Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 49
Found at i:2038830 original size:38 final size:38
Alignment explanation
Indices: 2038786--2038884 Score: 171
Period size: 38 Copynumber: 2.6 Consensus size: 38
2038776 TTCGAGATTT
*
2038786 ATGACAGGTTCTTCGGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
*
2038824 ATGACAGGTCCTTCAGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
*
2038862 ATGATAGGTCCTTCGGGACACAG
1 ATGACAGGTCCTTCGGGACACAG
2038885 TTTATACGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 57 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.24
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
Found at i:2039304 original size:6 final size:6
Alignment explanation
Indices: 2039293--2039364 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
2039283 AAATGGGTTC
* * * *
2039293 ATGATA ATGATA GA-GATC ATGATA ATGATA ATGATA TTGATG TTGATA
1 ATGATA ATGATA -ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
*
2039341 ATGATA GA-GATC ATGATA ATGATA
1 ATGATA -ATGATA ATGATA ATGATA
2039365 TTAATGTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
5 2 0.04
6 50 0.93
7 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (6 bp):
ATGATA
Found at i:2039314 original size:18 final size:18
Alignment explanation
Indices: 2039291--2039396 Score: 88
Period size: 18 Copynumber: 5.6 Consensus size: 18
2039281 TTAAATGGGT
2039291 TCATGATAATGATAGAGA
1 TCATGATAATGATAGAGA
2039309 TCATGATAATGATAATGATATTGA
1 TCATGATAATGAT-A-G--A--GA
**
2039333 TGTTGATAATGATAGAGA
1 TCATGATAATGATAGAGA
*
2039351 TCATGATAATGATATTA-A
1 TCATGATAATGATA-GAGA
** *
2039369 TGTTGAGAATGATAGAGA
1 TCATGATAATGATAGAGA
2039387 TCATGATAAT
1 TCATGATAAT
2039397 AATATTGAGG
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.01
18 47 0.69
19 2 0.03
20 2 0.03
22 2 0.03
23 1 0.01
24 13 0.19
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (18 bp):
TCATGATAATGATAGAGA
Found at i:2039325 original size:24 final size:24
Alignment explanation
Indices: 2039293--2039364 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
2039283 AAATGGGTTC
2039293 ATGATAATGATAGAGATCATGATA
1 ATGATAATGATAGAGATCATGATA
*
2039317 ATGATAATGAT----AT--TGATG
1 ATGATAATGATAGAGATCATGATA
*
2039335 TTGATAATGATAGAGATCATGATA
1 ATGATAATGATAGAGATCATGATA
2039359 ATGATA
1 ATGATA
2039365 TTAATGTTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
18 14 0.37
20 2 0.05
22 2 0.05
24 20 0.53
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (24 bp):
ATGATAATGATAGAGATCATGATA
Found at i:2039357 original size:36 final size:36
Alignment explanation
Indices: 2039317--2039404 Score: 149
Period size: 36 Copynumber: 2.4 Consensus size: 36
2039307 GATCATGATA
*
2039317 ATGATAATGATATTGATGTTGATAATGATAGAGATC
1 ATGATAATGATATTGATGTTGAGAATGATAGAGATC
*
2039353 ATGATAATGATATTAATGTTGAGAATGATAGAGATC
1 ATGATAATGATATTGATGTTGAGAATGATAGAGATC
*
2039389 ATGATAATAATATTGA
1 ATGATAATGATATTGA
2039405 GGTTAATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.42, C:0.02, G:0.20, T:0.35
Consensus pattern (36 bp):
ATGATAATGATATTGATGTTGAGAATGATAGAGATC
Found at i:2039411 original size:42 final size:38
Alignment explanation
Indices: 2039298--2039397 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 38
2039288 GGTTCATGAT
* *
2039298 AATGATAGAGATCATGATAATGATAATGATATTGATGTTGAT
1 AATGATAGAGATCATGATAAT-AT-ATG--ATTAATGTTGAG
*
2039340 AATGATAGAGATCATGATAAT-GAT-ATTAATGTTGAG
1 AATGATAGAGATCATGATAATATATGATTAATGTTGAG
2039376 AATGATAGAGATCATGATAATA
1 AATGATAGAGATCATGATAATA
2039398 ATATTGAGGT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
36 31 0.57
39 2 0.04
42 21 0.39
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (38 bp):
AATGATAGAGATCATGATAATATATGATTAATGTTGAG
Found at i:2041251 original size:70 final size:70
Alignment explanation
Indices: 2041166--2041319 Score: 218
Period size: 70 Copynumber: 2.2 Consensus size: 70
2041156 CGTTTCAATT
** * * *
2041166 AACACTAAATAAACATATTAGCGAAGATATAAATGAAAATATTGCCATACCTTAAATAAATATAT
1 AACACTAAACGAACATATTAACGAAGATATAAATGAAAATATTGCCAAACCTTAAATAAACATAT
2041231 TCATA
66 TCATA
* * **
2041236 AACACTAAACGAACATATTAACGAAGATATGAATGAAAATATTGTCAAATGTTAAATAAACATAT
1 AACACTAAACGAACATATTAACGAAGATATAAATGAAAATATTGCCAAACCTTAAATAAACATAT
2041301 TCATA
66 TCATA
*
2041306 CACACTAAACGAAC
1 AACACTAAACGAAC
2041320 CAAACACGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.26
Consensus pattern (70 bp):
AACACTAAACGAACATATTAACGAAGATATAAATGAAAATATTGCCAAACCTTAAATAAACATAT
TCATA
Found at i:2043881 original size:194 final size:200
Alignment explanation
Indices: 2043552--2043944 Score: 647
Period size: 194 Copynumber: 2.0 Consensus size: 200
2043542 TAAATTGATA
2043552 AAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATC
1 AAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATC
*
2043617 GAAATAATTTTAAATTGTGAGGTTTAAATTAATGCAAAAAATACTAAATTATACCCATTTAAAAA
66 GAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAATACTAAATTATACCCATTTAAAAA
2043682 GTTATGGACCAACT-AAAAA-TAGAAATAAGT-AT-G-A-GTCAATTTCAGATGCAAATATAATT
131 GTTATGGACCAACTAAAAAATTAGAAATAAGTAATAGTAGGTCAATTTCAGATGCAAATATAATT
2043741 TGACC
196 TGACC
* *
2043746 AAATATGAAATTACAAATAAAATTTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATT
1 AAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATC
*
2043811 GAAATAATTTTAAATTGTGAGGTTTAAATTAATACAACAAAGTACTAAATTATA-CCATTTAAAA
66 GAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA-AAAATACTAAATTATACCCATTTAAAA
* *
2043875 AGTTATGGGCCAACTAAAAAATTAGAAATAAGTAATAAGTATAGGTCAATTTCATATGCAAATAT
130 AGTTATGGACCAACTAAAAAATTAGAAATAAGTAAT-AG--TAGGTCAATTTCAGATGCAAATAT
2043940 AATTT
192 AATTT
2043945 TAAGGACTAA
Statistics
Matches: 183, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
194 123 0.67
195 20 0.11
196 11 0.06
197 2 0.01
199 1 0.01
202 1 0.01
203 25 0.14
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (200 bp):
AAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAGGGATCAAATC
GAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAATACTAAATTATACCCATTTAAAAA
GTTATGGACCAACTAAAAAATTAGAAATAAGTAATAGTAGGTCAATTTCAGATGCAAATATAATT
TGACC
Found at i:2044141 original size:20 final size:20
Alignment explanation
Indices: 2044118--2044161 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2044108 TATATATATA
2044118 ATATAAACTATATAGT-TTAT
1 ATATAAACTATAT-GTATTAT
*
2044138 ATATAAAGTATATGTATTAT
1 ATATAAACTATATGTATTAT
2044158 ATAT
1 ATAT
2044162 TGTAACAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATAAACTATATGTATTAT
Found at i:2044963 original size:5 final size:5
Alignment explanation
Indices: 2044919--2044951 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2044909 GACCCGAATT
*
2044919 GACCC GA-CC GACCC GACCC AACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC
2044952 TTTGACCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:2052197 original size:10 final size:9
Alignment explanation
Indices: 2052174--2052262 Score: 52
Period size: 10 Copynumber: 9.3 Consensus size: 9
2052164 ATGCTGGAAA
2052174 ACCGGTTTG
1 ACCGGTTTG
2052183 ACCGGTTTCG
1 ACCGGTTT-G
**
2052193 ACCGGTTCAA
1 ACCGGTT-TG
*
2052203 ACCGGTCTG
1 ACCGGTTTG
**
2052212 AACTAGTTTG
1 -ACCGGTTTG
* *
2052222 ATCGGTTCG
1 ACCGGTTTG
*
2052231 AACCGGTCTG
1 -ACCGGTTTG
2052241 AACCGGTTTG
1 -ACCGGTTTG
*
2052251 ACCGGTCTG
1 ACCGGTTTG
2052260 ACC
1 ACC
2052263 CGAACCGAAC
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
9 24 0.41
10 35 0.59
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:2052249 original size:29 final size:29
Alignment explanation
Indices: 2052172--2052256 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
2052162 AGATGCTGGA
*
2052172 AAACCGGTTTG-ACCGGTTTCGACCGGTTC
1 AAACCGGTCTGAACCGGTTT-GACCGGTTC
** *
2052201 AAACCGGTCTGAACTAGTTTGATCGGTTC
1 AAACCGGTCTGAACCGGTTTGACCGGTTC
*
2052230 GAACCGGTCTGAACCGGTTTGACCGGT
1 AAACCGGTCTGAACCGGTTTGACCGGT
2052257 CTGACCCGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 41 0.87
30 6 0.13
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (29 bp):
AAACCGGTCTGAACCGGTTTGACCGGTTC
Found at i:2053832 original size:2 final size:2
Alignment explanation
Indices: 2053825--2053908 Score: 61
Period size: 2 Copynumber: 42.5 Consensus size: 2
2053815 AGGGGGTTAC
* * *
2053825 AT AT AT AT A- AA ACT AT AT AT -T TT AT AT TT AT AT -T AT -T AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2053864 AT ACT AT AT AT -T AT AT AT AT AT AT ACT AT AT AT AA ACT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
