCCTG
1 TCCATATGTCCCGAAGAACATAGGTAA--ATG
*
5881524 TCCATATGTCCCGAAGGACATAG
1 TCCATATGTCCCGAAGAACATAG
5881547 ATAACCCTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
30 23 0.51
32 22 0.49
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAGGTAAATG
Found at i:5883090 original size:13 final size:13
Alignment explanation
Indices: 5883072--5883104 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
5883062 ATGACAAGTC
5883072 AAATTCAACTTCT
1 AAATTCAACTTCT
5883085 AAATTCAACTTCT
1 AAATTCAACTTCT
5883098 AAATTCA
1 AAATTCA
5883105 TTAACTCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATTCAACTTCT
Found at i:5885601 original size:19 final size:19
Alignment explanation
Indices: 5885577--5885616 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5885567 GAAGTTGAAT
5885577 ATACTTCAATAAGCAAATC
1 ATACTTCAATAAGCAAATC
5885596 ATACTTCAATAAGCAAATC
1 ATACTTCAATAAGCAAATC
5885615 AT
1 AT
5885617 TCTTAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (19 bp):
ATACTTCAATAAGCAAATC
Found at i:5886631 original size:32 final size:30
Alignment explanation
Indices: 5886561--5886651 Score: 119
Period size: 32 Copynumber: 2.9 Consensus size: 30
5886551 GAATGACCTA
* * *
5886561 TCCATATGTTCCGAAGAACATTGGGTAACTG
1 TCCATATGTCCCGAAGGACA-TAGGTAACTG
*
5886592 TTCATATGTCCCGAAGGACATAGGTAATCATG
1 TCCATATGTCCCGAAGGACATAGGTAA-C-TG
5886624 TCCATATGTCCCGAAGGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
5886652 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
30 6 0.11
31 19 0.36
32 28 0.53
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGGACATAGGTAACTG
Found at i:5890730 original size:5 final size:5
Alignment explanation
Indices: 5890722--5890765 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
5890712 TAAGCATCTG
*
5890722 ATAAA ATAAA ATAAA ATAAA ATAAA AT-AA ATAAA ATGAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
5890766 TTTGGCTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:5897597 original size:2 final size:2
Alignment explanation
Indices: 5897592--5897621 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5897582 CACATATATG
5897592 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5897622 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5897678 original size:6 final size:6
Alignment explanation
Indices: 5897644--5897696 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
5897634 TATATATACA
* * *
5897644 TATCAT CATCAT CATCA- T-TCAT TATCAT TATCAT TACCAT TATCAT
1 TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT TATCAT
5897690 TATCAT T
1 TATCAT T
5897697 CACGGTTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 3 0.07
5 1 0.02
6 37 0.90
ACGTcount: A:0.32, C:0.23, G:0.00, T:0.45
Consensus pattern (6 bp):
TATCAT
Found at i:5897686 original size:18 final size:16
Alignment explanation
Indices: 5897646--5897698 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
5897636 TATATACATA
* *
5897646 TCATCATCATCATCAT
1 TCATTATCATTATCAT
5897662 TCATTATCATTATCAT
1 TCATTATCATTATCAT
5897678 TACCATTATCATTATCAT
1 T--CATTATCATTATCAT
5897696 TCA
1 TCA
5897699 CGGTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
16 17 0.52
18 16 0.48
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (16 bp):
TCATTATCATTATCAT
Found at i:5898076 original size:45 final size:45
Alignment explanation
Indices: 5898027--5898113 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
5898017 TTTTCAGATT
*
5898027 TTCACATAGTTC-AGTATCACATAGTTTATATCATATGTTCACACG
1 TTCACATAGTTCGA-TATCACATAGTTTATATCACATGTTCACACG
* *
5898072 TTCACGTAGTTCGATATCATATAGTTTATATCACATGTTCAC
1 TTCACATAGTTCGATATCACATAGTTTATATCACATGTTCAC
5898114 GTAATTCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (45 bp):
TTCACATAGTTCGATATCACATAGTTTATATCACATGTTCACACG
Found at i:5898106 original size:37 final size:37
Alignment explanation
Indices: 5898065--5898178 Score: 183
Period size: 37 Copynumber: 3.1 Consensus size: 37
5898055 TATCATATGT
* * *
5898065 TCACACGTTCACGTAGTTCGATATCATATAGTTTATA
1 TCACATGTTCACGTAGTTCGGTATCACATAGTTTATA
*
5898102 TCACATGTTCACGTAATTCGGTATCACATAGTTTATA
1 TCACATGTTCACGTAGTTCGGTATCACATAGTTTATA
*
5898139 TCACATGTTCACGTAGTTCGGTATCACATAGCTTATA
1 TCACATGTTCACGTAGTTCGGTATCACATAGTTTATA
5898176 TCA
1 TCA
5898179 TTTTCTAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (37 bp):
TCACATGTTCACGTAGTTCGGTATCACATAGTTTATA
Found at i:5898335 original size:32 final size:32
Alignment explanation
Indices: 5898299--5898364 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5898289 CATGTACATT
5898299 TAGAAACCATATAAACAACATATTATTATTCC
1 TAGAAACCATATAAACAACATATTATTATTCC
5898331 TAGAAACCATATAAACAACATATTATTATTCC
1 TAGAAACCATATAAACAACATATTATTATTCC
5898363 TA
1 TA
5898365 AAATCATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (32 bp):
TAGAAACCATATAAACAACATATTATTATTCC
Found at i:5898772 original size:19 final size:20
Alignment explanation
Indices: 5898748--5898788 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5898738 GTAATTCGTT
*
5898748 CTTAAA-AATGGTATCGATA
1 CTTAAACAATGGTATCAATA
*
5898767 CTTAAACATTGGTATCAATA
1 CTTAAACAATGGTATCAATA
5898787 CT
1 CT
5898789 CATAGTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (20 bp):
CTTAAACAATGGTATCAATA
Found at i:5902592 original size:13 final size:13
Alignment explanation
Indices: 5902574--5902608 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
5902564 TTTTATGAAT
5902574 AGTGAACAGTAAC
1 AGTGAACAGTAAC
*
5902587 AGTGAACAGTACC
1 AGTGAACAGTAAC
*
5902600 CGTGAACAG
1 AGTGAACAG
5902609 CGGGGTATCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (13 bp):
AGTGAACAGTAAC
Found at i:5902686 original size:12 final size:12
Alignment explanation
Indices: 5902669--5902693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5902659 TACCGTTCAT
5902669 TGCTACAGTAAC
1 TGCTACAGTAAC
5902681 TGCTACAGTAAC
1 TGCTACAGTAAC
5902693 T
1 T
5902694 TACGAAAATA
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:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:5907863 original size:19 final size:19
Alignment explanation
Indices: 5907835--5907880 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
5907825 AGACTAGACC
*
5907835 TCTACTCTGGCTACCATCG
1 TCTACGCTGGCTACCATCG
*
5907854 TCTACGCTGGCTACCATTG
1 TCTACGCTGGCTACCATCG
5907873 TCTACGCT
1 TCTACGCT
5907881 AGTCTTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.15, C:0.35, G:0.17, T:0.33
Consensus pattern (19 bp):
TCTACGCTGGCTACCATCG
Found at i:5908979 original size:37 final size:37
Alignment explanation
Indices: 5908936--5909009 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
5908926 CAAACTTATA
5908936 GCTCTTTATCACACATCATGTAATACTCTTATAGAGT
1 GCTCTTTATCACACATCATGTAATACTCTTATAGAGT
5908973 GCTCTTTATCACACATCATGTAATACTCTTATAGAGT
1 GCTCTTTATCACACATCATGTAATACTCTTATAGAGT
5909010 TCCCTGTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (37 bp):
GCTCTTTATCACACATCATGTAATACTCTTATAGAGT
Found at i:5910977 original size:43 final size:43
Alignment explanation
Indices: 5910918--5911040 Score: 174
Period size: 43 Copynumber: 2.9 Consensus size: 43
5910908 TTTTTATACA
* **
5910918 AAAAACGCCGCAATAGGTATTGATATTTAGCGGCGTTTGTGTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
* *
5910961 ACAAACACCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
* * *
5911004 AAAAATGCCACAATAGGTGTTGATATTTAGCGACGTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTT
5911041 GATATTTAGC