2053906 AT A
1 AT A
2053909 CCATGTATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
1 5 0.07
2 56 0.84
3 6 0.09
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2053880 original size:7 final size:7
Alignment explanation
Indices: 2053838--2053896 Score: 64
Period size: 7 Copynumber: 8.0 Consensus size: 7
2053828 TATATAAAAC
2053838 TATATAT
1 TATATAT
*
2053845 TTTATATT
1 TATATA-T
2053853 TATATTAT
1 TATA-TAT
*
2053861 TATATAC
1 TATATAT
2053868 TATATAT
1 TATATAT
2053875 TATATAT
1 TATATAT
*
2053882 ATATATAC
1 -TATATAT
2053890 TATATAT
1 TATATAT
2053897 AAACTATATA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 26 0.60
8 15 0.35
9 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (7 bp):
TATATAT
Found at i:2053884 original size:11 final size:11
Alignment explanation
Indices: 2053826--2053908 Score: 75
Period size: 11 Copynumber: 7.7 Consensus size: 11
2053816 GGGGGTTACA
*
2053826 TATATATAAAAC
1 TATATAT-ATAC
*
2053838 TATATAT-T-T
1 TATATATATAC
* *
2053847 TATATTTATAT
1 TATATATATAC
2053858 TAT-TATATAC
1 TATATATATAC
2053868 TATATATTATA-
1 TATATA-TATAC
2053879 TATATATATAC
1 TATATATATAC
*
2053890 TATATATAAAC
1 TATATATATAC
2053901 TATATATA
1 TATATATA
2053909 CCATGTATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
9 6 0.10
10 13 0.22
11 30 0.50
12 11 0.18
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATATATAC
Found at i:2053997 original size:22 final size:20
Alignment explanation
Indices: 2053957--2054127 Score: 91
Period size: 22 Copynumber: 8.4 Consensus size: 20
2053947 ACTATTGAAC
* * *
2053957 TATATAGAAACTACATAGTT
1 TATATATAAATTATATAGTT
2053977 TATTAATATAAATTATATAGTT
1 TA-T-ATATAAATTATATAGTT
**
2053999 TATATATAAATTATATATGAAA
1 TATATATAAATTATATA-G-TT
* * * *
2054021 TATGTATAAACTATACAATT
1 TATATATAAATTATATAGTT
* * *
2054041 TATATTTATA-TAT-TA-TG
1 TATATATAAATTATATAGTT
* *
2054058 TATAGTTATAAATAATATA-TA
1 TATA--TATAAATTATATAGTT
*
2054079 T-TGTATAAATTATATAGTT
1 TATATATAAATTATATAGTT
*
2054098 TATTAATATAAACTATATAGTT
1 TA-T-ATATAAATTATATAGTT
2054120 TATATATA
1 TATATATA
2054128 TACATGGTTT
Statistics
Matches: 114, Mismatches: 25, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
17 5 0.04
18 13 0.11
19 9 0.08
20 31 0.27
21 9 0.08
22 47 0.41
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:2054061 original size:17 final size:17
Alignment explanation
Indices: 2054041--2054094 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
2054031 CTATACAATT
* *
2054041 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
2054058 TATAGTTATAAATAATA
1 TATATTTATAAATTATA
2054075 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
2054093 TA
1 TA
2054095 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:2054274 original size:13 final size:13
Alignment explanation
Indices: 2054248--2054287 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
2054238 CTATATAGTT
*
2054248 TATATATGAACTA
1 TATATATAAACTA
*
2054261 TATGTATAAACTA
1 TATATATAAACTA
2054274 TATATATAAACTA
1 TATATATAAACTA
2054287 T
1 T
2054288 GTAAACTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:2054340 original size:24 final size:24
Alignment explanation
Indices: 2054294--2054343 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2054284 CTATGTAAAC
*
2054294 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGAACTATA
*
2054318 TATATAGTTTA-TTAGTGAACTATA
1 TATATAGTTTACATA-TGAACTATA
2054342 TA
1 TA
2054344 AACTATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (24 bp):
TATATAGTTTACATATGAACTATA
Found at i:2054441 original size:27 final size:27
Alignment explanation
Indices: 2054382--2054441 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
2054372 ATATATAAAA
2054382 ATTATAGTTTATATTTATATACTACAT
1 ATTATAGTTTATATTTATATACTACAT
* *
2054409 ACTATAGTTTATATTTATATACTATAT
1 ATTATAGTTTATATTTATATACTACAT
*
2054436 TTTATA
1 ATTATA
2054442 CTATTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTATAGTTTATATTTATATACTACAT
Found at i:2054443 original size:12 final size:13
Alignment explanation
Indices: 2054391--2054466 Score: 52
Period size: 13 Copynumber: 5.8 Consensus size: 13
2054381 AATTATAGTT
2054391 TATATTTATATAC
1 TATATTTATATAC
* * *
2054404 TACATACTATAGT-T
1 TATAT-TTATA-TAC
2054418 TATATTTATATAC
1 TATATTTATATAC
2054431 TATATTT-TATAC
1 TATATTTATATAC
2054443 --TATTTATATAAGC
1 TATATTTATAT-A-C
2054456 TATAGTTTATA
1 TATA-TTTATA
2054467 GAAATCCTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
10 5 0.10
11 3 0.06
12 7 0.15
13 16 0.33
14 8 0.17
15 3 0.06
16 6 0.12
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:2054458 original size:25 final size:23
Alignment explanation
Indices: 2054407--2054466 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 23
2054397 TATATACTAC
2054407 ATACTATAG-TT-TA-TATTTAT
1 ATACTATAGTTTATACTATTTAT
*
2054427 ATACTATATTTTATACTATTTAT
1 ATACTATAGTTTATACTATTTAT
2054450 ATAAGCTATAGTTTATA
1 AT-A-CTATAGTTTATA
2054467 GAAATCCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 2 0.06
23 9 0.27
24 1 0.03
25 11 0.33
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.52
Consensus pattern (23 bp):
ATACTATAGTTTATACTATTTAT
Found at i:2054706 original size:35 final size:36
Alignment explanation
Indices: 2054635--2054708 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 36
2054625 ACAATAGTTA
**
2054635 ATATATGTAACCTATAGTATATGTATACATGTAAACT
1 ATATATGTAACCTATAGTATATGTATA-ATACAAACT
* * *
2054672 ATATATGTAACTTATAGTATTTGTAT-GTACAAACT
1 ATATATGTAACCTATAGTATATGTATAATACAAACT
2054707 AT
1 AT
2054709 GTATAGTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 8 0.25
37 24 0.75
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (36 bp):
ATATATGTAACCTATAGTATATGTATAATACAAACT
Found at i:2054717 original size:20 final size:20
Alignment explanation
Indices: 2054694--2054791 Score: 55
Period size: 20 Copynumber: 5.0 Consensus size: 20
2054684 TATAGTATTT
* *
2054694 GTATGTACAAACTATGTATA
1 GTATATACAAACTATATATA
*
2054714 GTATATATAAACTATATATA
1 GTATATACAAACTATATATA
2054734 -TATA-AC---CTATAGTATA
1 GTATATACAAACTATA-TATA
* *
2054750 TGTAAATATACAATCTATTTATA
1 -GT--ATATACAAACTATATATA
*
2054773 TGT-TATATAAACTATATAT
1 -GTATATACAAACTATATAT
2054792 GTAACCTATA
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
15 5 0.08
16 4 0.07
18 2 0.03
19 4 0.07
20 33 0.54
21 2 0.03
23 7 0.11
24 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (20 bp):
GTATATACAAACTATATATA
Found at i:2054733 original size:57 final size:56
Alignment explanation
Indices: 2054666--2054803 Score: 172
Period size: 57 Copynumber: 2.4 Consensus size: 56
2054656 TGTATACATG
* * *
2054666 TAAACTATATATGTAACTTATAGTATTTGT-ATGTACAAACTATGTATA-GTATATA
1 TAAACTATATATGTAACCTATAGTATATGTAATATACAAACTATGTATATGT-TATA
* * *
2054721 TAAACTATATATATATAACCTATAGTATATGTAAATATACAATCTATTTATATGTTATA
1 TAAAC--TATATATGTAACCTATAGTATATGT-AATATACAAACTATGTATATGTTATA
2054780 TAAACTATATATGTAACCTATAGT
1 TAAACTATATATGTAACCTATAGT
2054804 TTATAAACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
55 5 0.07
57 40 0.56
59 24 0.34
60 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (56 bp):
TAAACTATATATGTAACCTATAGTATATGTAATATACAAACTATGTATATGTTATA
Found at i:2054735 original size:15 final size:16
Alignment explanation
Indices: 2054710--2054759 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
2054700 ACAAACTATG
2054710 TATAGTATATATAAAC
1 TATAGTATATATAAAC
*
2054726 TATA-TATATATAACC
1 TATAGTATATATAAAC
*
2054741 TATAGTATATGTAAA-
1 TATAGTATATATAAAC
2054756 TATA
1 TATA
2054760 CAATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (16 bp):
TATAGTATATATAAAC
Found at i:2054767 original size:24 final size:23
Alignment explanation
Indices: 2054731--2054775 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
2054721 TAAACTATAT
*
2054731 ATATATAACCTATAGTATATGTAA
1 ATATACAACCTAT-GTATATGTAA
* *
2054755 ATATACAATCTATTTATATGT
1 ATATACAACCTATGTATATGT
2054776 TATATAAACT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (23 bp):
ATATACAACCTATGTATATGTAA
Found at i:2054941 original size:31 final size:29
Alignment explanation
Indices: 2054900--2055112 Score: 146
Period size: 31 Copynumber: 6.8 Consensus size: 29
2054890 TATTGTACTA
* *
2054900 TATAGTTTATATTAATGTTAATTATCTTAAC
1 TATAATTTATATTAATATTAATT-T-TTAAC
2054931 TATAATTTATATTAATATAGTATATAGTTTATAAAC
1 TATAATTTATATTAATAT--TA-AT--TTT-T-AAC
2054967 TAT-A-TTATATTAATATTAATTATATTAAC
1 TATAATTTATATTAATATTAATT-T-TTAAC
* * *
2054996 TATAGTTTATAAACTATACTATATAATTTATAAC