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAG
Found at i:5911043 original size:16 final size:16
Alignment explanation
Indices: 5911022--5911056 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5911012 CACAATAGGT
5911022 GTTGATATTTAGCGAC
1 GTTGATATTTAGCGAC
5911038 GTTGATATTTAGCGAC
1 GTTGATATTTAGCGAC
5911054 GTT
1 GTT
5911057 TTTTAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (16 bp):
GTTGATATTTAGCGAC
Found at i:5911101 original size:43 final size:43
Alignment explanation
Indices: 5911038--5911272 Score: 217
Period size: 42 Copynumber: 5.5 Consensus size: 43
5911028 ATTTAGCGAC
* * * ** *
5911038 GTTGATATTTAGCGACGTTTTTTAGATAAACGCCGCAGTAGGT
1 GTTGATGTTTTGCGGCGTTTTTTCCACAAACGCCGCAGTAGGT
* * *
5911081 GTTGATGTTTTGCGGTG-TTTTCCCACAAACGCCGCAGTAGAT
1 GTTGATGTTTTGCGGCGTTTTTTCCACAAACGCCGCAGTAGGT
* * * *
5911123 GTTGATGTTTTGCGGC-ATTTTCCCATAAACGCCGCAGTAGAT
1 GTTGATGTTTTGCGGCGTTTTTTCCACAAACGCCGCAGTAGGT
* * * * * *
5911165 GTTGATGTTTTACGTCGTTTATTCCACAAATGTCGTAGTAGG-
1 GTTGATGTTTTGCGGCGTTTTTTCCACAAACGCCGCAGTAGGT
* *
5911207 GTTTGATGTTTTGCAGCG-TTTTTCTCACAAACGCCGCAATAGGT
1 G-TTGATGTTTTGCGGCGTTTTTTC-CACAAACGCCGCAGTAGGT
* *
5911251 ATTGATTTTTTGCGGCGTTTTT
1 GTTGATGTTTTGCGGCGTTTTT
5911273 GCTAAAAACA
Statistics
Matches: 154, Mismatches: 32, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
42 79 0.51
43 71 0.46
44 4 0.03
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.38
Consensus pattern (43 bp):
GTTGATGTTTTGCGGCGTTTTTTCCACAAACGCCGCAGTAGGT
Found at i:5917159 original size:2 final size:2
Alignment explanation
Indices: 5917154--5917208 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
5917144 TTCTTCAACA
5917154 AT AT AT AT AT AT A- AT AT AT AT AT A- AT AT A- 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
5917193 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
5917209 TAAAAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5920912 original size:41 final size:41
Alignment explanation
Indices: 5920765--5921155 Score: 408
Period size: 41 Copynumber: 9.4 Consensus size: 41
5920755 TTATAAATAC
* *
5920765 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-TAA
* * * * * *
5920807 AAACGCCACAAAAGTACGAGTTTATAGTGTCGTTTGCATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTA-TAA
* *
5920849 AAATGCCACTAAAGTACGAGTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
5920890 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * * * *
5920931 AAATGCTACTAAAGTACGAGTCTTTAGCGGCGGTTT-CATTCA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGC-GTTTGTA-TAA
* * * * *
5920973 AAACGCCACTAAAGTACAAGTTTATAGCAGTGTTTAG-ATTTA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-GTA-TAA
* * *
5921015 AAACGCCACTAAAGTATGAGTATATAGCGGCGTTTGTATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * **
5921056 AAACGCCACTAAAGTACTAGTATATAGCGGTTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
5921097 AAACGCCACTAAATTACGATTCTATAGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
5921138 AAGCGCTACTAAAGTACG
1 AAACGCCACTAAAGTACG
5921156 TACCTATAAC
Statistics
Matches: 290, Mismatches: 54, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
41 158 0.54
42 132 0.46
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:5921025 original size:125 final size:124
Alignment explanation
Indices: 5920765--5921154 Score: 421
Period size: 125 Copynumber: 3.1 Consensus size: 124
5920755 TTATAAATAC
* * * *
5920765 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATTCAAAACGCCACAAAAGTACGAGTTT
1 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTA-TAAAAACGCCACTAAAGTACGAGTTT
* * * * *
5920830 ATAGTGTCGTTTGCATTCAAAATGCCACTAAAGTACGAGTCTATAGCGGTGTTTGTATAA