1 TATAATTTAT--A-T-TAATAT-TAATTTTTAAC
2055030 ATATAATTTATATTAATATTAATTTTATAGAC
1 -TATAATTTATATTAATATTAATTTT-TA-AC
*
2055062 TATAATTTATATTAATATTAA-TTATAA-
1 TATAATTTATATTAATATTAATTTTTAAC
* *
2055089 TATATAATTATTTTAATATTAATT
1 TATA-ATTTATATTAATATTAATT
2055113 AAATAGTTTA
Statistics
Matches: 150, Mismatches: 11, Indels: 44
0.73 0.05 0.21
Matches are distributed among these distances:
27 4 0.03
28 16 0.11
29 10 0.07
30 10 0.07
31 51 0.34
32 5 0.03
33 4 0.03
34 20 0.13
35 18 0.12
36 12 0.08
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (29 bp):
TATAATTTATATTAATATTAATTTTTAAC
Found at i:2055003 original size:43 final size:43
Alignment explanation
Indices: 2054939--2055087 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
2054929 ACTATAATTT
*
2054939 ATATTAA-TATAGT-ATATAGTTTATAAACTATA-TTATATTA
1 ATATTAATTATATTAATATAGTTTATAAACTATACTTATATTA
2054979 ATATTAATTATATTAACTATAGTTTATAAACTATACTATATAATTTATA
1 ATATTAATTATATTAA-TATAGTTTATAAACTATACT-TAT-A--T-TA
* * * *
2055028 ACATATAATTTATATTAATATTAATTTTATAGACTATAATTTATATTA
1 ATAT-TAA-TTATATTAATA-T-AGTTTATAAACTAT-ACTTATATTA
2055076 ATATTAATTATA
1 ATATTAATTATA
2055088 ATATATAATT
Statistics
Matches: 89, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
40 7 0.08
41 5 0.06
42 1 0.01
43 18 0.20
44 1 0.01
45 3 0.03
46 6 0.07
47 3 0.03
48 6 0.07
49 6 0.07
50 5 0.06
51 11 0.12
52 15 0.17
53 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (43 bp):
ATATTAATTATATTAATATAGTTTATAAACTATACTTATATTA
Found at i:2055020 original size:14 final size:14
Alignment explanation
Indices: 2054960--2055021 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2054950 GTATATAGTT
2054960 TATAAACTATATTA
1 TATAAACTATATTA
*
2054974 TATTAA-TATTAATTA
1 TATAAACTA-T-ATTA
*
2054989 TATTAACTATAGTT-
1 TATAAACTATA-TTA
*
2055003 TATAAACTATACTA
1 TATAAACTATATTA
2055017 TATAA
1 TATAA
2055022 TTTATAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.08
14 22 0.55
15 13 0.32
16 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (14 bp):
TATAAACTATATTA
Found at i:2057152 original size:36 final size:36
Alignment explanation
Indices: 2057100--2057368 Score: 394
Period size: 36 Copynumber: 7.3 Consensus size: 36
2057090 AGAAATACAA
*
2057100 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
*
2057136 GAATGGAAGGAGGCATCGGCACTTCCGTTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCA----C--TTCCGATTCAAGTC
2057178 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
*
2057214 GAACGGAAGGAAGCATCGGCACTTCCGATTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * *
2057250 GAACGGAAGGAAGCATCGGCACCTCCGAGTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
* * *
2057286 GAACGGAATGAGGCATCGGCCCTTCCGAGTCAAGTC
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
*
2057322 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTA
1 GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
2057358 GAACGGAAGGA
1 GAACGGAAGGA
2057369 TGTATCGCAC
Statistics
Matches: 213, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
36 177 0.83
38 1 0.00
40 1 0.00
42 34 0.16
ACGTcount: A:0.29, C:0.25, G:0.30, T:0.16
Consensus pattern (36 bp):
GAACGGAAGGAGGCATCGGCACTTCCGATTCAAGTC
Found at i:2061724 original size:13 final size:13
Alignment explanation
Indices: 2061705--2061742 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2061695 TAATTTAGTG
2061705 ATTATAAATAA-A
1 ATTATAAATAAGA
2061717 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
2061732 ATTATAAATAA
1 ATTATAAATAA
2061743 TATAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:2061798 original size:38 final size:39
Alignment explanation
Indices: 2061739--2061815 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
2061729 AGAATTATAA
2061739 ATAATATAAAGAATTAGAATTAATATAAAAA-TCAAATTT
1 ATAATATAAAGAATTAGAATTAATATAAAAACT-AAATTT
* *
2061778 ATAATATACA-AATTATAATTAATATAAAAACTAAATTT
1 ATAATATAAAGAATTAGAATTAATATAAAAACTAAATTT
2061816 CAAAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 25 0.71
39 10 0.29
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (39 bp):
ATAATATAAAGAATTAGAATTAATATAAAAACTAAATTT
Found at i:2061802 original size:18 final size:19
Alignment explanation
Indices: 2061722--2061805 Score: 77
Period size: 19 Copynumber: 4.5 Consensus size: 19
2061712 ATAAAATTTA
*
2061722 TAATAT-AAGAATTATAAA
1 TAATATAAAGAATTATAAT
*
2061740 TAATATAAAGAATTAGAAT
1 TAATATAAAGAATTATAAT
*
2061759 TAATATAAA-AATCA-AATTT
1 TAATATAAAGAATTATAA--T
*
2061778 ATAATATACA-AATTATAAT
1 -TAATATAAAGAATTATAAT
2061797 TAATATAAA
1 TAATATAAA
2061806 AACTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
17 2 0.04
18 18 0.33
19 21 0.38
20 12 0.22
21 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
TAATATAAAGAATTATAAT
Found at i:2062858 original size:17 final size:17
Alignment explanation
Indices: 2062836--2062874 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
2062826 TGAATCAAAT
2062836 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2062853 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
2062870 -AATTA
1 TAATTA
2062875 ATTGTAAATT
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:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:2063402 original size:37 final size:36
Alignment explanation
Indices: 2063306--2063423 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
2063296 GACAATCAAC
*
2063306 TTTTAAAAAATAG-TTTTCAAAGTTTGGTAAATGTT
1 TTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
2063341 TATTTG-AAAAT-GTTTTTCAAAGTTTGGTAAATGTT
1 T-TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
*
2063376 TCTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTT
1 T-TTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
*
2063413 TGTTGAAAAAT
1 TTTTGAAAAAT
2063424 TGTAATGTGA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
34 1 0.01
35 33 0.44
36 17 0.23
37 24 0.32
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (36 bp):
TTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTT
Found at i:2067431 original size:18 final size:19
Alignment explanation
Indices: 2067396--2067432 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2067386 CACGGAATGT
2067396 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2067416 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2067433 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2068579 original size:37 final size:36
Alignment explanation
Indices: 2068496--2068598 Score: 165
Period size: 35 Copynumber: 2.9 Consensus size: 36
2068486 TTGTTAAAAG
2068496 TTCAAAGTTTGGTAAATGTTTCTTTG-AAAATGGTT
1 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTT
2068531 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTT
1 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGG-TT
* *
2068568 TTCAAAGTTTGGTAGATGTTT-ATTGAAAAAT
1 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAAT
2068599 TGTAATGTGA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
35 26 0.41
36 16 0.25
37 22 0.34
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (36 bp):
TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTT
Found at i:2069553 original size:4 final size:4
Alignment explanation
Indices: 2069544--2069574 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2069534 CAATGCATGT
2069544 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
2069575 GTTGAGCAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2076035 original size:30 final size:28
Alignment explanation
Indices: 2075984--2076044 Score: 70
Period size: 31 Copynumber: 2.1 Consensus size: 28
2075974 ACCCACCATT
*
2075984 TTTCAAAATTACCAATTTGGTCCCCTAACA
1 TTTCAAAATTACCAATATGGT-CCCTAA-A
*
2076014 TTTCAAAAATTATCAA-ATGGTCCCTAAA
1 TTTC-AAAATTACCAATATGGTCCCTAAA
2076042 TTT
1 TTT
2076045 TTTTAAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.14
29 6 0.21
30 8 0.29
31 10 0.36
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (28 bp):
TTTCAAAATTACCAATATGGTCCCTAAA
Found at i:2085217 original size:29 final size:29
Alignment explanation
Indices: 2085172--2085342 Score: 192
Period size: 29 Copynumber: 6.0 Consensus size: 29
2085162 ACCGTTGACC
*
2085172 GGGTGTTAGTTTT-GTAATTATTTTTAAAA
1 GGGTGTTA-TTTTCGTAAATATTTTTAAAA
* * *
2085201 TGGTGCTATTTTCGTAATTATTTTTAAAA
1 GGGTGTTATTTTCGTAAATATTTTTAAAA
*
2085230 GGGTGTTATTTTCGT--AT-TTTTAAAAAA
1 GGGTGTTATTTTCGTAAATATTTT-TAAAA
**
2085257 ATGTGTTA-TTTCGTAAATATTTTTTAAAA
1 GGGTGTTATTTTCGTAAATA-TTTTTAAAA
*
2085286 -GGTTTTATTTTCGTAAATATTTTTAAAA
1 GGGTGTTATTTTCGTAAATATTTTTAAAA
*
2085314 GGGTGTTAGTTTCGTAAATATTTTTAAAA
1 GGGTGTTATTTTCGTAAATATTTTTAAAA
2085343 AGGGCGATAA
Statistics
Matches: 121, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
26 10 0.08
27 11 0.09
28 20 0.17
29 76 0.63
30 4 0.03
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (29 bp):
GGGTGTTATTTTCGTAAATATTTTTAAAA
Found at i:2085316 original size:84 final size:85
Alignment explanation
Indices: 2085174--2085329 Score: 235
Period size: 84 Copynumber: 1.8 Consensus size: 85
2085164 CGTTGACCGG
* * * *
2085174 GTGTTAGTTTTGTAATTATTTTTAAAATGGTGCTATTTTCGTAATTATTTTTAAAAGGGTGTTAT
1 GTGTTAGTTTCGTAAATATTTTTAAAATGGTGCTATTTTCGTAAATATTTTTAAAAGGGTGTTAG
2085239 TTTCGTATTTTTAAAAAAAT
66 TTTCGTATTTTTAAAAAAAT
**
2085259 GTGTTA-TTTCGTAAATATTTTTTAAAA-GGTTTTATTTTCGTAAATATTTTTAAAAGGGTGTTA
1 GTGTTAGTTTCGTAAATA-TTTTTAAAATGGTGCTATTTTCGTAAATATTTTTAAAAGGGTGTTA
2085322 GTTTCGTA
65 GTTTCGTA
2085330 AATATTTTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
84 49 0.77
85 15 0.23
ACGTcount: A:0.29, C:0.04, G:0.16, T:0.51
Consensus pattern (85 bp):
GTGTTAGTTTCGTAAATATTTTTAAAATGGTGCTATTTTCGTAAATATTTTTAAAAGGGTGTTAG
TTTCGTATTTTTAAAAAAAT
Found at i:2085361 original size:30 final size:29
Alignment explanation
Indices: 2085264--2085354 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 29
2085254 AAAATGTGTT
***
2085264 ATTTCGTAAATATTTTTTAAAA-GGTTTTA
1 ATTTCGTAAATA-TTTTTAAAAGGGCGATA
* * *
2085293 TTTTCGTAAATATTTTTAAAAGGGTGTTA
1 ATTTCGTAAATATTTTTAAAAGGGCGATA
*
2085322 GTTTCGTAAATATTTTTAAAAAGGGCGATA
1 ATTTCGTAAATATTTTT-AAAAGGGCGATA
2085352 ATT
1 ATT
2085355 GTGTAAAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
28 9 0.17
29 33 0.61
30 12 0.22
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.46
Consensus pattern (29 bp):
ATTTCGTAAATATTTTTAAAAGGGCGATA
Found at i:2085986 original size:2 final size:2
Alignment explanation
Indices: 2085979--2086019 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2085969 TGTTTTAAAG
2085979 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
2086020 TTGAATATTG
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:2092492 original size:29 final size:29
Alignment explanation
Indices: 2092451--2092529 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
2092441 CGGGTGTTAG
*
2092451 TTTTGTAATTATTTTTAAAATGATGCTAT
1 TTTTGTAATTATTTTTAAAAGGATGCTAT
*
2092480 TTTTGTAATTATTTTTAAAAGGGTGCTAT
1 TTTTGTAATTATTTTTAAAAGGATGCTAT
** *
2092509 TTTCATAATTTTTTTTTAAAA
1 TTTTGTAA-TTATTTTTAAAA
2092530 AAAGTGCTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.30, C:0.04, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTTGTAATTATTTTTAAAAGGATGCTAT
Found at i:2092578 original size:29 final size:29
Alignment explanation
Indices: 2092539--2092611 Score: 121
Period size: 29 Copynumber: 2.6 Consensus size: 29
2092529 AAAAGTGCTG
* *
2092539 GTAAATATTTTTAAAA-TGTGTTATTTTC
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
2092567 GTAAATATTTTTAAAAGGGTGTTAGTTTC
1 GTAAATATTTTTAAAAGGGTGTTAGTTTC
2092596 GTAAATATTTTTAAAA
1 GTAAATATTTTTAAAA
2092612 AAGGTGATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
28 16 0.38
29 26 0.62
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.48
Consensus pattern (29 bp):
GTAAATATTTTTAAAAGGGTGTTAGTTTC
Found at i:2092607 original size:83 final size:83
Alignment explanation
Indices: 2092455--2092613 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 83
2092445 TGTTAGTTTT
* * * * *
2092455 GTAATTATTTTTAAAATGATGCTATTTTTGTAATTATTTTTAAAAGGGTGCTATTTTCATAATTT
1 GTAAATATTTTTAAAATGATGCTATTTTCGTAAATATTTTTAAAAGGGTGCTAGTTTCATAA-AT
*
2092520 TTTTTTAAAAAAAGTGCTG
65 ATTTTTAAAAAAAGTGCTG
* * *
2092539 GTAAATATTTTTAAAATG-TGTTATTTTCGTAAATATTTTTAAAAGGGTGTTAGTTTCGTAAATA
1 GTAAATATTTTTAAAATGATGCTATTTTCGTAAATATTTTTAAAAGGGTGCTAGTTTCATAAATA
2092603 TTTTTAAAAAA
66 TTTTTAAAAAA
2092614 GGTGATAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
82 12 0.18
83 37 0.56
84 17 0.26
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (83 bp):
GTAAATATTTTTAAAATGATGCTATTTTCGTAAATATTTTTAAAAGGGTGCTAGTTTCATAAATA
TTTTTAAAAAAAGTGCTG
Found at i:2107415 original size:10 final size:10
Alignment explanation
Indices: 2107372--2107409 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
2107362 AACAAAGGAG
2107372 CTCT-CCTCT
1 CTCTCCCTCT
2107381 CTCTCCCTCT
1 CTCTCCCTCT
2107391 CTCTCCCTCT
1 CTCTCCCTCT
2107401 CTCTCCCTC
1 CTCTCCCTC
2107410 CTTCTCGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 4 0.14
10 24 0.86
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCCCTCT
Found at i:2110830 original size:55 final size:55
Alignment explanation
Indices: 2110769--2110879 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 55
2110759 ACTTACGATA
* * * *
2110769 AACCAAAATCTTTCAATTTTCCCAACAATTTGGTGTCAAATTCCTTCATAAAGAC
1 AACCAAAATCCTTCAATTTTCCCAACAAATTGATGTCAAATTCCTTCAGAAAGAC
2110824 AACCAAAATCCTTCAATTTTCCCAACAAATTGATGTCAAATTCCTTCAGAAAGAC
1 AACCAAAATCCTTCAATTTTCCCAACAAATTGATGTCAAATTCCTTCAGAAAGAC
2110879 A
1 A
2110880 TTCTTTCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.39, C:0.24, G:0.07, T:0.30
Consensus pattern (55 bp):
AACCAAAATCCTTCAATTTTCCCAACAAATTGATGTCAAATTCCTTCAGAAAGAC
Found at i:2111344 original size:21 final size:21
Alignment explanation
Indices: 2111318--2111372 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
2111308 ATTCTGACTA
2111318 TCGCGTTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTCCCAAAT
* *
2111339 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTCCCAAAT
**
2111360 TCGCAATGCGATT
1 TCGCGTTGCGATT
2111373 AATTCGCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATTTCCCAAAT
Found at i:2111377 original size:16 final size:16
Alignment explanation
Indices: 2111356--2111389 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2111346 GCGATTTTCC
2111356 TAATTCGCAATGCGAT
1 TAATTCGCAATGCGAT
2111372 TAATTCGCAATGCGAT
1 TAATTCGCAATGCGAT
2111388 TA
1 TA
2111390 CGTAAATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (16 bp):
TAATTCGCAATGCGAT
Found at i:2111401 original size:20 final size:20
Alignment explanation
Indices: 2111376--2111429 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
2111366 TGCGATTAAT
*
2111376 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGAAAA
* **
2111396 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTACGAAAA
2111417 TCGCAATGCGATT
1 TCGCAATGCGATT
2111430 TACATAGCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGATTACGAAAA
Found at i:2111630 original size:22 final size:22
Alignment explanation
Indices: 2111605--2111666 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 22
2111595 GGCGACATCC
2111605 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
2111627 GTCCCCA----CGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
2111645 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
2111667 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:2112013 original size:14 final size:14
Alignment explanation
Indices: 2111994--2112027 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2111984 ACTATCGCAA
2111994 TGCGATTC-TGTCGT
1 TGCGATTCTTG-CGT
2112008 TGCGATTCTTGCGT
1 TGCGATTCTTGCGT
2112022 TGCGAT
1 TGCGAT
2112028 AGTCAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.09, C:0.21, G:0.29, T:0.41
Consensus pattern (14 bp):
TGCGATTCTTGCGT
Found at i:2112043 original size:20 final size:20
Alignment explanation
Indices: 2112018--2112067 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2112008 TGCGATTCTT
2112018 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
2112038 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
2112058 GTGTTGCGAT
1 GCGTTGCGAT
2112068 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:2112073 original size:20 final size:20
Alignment explanation
Indices: 2112035--2112089 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
2112025 GATAGTCAAA
* **
2112035 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
2112055 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
2112075 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
2112090 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:2112097 original size:20 final size:20
Alignment explanation
Indices: 2112054--2112097 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2112044 CGATAGTCAT
** *
2112054 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
2112074 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