65 ATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACAAGTCTATAGCAGTGTTTGTATAA
* * *
5920890 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTATATAAAAATGCTACTAAAGTACGAGTCTT
1 AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGT-TT
* *
5920955 -TAGCGGCGGTTT-CATTCAAAACGCCACTAAAGTACAAGTTTATAGCAGTGTTTAG-ATTTA
65 ATAGCGGC-GTTTGCATTCAAAACGCCACTAAAGTACAAGTCTATAGCAGTGTTT-GTA-TAA
* * * *
5921015 AAACGCCACTAAAGTA-TGAGTATATAGCGGCGTTTGTATAGAAACGCCACTAAAGTACTAGTAT
1 AAACGCCACTAAAGTACT-AGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTTT
** * * * * * * * *
5921079 ATAGCGGTTTTTGTA-TAAAAACGCCACTAAATTACGATTCTATAGCGGCGTTTTTATAA
65 ATAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACAAGTCTATAGCAGTGTTTGTATAA
* *
5921138 AAGCGCTACTAAAGTAC
1 AAACGCCACTAAAGTAC
5921155 GTACCTATAA
Statistics
Matches: 221, Mismatches: 35, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
123 16 0.07
124 100 0.45
125 105 0.48
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (124 bp):
AAACGCCACTAAAGTACTAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTTTA
TAGCGGCGTTTGCATTCAAAACGCCACTAAAGTACAAGTCTATAGCAGTGTTTGTATAA
Found at i:5921052 original size:166 final size:166
Alignment explanation
Indices: 5920765--5921154 Score: 520
Period size: 166 Copynumber: 2.4 Consensus size: 166
5920755 TTATAAATAC
* *
5920765 AAACGCCACTAAAGTACGAGTCTTTAGCGGC-GTTTGTATTCAAAACGCCACAAAAGTACGAGTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGGTTT-TATTCAAAACGCCACTAAAGTACAAGTT
* * * *
5920829 TATAGTGTCGTTTGCATTCAAAATGCCACTAAAGTACGAGTCTATAGCGGTGTTTGTATAAAAAC
65 TATAGAGTCGTTTGCATTCAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTATAAAAAC
*
5920894 GCCACTAAAGTACTAGTCTATAGCGGCGTTTATATAA
130 GCCACTAAAGTACTAGTATATAGCGGCGTTTATATAA
* * *
5920931 AAATGCTACTAAAGTACGAGTCTTTAGCGGCGGTTTCATTCAAAACGCCACTAAAGTACAAGTTT
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGGTTTTATTCAAAACGCCACTAAAGTACAAGTTT
* * *
5920996 ATAGCAGT-GTTTAG-ATTTAAAACGCCACTAAAGTATGAGTATATAGCGGCGTTTGTATAGAAA
66 ATAG-AGTCGTTT-GCATTCAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTATAAAAA
** *
5921059 CGCCACTAAAGTACTAGTATATAGCGGTTTTTGTATAA
129 CGCCACTAAAGTACTAGTATATAGCGGCGTTTATATAA
* * * * *
5921097 AAACGCCACTAAATTACGATTCTATAGCGGCGTTTTTA-T-AAAAGCGCTACTAAAGTAC
1 AAACGCCACTAAAGTACGAGTCTTTAGCGGCGGTTTTATTCAAAA-CGCCACTAAAGTAC
5921155 GTACCTATAA
Statistics
Matches: 196, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
164 4 0.02
165 14 0.07
166 171 0.87
167 7 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (166 bp):
AAACGCCACTAAAGTACGAGTCTTTAGCGGCGGTTTTATTCAAAACGCCACTAAAGTACAAGTTT
ATAGAGTCGTTTGCATTCAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTTGTATAAAAACG
CCACTAAAGTACTAGTATATAGCGGCGTTTATATAA
Found at i:5921643 original size:40 final size:40
Alignment explanation
Indices: 5921573--5921747 Score: 156
Period size: 41 Copynumber: 4.3 Consensus size: 40
5921563 ATTTAACATT
** *
5921573 TTGCGGCGTTTATAAAAAAAACGCTACTATTGATTACACAA
1 TTGCGGCGTTTAT-CTAAAAACGCCACTATTGATTACACAA
* * * * *
5921614 TTGTGGCGTTTGT-TAAAAAGTGCCACTATTGATTAAAACTA
1 TTGCGGCGTTTATCTAAAAA-CGCCACTATTGATT-ACACAA
* *
5921655 TTGCGGCGTTTTTCTAAAAACGCCACTAGTGATTA-ACATTA
1 TTGCGGCGTTTATCTAAAAACGCCACTATTGATTACACA--A
* * *
5921696 TTGCGGCGTTTATCTAAAAACGCCATTATTTATTATCACTA
1 TTGCGGCGTTTATCTAAAAACGCCACTATTGATTA-CACAA
*
5921737 TTGTGGCGTTT
1 TTGCGGCGTTT
5921748 TAAGAATAAA
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
39 7 0.06
40 13 0.12
41 81 0.74
42 6 0.06
43 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGGCGTTTATCTAAAAACGCCACTATTGATTACACAA
Found at i:5921704 original size:82 final size:81
Alignment explanation
Indices: 5921589--5921748 Score: 189