2112094 TTTC
1 TTTC
2112098 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:2113998 original size:20 final size:20
Alignment explanation
Indices: 2113973--2114076 Score: 123
Period size: 20 Copynumber: 5.5 Consensus size: 20
2113963 AGAATAGTTT
2113973 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2113993 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
2114009 A--ATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
2114027 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
2114047 ACTATCGCAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
2114067 ACTATCGCAA
1 ACTATCGCAA
2114077 CGAAAGAATC
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.08
16 4 0.06
17 4 0.06
18 4 0.06
19 3 0.04
20 51 0.71
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:2114175 original size:20 final size:20
Alignment explanation
Indices: 2114121--2114189 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
2114111 GCGATTCTCT
**
2114121 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
2114141 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
*
2114161 CATTGCGATAGTCATTTTTG
1 CATTGCGATAGTCATTTTCG
*
2114181 CGTTGCGAT
1 CATTGCGAT
2114190 TTTGTTGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:2125406 original size:14 final size:14
Alignment explanation
Indices: 2125387--2125422 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2125377 ATTGTTTAAT
2125387 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
2125401 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
2125415 TGATTTGT
1 TGATTTGT
2125423 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2125562 original size:34 final size:34
Alignment explanation
Indices: 2125524--2125619 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
2125514 AAAACAAACT
* *
2125524 ATCGCAACGCGGAAATGAATATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
2125558 ATCGCAATGC-GAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
2125591 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
2125620 CGAAATTAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2125615 original size:20 final size:19
Alignment explanation
Indices: 2125557--2125625 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
2125547 GCAACGAGAG
2125557 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2125576 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2125590 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
2125610 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
2125626 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.07
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2125673 original size:19 final size:20
Alignment explanation
Indices: 2125629--2125682 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2125619 GCGAAATTAG
*
2125629 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
2125649 TTTCGCATTGCGATTTTCA-
1 TTTCGCATTGCGATTTTCAT
2125668 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
2125683 CTCTCGTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:2125750 original size:40 final size:40
Alignment explanation
Indices: 2125687--2125778 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
2125677 GCGATTCTCT
*
2125687 CGTTACGATAGTCATTTCCGTGTTACAATAGTCA-ATTCCG
1 CGTTGCGATAGTCATTTCCGTGTTACAATAGTCATATT-CG
* * *
2125727 CGTTGCGATAGTCATTTCTGTGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCATTTCCGTGTTACAATAGTCATATTCG
2125767 CGTTGCGATAGT
1 CGTTGCGATAGT
2125779 TAAATGAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 44 0.94
41 3 0.06
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (40 bp):
CGTTGCGATAGTCATTTCCGTGTTACAATAGTCATATTCG
Found at i:2125771 original size:20 final size:20
Alignment explanation
Indices: 2125687--2125778 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
2125677 GCGATTCTCT
*
2125687 CGTTACGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * * *
2125707 TGTTACAATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
2125727 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
*
2125747 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
2125767 CGTTGCGATAGT
1 CGTTGCGATAGT
2125779 TAAATGAATG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:2128228 original size:24 final size:24
Alignment explanation
Indices: 2128194--2128247 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2128184 CTGAAAAATC
2128194 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
2128218 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
2128242 ATCAAA
1 ATCAAA
2128248 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:2128261 original size:24 final size:24
Alignment explanation
Indices: 2128194--2128261 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2128184 CTGAAAAATC
* * *
2128194 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
2128218 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
2128242 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
2128262 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:2129132 original size:20 final size:20
Alignment explanation
Indices: 2129109--2129177 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
2129099 CAGAATCTCG
*
2129109 TTGCGATTTACAG-ATTTGCA
1 TTGCGATTTAC-GTATTCGCA
2129129 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
2129149 TTACGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
*
2129169 TTACGATTT
1 TTGCGATTT
2129178 TCCAAAGAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:2129373 original size:41 final size:41
Alignment explanation
Indices: 2129326--2129590 Score: 426
Period size: 41 Copynumber: 6.5 Consensus size: 41
2129316 ATTCGCGCTG
* * *
2129326 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTCT-ACAGT-GTCGTTGCGATTTTC
2129367 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
2129408 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGGTTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
2129449 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
2129490 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
* **
2129531 CATTTCGCGTTCCGATAGTCTACAGTGTCGTTGTAATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
*
2129572 CATTTTGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2129591 TTTAAAAATG
Statistics
Matches: 212, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
40 1 0.00
41 210 0.99
42 1 0.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTC
Found at i:2129376 original size:20 final size:20
Alignment explanation
Indices: 2129351--2129546 Score: 93
Period size: 20 Copynumber: 9.6 Consensus size: 20
2129341 TAGTTGAAAA
*
2129351 TCGCGTTGCGGTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
2129371 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
2129392 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
* * *
2129412 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
*
2129433 T-GTCGTTGCGGTTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
* * *
2129453 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
2129474 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
* * *
2129494 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
2129515 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
*
2129535 TCGCGTTCCGAT
1 TCGCGTTGCGAT
2129547 AGTCTACAGT
Statistics
Matches: 128, Mismatches: 28, Indels: 40
0.65 0.14 0.20
Matches are distributed among these distances:
19 16 0.12
20 53 0.41
21 43 0.34
22 16 0.12
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2130412 original size:6 final size:6
Alignment explanation
Indices: 2130396--2130427 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
2130386 TCTTGTCTCG
2130396 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2130428 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2130567 original size:41 final size:41
Alignment explanation
Indices: 2130509--2130774 Score: 319
Period size: 41 Copynumber: 6.5 Consensus size: 41
2130499 CCATTTTTAA
*
2130509 AACTATCGCAACGCGAAATGGAAAATCACAACGAC-ACTGT-
1 AACTATCGCAACGCGAAATGGAAAATCGCAACG-CGACTGTC
2130549 AGACTATCGCAACGCGAAATGGAAAATCGCAACGAC-ACTGT-
1 A-ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGACTGTC
*
2130590 AGACTATCGCAACGCGAAATGGAAAATCACAACGAC-ACTGT-
1 A-ACTATCGCAACGCGAAATGGAAAATCGCAACG-CGACTGTC
* * * * * *
2130631 AGACTATCGCAACGTGAAATAGAAAACCGCAATGCGATTTTC
1 A-ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTC
* * *