Period size: 82 Copynumber: 2.0 Consensus size: 81
5921579 CGTTTATAAA
* * * * *
5921589 AAAAACGCTACTATTGATTACACAATTGTGGCGTTTGT-TAAAAAGTGCCACTATTGATTAAAAC
1 AAAAACGCCACTAGTGATTACACAATTGCGGCGTTTATCTAAAAA-CGCCACTATTGATTAAAAC
5921653 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
* * **
5921670 AAAAACGCCACTAGTGATTA-ACATTATTGCGGCGTTTATCTAAAAACGCCATTATTTATTATCA
1 AAAAACGCCACTAGTGATTACACA--ATTGCGGCGTTTATCTAAAAACGCCACTATTGATTAAAA
*
5921734 CTATTGTGGCGTTTT
64 CTATTGCGGCGTTTT
5921749 AAGAATAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
80 3 0.05
81 18 0.27
82 39 0.59
83 6 0.09
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (81 bp):
AAAAACGCCACTAGTGATTACACAATTGCGGCGTTTATCTAAAAACGCCACTATTGATTAAAACT
ATTGCGGCGTTTTTCT
Found at i:5926021 original size:15 final size:15
Alignment explanation
Indices: 5926003--5926032 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5925993 ATTATAAAAA
*
5926003 AATATTATTCTTTTT
1 AATAATATTCTTTTT
5926018 AATAATATTCTTTTT
1 AATAATATTCTTTTT
5926033 CGCAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
AATAATATTCTTTTT
Found at i:5937079 original size:31 final size:31
Alignment explanation
Indices: 5937041--5937101 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
5937031 AGACAACATG
*
5937041 ATTGTAAAATCTCAACCGGCTTGTAAATTGA
1 ATTGTAAAATCTCAACCGACTTGTAAATTGA
5937072 ATTGTAAAATCTCAACCGACTTGTAAATTG
1 ATTGTAAAATCTCAACCGACTTGTAAATTG
5937102 TAGTCTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (31 bp):
ATTGTAAAATCTCAACCGACTTGTAAATTGA
Found at i:5943796 original size:17 final size:17
Alignment explanation
Indices: 5943769--5943807 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
5943759 AATTTACAAT
5943769 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
5943785 TAATTATAAATAATATC
1 TAATTATAAATAATATC
5943802 TAATTA
1 TAATTA
5943808 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:5950955 original size:25 final size:25
Alignment explanation
Indices: 5950910--5950957 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5950900 TCTTTTACCA
*
5950910 TCTTTCTTTATAATGGTTTCTTTCT
1 TCTTTCTTTATAATGATTTCTTTCT
*
5950935 TCTTTCTTT-TGATGATATTCTTT
1 TCTTTCTTTATAATGAT-TTCTTT
5950958 ATAACATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.65
Consensus pattern (25 bp):
TCTTTCTTTATAATGATTTCTTTCT
Found at i:5961669 original size:2 final size:2
Alignment explanation
Indices: 5961664--5961691 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5961654 CTTTATGTTC
5961664 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
5961692 GCATGTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5969535 original size:30 final size:32
Alignment explanation
Indices: 5969489--5969566 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
5969479 TTTAAATAGT
5969489 TATTATATTTTATATT-AAT-ATAATTATATAAA
1 TATTAT-TTTT-TATTAAATAATAATTATATAAA
* *
5969521 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATT-AAATAATAATTATATAAA
5969554 TATTATTTATTTA
1 TATTATTT-TTTA
5969567 AATTTATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 9 0.22
33 19 0.47
34 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTTTTATTAAATAATAATTATATAAA
Found at i:5969558 original size:33 final size:30
Alignment explanation
Indices: 5969468--5969589 Score: 90
Period size: 32 Copynumber: 4.0 Consensus size: 30
5969458 TATTTTTCAG
* * * *
5969468 TTATTATTATTTTTAAATAGTTATTATATTT
1 TTATTAATATATTTATATAATTATTAT-TTT
* *
5969499 TATATTAATATAATTATATAAATATTATTTT
1 T-TATTAATATATTTATATAATTATTATTTT
5969530 TTATTAAAATAATATTTATATAATTATTATTTAT
1 TTATT--AAT-ATATTTATATAATTATTATTT-T
* *
5969564 TTA--AATTTATTAAT-TAATTATT-TTTT
1 TTATTAATATATTTATATAATTATTATTTT
5969590 GTGCTAATTA