2130673 AACTATCGCAACGCGAAATGGAAAACCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTC
* *
2130714 AACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTC
2130755 AACTATCGCAACGCGAAATG
1 AACTATCGCAACGCGAAATG
2130775 CAGCGCGAAT
Statistics
Matches: 210, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
40 2 0.01
41 207 0.99
42 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (41 bp):
AACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGTC
Found at i:2130600 original size:21 final size:21
Alignment explanation
Indices: 2130537--2130644 Score: 75
Period size: 21 Copynumber: 5.2 Consensus size: 21
2130527 TGGAAAATCA
2130537 CAACGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
* **
2130558 CAACG-CGAAATG--GAAAATCG
1 CAACGAC--ACTGTAGACTATCG
2130578 CAACGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
* ** *
2130599 CAACG-CGAAATG--GAAAATCA
1 CAACGAC--ACTGTAGACTATCG
2130619 CAACGACACTGTAGACTATCG
1 CAACGACACTGTAGACTATCG
2130640 CAACG
1 CAACG
2130645 TGAAATAGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 20
0.65 0.14 0.21
Matches are distributed among these distances:
19 6 0.10
20 23 0.37
21 28 0.44
22 6 0.10
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (21 bp):
CAACGACACTGTAGACTATCG
Found at i:2130650 original size:82 final size:82
Alignment explanation
Indices: 2130509--2130774 Score: 378
Period size: 82 Copynumber: 3.2 Consensus size: 82
2130499 CCATTTTTAA
2130509 AACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
1 AACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
* *
2130574 ATCGCAACGAC-ACTGT-
66 ATCGCAACG-CGATTTTC
* *
2130590 AGACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGTGAAATAGAA
1 A-ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGGAA
* *
2130655 AACCGCAATGCGATTTTC
65 AATCGCAACGCGATTTTC
* * * *
2130673 AACTATCGCAACGCGAAATGGAAAACCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAATGGA
1 AACTATCGCAACGCGAAATGGAAAATCACAACGAC-ACTGT-AGACTATCGCAACGCGAAATGGA
2130736 AAATCGCAACGCGATTTTC
64 AAATCGCAACGCGATTTTC
2130755 AACTATCGCAACGCGAAATG
1 AACTATCGCAACGCGAAATG
2130775 CAGCGCGAAT
Statistics
Matches: 166, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
81 3 0.02
82 161 0.97
83 2 0.01
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (82 bp):
AACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAGACTATCGCAACGCGAAATGGAAA
ATCGCAACGCGATTTTC
Found at i:2130688 original size:21 final size:21
Alignment explanation
Indices: 2130658--2130770 Score: 104
Period size: 21 Copynumber: 5.5 Consensus size: 21
2130648 AATAGAAAAC
*
2130658 CGCAATGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** ** * *
2130679 CGCAACGCGAAATGGAA-AAC
1 CGCAACGCGATTTTCAACTAT
2130699 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
** ** *
2130720 CGCAACGCGAAATGGAA-AAT
1 CGCAACGCGATTTTCAACTAT
2130740 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
2130761 CGCAACGCGA
1 CGCAACGCGA
2130771 AATGCAGCGC
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
20 29 0.43
21 38 0.57
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:2130977 original size:21 final size:21
Alignment explanation
Indices: 2130953--2130998 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
2130943 TATTCGCATT
2130953 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
2130974 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
2130995 GCGA
1 GCGA
2130999 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:2134296 original size:64 final size:64
Alignment explanation
Indices: 2134195--2134322 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
2134185 TACATGCAGC
* *
2134195 AACAGTGATGGACTAGGGGAATGACCAGAGATGGATGAGGGAGAACATAGGAATTTTTTTTTGT
1 AACAGTGATGGACTAGGGGAATGACCAGAGATAGATGAGGGAGAACATAGGAATTTATTTTTGT
*
2134259 AACAGTGATGGACTAGGGGAATGACCAGAGATAGATGAGGGAGAACATAGGGATTTATTTTTGT
1 AACAGTGATGGACTAGGGGAATGACCAGAGATAGATGAGGGAGAACATAGGAATTTATTTTTGT
2134323 GATAACATAG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.34, C:0.08, G:0.33, T:0.26
Consensus pattern (64 bp):
AACAGTGATGGACTAGGGGAATGACCAGAGATAGATGAGGGAGAACATAGGAATTTATTTTTGT
Found at i:2134512 original size:21 final size:21
Alignment explanation
Indices: 2134488--2134552 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2134478 GGAATAAGAC
2134488 GAATGCTACAGTACTGCACAA
1 GAATGCTACAGTACTGCACAA
*
2134509 GAATGCTACGGTACTGCACAA
1 GAATGCTACAGTACTGCACAA
* *
2134530 GAATGCTACAGTACCGTACAA
1 GAATGCTACAGTACTGCACAA
2134551 GA
1 GA
2134553 CGACACATGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (21 bp):
GAATGCTACAGTACTGCACAA
Found at i:2134794 original size:33 final size:33
Alignment explanation
Indices: 2134717--2134795 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
2134707 TACTCAAACT
* * *
2134717 ATGTCTTGCTACCTTAATAAAGTTGTTCGAATC
1 ATGTCTTACTATCTTAATAAAGTTGTTCGAACC
* *
2134750 ATGTCTTACTATCTTGATCAAGTTGCTT-GAACC
1 ATGTCTTACTATCTTAATAAAGTTG-TTCGAACC
2134783 ATGTCTTACTATC
1 ATGTCTTACTATC
2134796 AAGTTGCTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (33 bp):
ATGTCTTACTATCTTAATAAAGTTGTTCGAACC
Found at i:2134905 original size:26 final size:26
Alignment explanation
Indices: 2134861--2134933 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
2134851 GATAACAAGG
* * * * *
2134861 CATGGTTCAAGCAATTTAGTAATATA
1 CATGGTTCGAGAAACTTAGTAACAGA
* *
2134887 TATGGTTCGAGAAACTTAGTAGCAGA
1 CATGGTTCGAGAAACTTAGTAACAGA
2134913 CATGGTTCGAGAAACTTAGTA
1 CATGGTTCGAGAAACTTAGTA
2134934 GCAGGGAATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (26 bp):
CATGGTTCGAGAAACTTAGTAACAGA
Found at i:2134934 original size:26 final size:26
Alignment explanation
Indices: 2134888--2134937 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
2134878 AGTAATATAT
2134888 ATGGTTCGAGAAACTTAGTAGCAGAC
1 ATGGTTCGAGAAACTTAGTAGCAGAC
2134914 ATGGTTCGAGAAACTTAGTAGCAG
1 ATGGTTCGAGAAACTTAGTAGCAG
2134938 GGAATGATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (26 bp):
ATGGTTCGAGAAACTTAGTAGCAGAC
Found at i:2135110 original size:33 final size:32
Alignment explanation
Indices: 2135031--2135111 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
2135021 TAGCAGGGTT
* * *
2135031 TGATTCGAGCAACTTTATTAGGGTAGCAGGCA
1 TGATTCGAGCAACTTGATTAAGGTAACAGGCA
* *
2135063 TGACTCGAGCAACTTGATTAAGGTAACAAGGTA
1 TGATTCGAGCAACTTGATTAAGGTAAC-AGGCA
*
2135096 TGATTCGAGAAACTTG
1 TGATTCGAGCAACTTG
2135112 TGACCATAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (32 bp):
TGATTCGAGCAACTTGATTAAGGTAACAGGCA
Found at i:2136429 original size:31 final size:31
Alignment explanation
Indices: 2136391--2136457 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
2136381 TACATCTAGA
* *
2136391 TGTCTAATGTTACAAATGTTGTCATTTTAAG
1 TGTCTAATGTTACAAATGTTATCACTTTAAG
* *
2136422 TGTCTAATGTTACAATTGTTATCACTTTAGG
1 TGTCTAATGTTACAAATGTTATCACTTTAAG
2136453 TGTCT
1 TGTCT
2136458 CGGTCATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (31 bp):
TGTCTAATGTTACAAATGTTATCACTTTAAG
Found at i:2136501 original size:34 final size:33
Alignment explanation
Indices: 2136439--2136509 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
2136429 TGTTACAATT
* *
2136439 GTTATCACTTTAGGTGTCTCGGTCATAACAACCC
1 GTTACCACTTTAGGTGTCTCGATCATAACAA-CC
* *
2136473 GTTACCACTTTAGGTGTCTCGATTATAACGACC
1 GTTACCACTTTAGGTGTCTCGATCATAACAACC
2136506 GTTA
1 GTTA
2136510 TAAATCTCCG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 6 0.18
34 27 0.82
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (33 bp):
GTTACCACTTTAGGTGTCTCGATCATAACAACC
Found at i:2137079 original size:20 final size:21
Alignment explanation
Indices: 2137054--2137104 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
2137044 GACCAACAAA
2137054 TTCGCAACGCGAACTT-CAAT
1 TTCGCAACGCGAACTTCCAAT
* **
2137074 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAACTTCCAAT
2137094 TTCGCAACGCG
1 TTCGCAACGCG
2137105 GTAGTCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 4 0.16
20 20 0.80
21 1 0.04
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCGCAACGCGAACTTCCAAT
Found at i:2137313 original size:16 final size:15
Alignment explanation
Indices: 2137278--2137316 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2137268 TCCCCATCTC
*
2137278 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
2137293 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2137309 TAATTTTT
1 TAATTTTT
2137317 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2138043 original size:24 final size:24
Alignment explanation
Indices: 2138016--2138069 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2138006 GTATTCAAAA
2138016 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2138040 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2138064 TTTGAT
1 TTTGAT
2138070 GATGTGATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:2138824 original size:23 final size:23
Alignment explanation
Indices: 2138798--2138866 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2138788 CACCACAGCT
*
2138798 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2138821 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2138844 CGTAGAAATGCACCTAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2138867 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2139509 original size:250 final size:250
Alignment explanation
Indices: 2139061--2139546 Score: 945
Period size: 250 Copynumber: 1.9 Consensus size: 250
2139051 GGGCATCATC
*
2139061 ATTTATTTCATTTCACATTTTCACATAAACACGTAGTTCACTTTCACATGGCACGTAGATTATGT
1 ATTTATGTCATTTCACATTTTCACATAAACACGTAGTTCACTTTCACATGGCACGTAGATTATGT
2139126 CACATAAGTTGAATCACATATACGTATAAACACGTAAATCACTTTCACATATCACGTAGCTCATA
66 CACATAAGTTGAATCACATATACGTATAAACACGTAAATCACTTTCACATATCACGTAGCTCATA
2139191 TCCATTTTTCATACTATTTCACATTTCTTGTCACGTTGCTTAAATCTTATTTTTATATCTTATCC
131 TCCATTTTTCATACTATTTCACATTTCTTGTCACGTTGCTTAAATCTTATTTTTATATCTTATCC
2139256 TATATATATATAGATAGTCACATGTTCATATAATCCATCATATCTTATCCTATAT
196 TATATATATATAGATAGTCACATGTTCATATAATCCATCATATCTTATCCTATAT
2139311 ATTTATGTCATTTCACATTTTCACATAAACACGTAGTTCACTTTCACATGGCACGTAGATTATGT
1 ATTTATGTCATTTCACATTTTCACATAAACACGTAGTTCACTTTCACATGGCACGTAGATTATGT
2139376 CACATAAGTTGAATCACATATACGTATAAACACGTAAATCACTTTCACATATCACGTAGCTCATA
66 CACATAAGTTGAATCACATATACGTATAAACACGTAAATCACTTTCACATATCACGTAGCTCATA
*
2139441 TCCATTTTTCATACTATTTCACATTTCTTGTCACGTTGCTTATATCTTATTTTTATATCTTATCC
131 TCCATTTTTCATACTATTTCACATTTCTTGTCACGTTGCTTAAATCTTATTTTTATATCTTATCC
*
2139506 TATATATATATAGATAGTCATATGTTCATATAATCCATCAT
196 TATATATATATAGATAGTCACATGTTCATATAATCCATCAT
2139547 TTCCTCATCT
Statistics
Matches: 233, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
250 233 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.40
Consensus pattern (250 bp):
ATTTATGTCATTTCACATTTTCACATAAACACGTAGTTCACTTTCACATGGCACGTAGATTATGT
CACATAAGTTGAATCACATATACGTATAAACACGTAAATCACTTTCACATATCACGTAGCTCATA
TCCATTTTTCATACTATTTCACATTTCTTGTCACGTTGCTTAAATCTTATTTTTATATCTTATCC
TATATATATATAGATAGTCACATGTTCATATAATCCATCATATCTTATCCTATAT
Found at i:2139591 original size:2 final size:2
Alignment explanation
Indices: 2139584--2139645 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
2139574 ATTCATCTTC
2139584 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
2139626 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
2139646 CATTTTTCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2140775 original size:24 final size:21
Alignment explanation
Indices: 2140727--2140803 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 21
2140717 TTCCCTTGAA
*
2140727 GTGCATCGATGCATTCTACAT
1 GTGCATCGATGCATCCTACAT
2140748 -TGCATCGATGCATCCCTTAACAT
1 GTGCATCGATGCAT-CC-T-ACAT
2140771 GTGCATCGATGCACTCCT---T
1 GTGCATCGATGCA-TCCTACAT
*
2140790 ATGCATCGATGCAT
1 GTGCATCGATGCAT
2140804 TAATTGCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
18 1 0.02
19 13 0.27
20 13 0.27
21 1 0.02
22 1 0.02
23 5 0.10
24 14 0.29
25 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (21 bp):
GTGCATCGATGCATCCTACAT
Found at i:2141805 original size:23 final size:23
Alignment explanation
Indices: 2141779--2141847 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2141769 CACCACAGCT
*
2141779 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2141802 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2141825 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2141848 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2143027 original size:20 final size:21
Alignment explanation
Indices: 2142980--2143032 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2142970 TCAAAGATCT
* * *
2142980 TATCACATAACTTCTCTTTTA
1 TATCATATAACTTCTCTATCA
2143001 TATTCATATAACTTCT-TATCA
1 TA-TCATATAACTTCTCTATCA
2143022 TATCATCATAA
1 TATCAT-ATAA
2143033 TATAACATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 12 0.44
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (21 bp):
TATCATATAACTTCTCTATCA
Found at i:2143507 original size:24 final size:24
Alignment explanation
Indices: 2143444--2143500 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2143434 TCTACAGTGT
2143444 ATCGATGCATCCCTTAAAATGTAC
1 ATCGATGCATCCCTTAAAATGTAC
* *
2143468 ATCGATGCATCCCTTAACATGTGC
1 ATCGATGCATCCCTTAAAATGTAC
2143492 ATCGATGCA
1 ATCGATGCA
2143501 CTCCTTATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (24 bp):
ATCGATGCATCCCTTAAAATGTAC
Found at i:2146049 original size:18 final size:18
Alignment explanation
Indices: 2146026--2146061 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2146016 CAAGAAAAGG
*
2146026 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2146044 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2146062 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2146462 original size:20 final size:20
Alignment explanation
Indices: 2146439--2146498 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
2146429 AATCGCAAAC
*
2146439 CGAAATTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
*
2146459 CGAATTTGACTTTCGTGTTG
1 CGAATTTGACTTTCGCGTTG
* *
2146479 AGAATTTGACTATCGCGTTG
1 CGAATTTGACTTTCGCGTTG
2146499 TACATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:2146941 original size:18 final size:18
Alignment explanation
Indices: 2146920--2146956 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2146910 GTAATTGGAG
2146920 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
2146938 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
2146956 T
1 T
2146957 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:2146963 original size:24 final size:24
Alignment explanation
Indices: 2146912--2146964 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2146902 TTTCATATGT
* * *
2146912 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
2146936 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
2146960 AATTT
1 AATTT
2146965 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2147309 original size:39 final size:39
Alignment explanation
Indices: 2147266--2147352 Score: 149
Period size: 39 Copynumber: 2.2 Consensus size: 39
2147256 TCCGATGCTC
*
2147266 ATCAAAATCCAAAGT-TCATATGGTGCCAAGCAAAATGAA
1 ATCAAAATCCAAA-TCTCATATGGTGCCAAGCAAAAGGAA
2147305 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
2147344 ATCAAAATC
1 ATCAAAATC
2147353 TACAACTTGA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 1 0.02
39 45 0.98
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
Found at i:2147729 original size:14 final size:14
Alignment explanation
Indices: 2147710--2147749 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
2147700 ATAATTCTTA
*
2147710 TTTACACATCAACT
1 TTTACAAATCAACT
2147724 TTTACAAATCAACT
1 TTTACAAATCAACT
2147738 TTTACAAATCAA
1 TTTACAAATCAA
2147750 TTAATCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:2149247 original size:21 final size:21
Alignment explanation
Indices: 2149175--2149263 Score: 63
Period size: 21 Copynumber: 4.2 Consensus size: 21
2149165 GCGGGACCTT
* * *
2149175 TTGAACGATGACAGAGGCCTC
1 TTGAACGATAAGAGGGGCCTC
* ** *
2149196 TTGAACGGTGGGAGGGGCTTC
1 TTGAACGATAAGAGGGGCCTC
*
2149217 TTCG-ATGATAAGAGGGGCCTC
1 TT-GAACGATAAGAGGGGCCTC
* **
2149238 TTGAACGATAGGAGGCACCTC
1 TTGAACGATAAGAGGGGCCTC
2149259 TTGAA
1 TTGAA
2149264 TGATGATAGG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 50 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (21 bp):
TTGAACGATAAGAGGGGCCTC
Found at i:2151966 original size:20 final size:20
Alignment explanation
Indices: 2151941--2152142 Score: 235
Period size: 20 Copynumber: 10.4 Consensus size: 20
2151931 GCGTAAAAAC
2151941 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2151961 ATTTGACTATT-GCGTTGCGA
1 ATTTGACT-TTCGCGTTGCGA
* *
2151981 ATTTGACTTTTGTGTTGCG-
1 ATTTGACTTTCGCGTTGCGA
*
2152000 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* *
2152021 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
2152041 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2152061 ATTTG----T---GTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