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
26 1 0.01
27 3 0.04
28 8 0.11
29 6 0.08
30 7 0.09
31 5 0.07
32 23 0.30
33 19 0.25
34 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (30 bp):
TTATTAATATATTTATATAATTATTATTTT
Found at i:5971342 original size:42 final size:42
Alignment explanation
Indices: 5971266--5971370 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
5971256 ATGCCACAAT
* * * *
5971266 GGTACATGCCCAGCCCTCCACTTCAGATGCCATCTCCTCAGG
1 GGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGG
* * *
5971308 GGTATATGCCAAGCCCACCAGTTCATATGTCATCTCCGCAGG
1 GGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGG
* * *
5971350 GTTACATTCCTAGCCCACCAG
1 GGTACATGCCAAGCCCACCAG
5971371 GTTACATGCC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
GGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCGCAGG
Found at i:5971959 original size:34 final size:34
Alignment explanation
Indices: 5971916--5972014 Score: 162
Period size: 34 Copynumber: 2.9 Consensus size: 34
5971906 ATAAATGTTT
5971916 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
5971950 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
*
5971984 TTAAAATATAAATTATAGTATTCGAAATTTA
1 TTAAAATACAAATTATAGTATTCGAAATTTA
5972015 GCATTAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:5972672 original size:127 final size:126
Alignment explanation
Indices: 5972445--5973077 Score: 1025
Period size: 127 Copynumber: 5.0 Consensus size: 126
5972435 GCGCTTTAAA
*
5972445 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGATATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATA-GG
5972510 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
65 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
5972572 GTCCCCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGC
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGC
* * *
5972637 TAATGATAACATATTCTCTGACAAAATAATAGAAGGCGTGCCCCCGGGAATGCGCCTTCACG
66 -AATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
5972699 GTCCCCTAAGGAATAATAGGTATTGATATGAATAGTTCCC-GGGGACATAAGTTACATAATAGGA
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGG-
* * * **
5972763 CAATAATAACATATTCTCTGACAAAATAATGGAAGGTGCGCCCCGGGGAATACGCCTTCACG
65 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
5972825 GTCCCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATA-GG
* * * *
5972890 TAATGATAACATATTCTCTGACAAAATAATGGAAGGTGCGCCCCCGGGAACGCGCTTTCATG
65 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
5972952 GTCCCCTAAGGAACAATAGGAATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATA-GG
*
5973017 CAATGATATCATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAC
65 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAC
5973078 ATGAATAGTA
Statistics
Matches: 468, Mismatches: 34, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
126 117 0.25
127 349 0.75
128 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (126 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGC
AATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:5972896 original size:253 final size:254
Alignment explanation
Indices: 5972445--5973077 Score: 1061
Period size: 253 Copynumber: 2.5 Consensus size: 254
5972435 GCGCTTTAAA
*
5972445 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGATATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
5972510 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTC
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTC
5972575 CCCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGCTAA
131 CCCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGCTAA
* *
5972640 TGATAACATATTCTCTGACAAAATAATAGAAGGCGTGCCCCCGGGAATGCGCCTTCACG
196 TGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* * *
5972699 GTCCCCTAAGGAATAATAGGTATTGATATGAATAGTTCCC-GGGGACATAAGTTACATAATAGGA
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* * * **
5972763 CAATAATAACATATTCTCTGACAAAATAATGGAAGGTGCGCCCCGGGGAATACGCCTTCACGGTC
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTC
* * * *
5972828 CCTTAAGGAATAATAGGTATTGACATGAATAGTTCTCGGGGGACATAAGTGACATAATAGGGTAA
131 CCCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGCTAA
* * * *
5972893 TGATAACATATTCTCTGACAAAATAATGGAAGGTGCGCCCCCGGGAACGCGCTTTCATG
196 TGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
5972952 GTCCCCTAAGGAACAATAGGAATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
*
5973017 CAATGATATCATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAC
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAC
5973078 ATGAATAGTA
Statistics
Matches: 348, Mismatches: 30, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
253 232 0.67
254 116 0.33
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (254 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGGTC
CCCTAAGGAATAATAAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGCTAA
TGATAACATATTCTCTGACAAAATAATAGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:5977183 original size:2 final size:2
Alignment explanation
Indices: 5977178--5977218 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5977168 GCCAAAAAAC
5977178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5977219 TCTTTTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5980407 original size:18 final size:18
Alignment explanation
Indices: 5980384--5980433 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
5980374 CCAGTTCAAC
5980384 TCCAAGACCAAACTCAGA
1 TCCAAGACCAAACTCAGA
* *
5980402 TCCAAGTACCCACCTCAGA
1 TCCAAG-ACCAAACTCAGA
*
5980421 TCCAAGACAAAAC
1 TCCAAGACCAAAC
5980434 CAATCCTCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.42, C:0.36, G:0.10, T:0.12
Consensus pattern (18 bp):
TCCAAGACCAAACTCAGA
Found at i:5984732 original size:32 final size:30
Alignment explanation
Indices: 5984696--5984772 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
5984686 CGGGGCCGTG
*
5984696 AGGCCTACCTAAGAACACATCTTAGGGCCGC
1 AGGCCTACCTAAGAA-ACATCTCAGGGCCGC
** **
5984727 AAGGCCTACCCGAGAATGATCTCAGGGCCGC
1 -AGGCCTACCTAAGAAACATCTCAGGGCCGC
5984758 AGAGCCTACCTAAGA
1 AG-GCCTACCTAAGA
5984773 GTCACATTAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 2 0.05
31 22 0.59
32 13 0.35
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.14
Consensus pattern (30 bp):
AGGCCTACCTAAGAAACATCTCAGGGCCGC
Found at i:5984755 original size:63 final size:63
Alignment explanation
Indices: 5984649--5984772 Score: 148
Period size: 63 Copynumber: 2.0 Consensus size: 63
5984639 CCCTAAGGGA
* * *
5984649 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGA-GCCTACCTAAGAAC
*
5984712 ACATCTTAGGGCC-GCA-AGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGA-GCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
5984773 GTCACATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
62 3 0.06
63 48 0.91
64 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:5985653 original size:7 final size:7
Alignment explanation
Indices: 5985641--5985671 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
5985631 GTCAAAGGAA
5985641 GTCAACG
1 GTCAACG
5985648 GTCAACG
1 GTCAACG
5985655 GTCAACG
1 GTCAACG
*
5985662 ATCAACG
1 GTCAACG
5985669 GTC
1 GTC
5985672 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:5985689 original size:17 final size:17
Alignment explanation
Indices: 5985663--5985737 Score: 96
Period size: 17 Copynumber: 4.3 Consensus size: 17
5985653 CGGTCAACGA
*
5985663 TCAACGGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
*
5985680 TCAACAGTCGGGTCGGA
1 TCAACAGTCGGGTCGGG
5985697 TCAACAGTCGGGTCGGG
1 TCAACAGTCGGGTCGGG
**
5985714 TCGGGTCAGTCGGGTCGGG
1 TC--AACAGTCGGGTCGGG
5985733 TCAAC
1 TCAAC
5985738 CCGGTTCAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
17 34 0.69
19 15 0.31
ACGTcount: A:0.16, C:0.24, G:0.41, T:0.19
Consensus pattern (17 bp):
TCAACAGTCGGGTCGGG
Found at i:5985727 original size:14 final size:14
Alignment explanation
Indices: 5985708--5985735 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5985698 CAACAGTCGG
5985708 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
5985722 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
5985736 ACCCGGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:5985776 original size:20 final size:19
Alignment explanation
Indices: 5985731--5985782 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
5985721 AGTCGGGTCG
* *
5985731 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
* *
5985750 GGCCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
5985770 GGTCAAACCGGTT
1 GGTCAAACCGGTT
5985783 TTCCAGCAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.27, C:0.31, G:0.25, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:5990431 original size:21 final size:21
Alignment explanation
Indices: 5990405--5990487 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
5990395 CAGATCCCCA
*
5990405 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
5990426 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* * *
5990446 CAAAGGGGGAATCGGTTCCCTCAG-
1 ---GGGGGGAATCGATTCCC-CTGT
5990470 GGGGAGGAATCGATTCCC
1 GGGG-GGAATCGATTCCC
5990488 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 20 0.40
22 12 0.24
23 16 0.32
24 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:5990466 original size:22 final size:22
Alignment explanation
Indices: 5990427--5990488 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
5990417 TTCCCCTGTG
5990427 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCCTTCAAA
**
5990450 GGGGGAATCGGTTCCC-TCAGG
1 GGGGGAATCGGTTCCCTTCAAA
*
5990471 GGGAGGAATCGATTCCCT
1 GGG-GGAATCGGTTCCCT
5990489 CTGCACCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.18
22 15 0.44
23 13 0.38
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.21
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCTTCAAA
Found at i:6001122 original size:32 final size:31
Alignment explanation
Indices: 6001036--6001160 Score: 92
Period size: 31 Copynumber: 4.0 Consensus size: 31
6001026 ACCCTAAGGG
* *
6001036 AACATCTTAGGGCCTG-AGAGCCTACCCAAGA
1 AACATCTCAGGGCC-GCAGAGCCTACCTAAGA
* * * * *
6001067 TAGATTTCGGGGCCG-TGAAGCCTACCTAAGA
1 AACATCTCAGGGCCGCAG-AGCCTACCTAAGA
* * **
6001098 ACACATCTTAGGGCCGCAGGGCCTACCCGAGA
1 A-ACATCTCAGGGCCGCAGAGCCTACCTAAGA
**
6001130 ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 AACATCTCAGGGCCGCAGAGCCTACCTAAGA
6001161 GTCACATTAG
Statistics
Matches: 69, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
30 2 0.03
31 45 0.65
32 21 0.30
33 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.26, T:0.17
Consensus pattern (31 bp):
AACATCTCAGGGCCGCAGAGCCTACCTAAGA
Found at i:6001143 original size:63 final size:63
Alignment explanation
Indices: 6001037--6001160 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
6001027 CCCTAAGGGA
* * *
6001037 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCG-TGAAGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAG-AGCCTACCTAAGAAC
* *
6001100 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
6001161 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 2 0.04
63 50 0.94
64 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Done.