2152074 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
2152094 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2152114 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
2152134 ATTTGACTT
1 ATTTGACTT
2152143 ATGTGTTGCG
Statistics
Matches: 158, Mismatches: 11, Indels: 26
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.08
16 1 0.01
17 1 0.01
18 2 0.01
19 6 0.04
20 128 0.81
21 6 0.04
22 2 0.01
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:2152071 original size:33 final size:33
Alignment explanation
Indices: 2152029--2152138 Score: 148
Period size: 33 Copynumber: 3.1 Consensus size: 33
2152019 GAATTTGACT
2152029 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAA
1 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAA
2152062 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAA
1 TTTGTGTTGCGAATTTGACTATCGCGTTGCGAA
*
2152095 TTTGACTATCGCGTTGCGAATTTGACTTTCGCGTTGCGAA
1 TTTG----T---GTTGCGAATTTGACTATCGCGTTGCGAA
2152135 TTTG
1 TTTG
2152139 ACTTATGTGT
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
33 37 0.54
37 1 0.01
40 31 0.45
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.40
Consensus pattern (33 bp):
TTTGTGTTGCGAATTTGACTATCGCGTTGCGAA
Found at i:2152072 original size:13 final size:13
Alignment explanation
Indices: 2152054--2152078 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2152044 TGACTATCGC
2152054 GTTGCGAATTTGT
1 GTTGCGAATTTGT
2152067 GTTGCGAATTTG
1 GTTGCGAATTTG
2152079 ACTATCGCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (13 bp):
GTTGCGAATTTGT
Found at i:2152094 original size:53 final size:53
Alignment explanation
Indices: 2152014--2152118 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
2152004 ACAAATTCGC
* * *
2152014 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGT
2152067 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTG
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTG
2152119 ACTTTCGCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (53 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGT
Found at i:2152111 original size:73 final size:73
Alignment explanation
Indices: 2151989--2152138 Score: 223
Period size: 73 Copynumber: 2.1 Consensus size: 73
2151979 GAATTTGACT
* * *
2151989 TTTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 TTTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGC
2152054 GTTGCGAA
66 GTTGCGAA
* *
2152062 TTTGTGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTC
1 TTTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATC
2152125 GCGTTGCGAA
64 GCGTTGCGAA
2152135 TTTG
1 TTTG
2152139 ACTTATGTGT
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
73 63 0.90
74 5 0.07
75 2 0.03
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (73 bp):
TTTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGC
GTTGCGAA
Found at i:2152150 original size:20 final size:21
Alignment explanation
Indices: 2152067--2152153 Score: 137
Period size: 20 Copynumber: 4.3 Consensus size: 21
2152057 GCGAATTTGT
2152067 GTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACTTATCGC
2152087 GTTGCGAATTTGAC-TATCGC
1 GTTGCGAATTTGACTTATCGC
2152107 GTTGCGAATTTGACTT-TCGC
1 GTTGCGAATTTGACTTATCGC
*
2152127 GTTGCGAATTTGACTTAT-GT
1 GTTGCGAATTTGACTTATCGC
2152147 GTTGCGA
1 GTTGCGA
2152154 TTTACAGATT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTGACTTATCGC
Found at i:2152233 original size:21 final size:21
Alignment explanation
Indices: 2152209--2152357 Score: 70
Period size: 21 Copynumber: 7.2 Consensus size: 21
2152199 ATATTCGCGT
*
2152209 TGCGAATTTGGAAAATCGCAA
1 TGCGAACTTGGAAAATCGCAA
** * * **
2152230 TGCG-ACTTACATATTCGCGT
1 TGCGAACTTGGAAAATCGCAA
*
2152250 TGCGAATTTGGAAAATCGCAA
1 TGCGAACTTGGAAAATCGCAA
** * * **
2152271 TGCG-ACTTACATATTCGCGT
1 TGCGAACTTGGAAAATCGCAA
*
2152291 TGCGAAATTGGAAAATCGCAA
1 TGCGAACTTGGAAAATCGCAA
** * * * **
2152312 TGCG-ACTTACATATTCACGT
1 TGCGAACTTGGAAAATCGCAA
*
2152332 TGCGAAATTGGAAAATCGCAA
1 TGCGAACTTGGAAAATCGCAA
2152353 TGCGA
1 TGCGA
2152358 CTTATATATT
Statistics
Matches: 81, Mismatches: 44, Indels: 6
0.62 0.34 0.05
Matches are distributed among these distances:
20 38 0.47
21 43 0.53
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCGAACTTGGAAAATCGCAA
Found at i:2152294 original size:20 final size:20
Alignment explanation
Indices: 2152148--2152327 Score: 90
Period size: 20 Copynumber: 8.8 Consensus size: 20
2152138 GACTTATGTG
* *
2152148 TTGCGATTTACAGATTCGCA
1 TTGCGACTTACATATTCGCA
* * *
2152168 TAGCGATTTACAGATTCGCA
1 TTGCGACTTACATATTCGCA
* *
2152188 ATGCGACTTACATATTCGCG
1 TTGCGACTTACATATTCGCA
* ** * *
2152208 TTGCGAATTTGGAAAATCGCA
1 TTGCG-ACTTACATATTCGCA
* *
2152229 ATGCGACTTACATATTCGCG
1 TTGCGACTTACATATTCGCA
* ** * *
2152249 TTGCGAATTTGGAAAATCGCA
1 TTGCG-ACTTACATATTCGCA
* *
2152270 ATGCGACTTACATATTCGCG
1 TTGCGACTTACATATTCGCA
* ** * *
2152290 TTGCGAAATTGGAAAATCGCA
1 TTGCG-ACTTACATATTCGCA
*
2152311 ATGCGACTTACATATTC
1 TTGCGACTTACATATTC
2152328 ACGTTGCGAA
Statistics
Matches: 110, Mismatches: 47, Indels: 6
0.67 0.29 0.04
Matches are distributed among these distances:
20 71 0.65
21 39 0.35
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (20 bp):
TTGCGACTTACATATTCGCA
Found at i:2152382 original size:41 final size:41
Alignment explanation
Indices: 2152183--2152374 Score: 348
Period size: 41 Copynumber: 4.7 Consensus size: 41
2152173 ATTTACAGAT
*
2152183 TCGCAATGCGACTTACATATTCGCGTTGCGAATTTGGAAAA
1 TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
*
2152224 TCGCAATGCGACTTACATATTCGCGTTGCGAATTTGGAAAA
1 TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
2152265 TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
1 TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
*
2152306 TCGCAATGCGACTTACATATTCACGTTGCGAAATTGGAAAA
1 TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
*
2152347 TCGCAATGCGACTTATATATTCGCGTTG
1 TCGCAATGCGACTTACATATTCGCGTTG
2152375 TAAAATTGAA
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 147 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
TCGCAATGCGACTTACATATTCGCGTTGCGAAATTGGAAAA
Found at i:2160121 original size:20 final size:22
Alignment explanation
Indices: 2160098--2160137 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2160088 AAGACTCAAG
2160098 AAAAAA-AAG-GAAATAATATA
1 AAAAAATAAGAGAAATAATATA
*
2160118 AAAAAATAAGAGAACTAATA
1 AAAAAATAAGAGAAATAATA
2160138 ATCCCCAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAAATAAGAGAAATAATATA
Found at i:2160601 original size:40 final size:40
Alignment explanation
Indices: 2160542--2160622 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
2160532 TACATCATTC
*
2160542 ATCACTAAAACTATTTTCTCACTCTTATTTTGGTCACAAA
1 ATCACTAAAACTATCTTCTCACTCTTATTTTGGTCACAAA
2160582 ATCACTAAAACTATCTTCTCACTCTTATTTTGGTCACAAA
1 ATCACTAAAACTATCTTCTCACTCTTATTTTGGTCACAAA
2160622 A
1 A
2160623 GTATAATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (40 bp):
ATCACTAAAACTATCTTCTCACTCTTATTTTGGTCACAAA
Found at i:2160789 original size:31 final size:28
Alignment explanation
Indices: 2160730--2160810 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 28
2160720 TTATTAAAAT
*
2160730 AAAAAATGAAAGTTAGAGTGAATAAATTAGA
1 AAAAAATTAAAGTTA-AGT-AATAAATTA-A
* *
2160761 AGAAATTTAAAAGTTAAGTAATTAAATTAA
1 AAAAAATT-AAAGTTAAGTAA-TAAATTAA
*
2160791 AAAAAATTAAAGTTTAGTAA
1 AAAAAATTAAAGTTAAGTAA
2160811 CGAAAAATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 11 0.26
30 9 0.21
31 15 0.36
32 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (28 bp):
AAAAAATTAAAGTTAAGTAATAAATTAA
Found at i:2162513 original size:22 final size:22
Alignment explanation
Indices: 2162488--2162553 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2162478 ACTATATAGT
*
2162488 ATGAACAGTACCGTG-AGCAGTA
1 ATGAACAGTACCATGTA-CAGTA
* *
2162510 ATGAACATTACTATGTACAGTA
1 ATGAACAGTACCATGTACAGTA
* * *
2162532 ATGAACAATATCATGAACAGTA
1 ATGAACAGTACCATGTACAGTA
2162554 CCAAATGCTA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (22 bp):
ATGAACAGTACCATGTACAGTA
Found at i:2163408 original size:31 final size:31
Alignment explanation
Indices: 2163381--2163489 Score: 184
Period size: 31 Copynumber: 3.5 Consensus size: 31
2163371 CTATATGTTT
2163381 CGAAGAACATAGGTAATCAGTCCATATGTCC
1 CGAAGAACATAGGTAATCAGTCCATATGTCC
2163412 CGAAGAACATAGGTAAAT-AGTCCATATGTCC
1 CGAAGAACATAGGT-AATCAGTCCATATGTCC
* *
2163443 CGAAGAACATAGGTAAACAGTCCATATATCC
1 CGAAGAACATAGGTAATCAGTCCATATGTCC
2163474 CGAAGAACATAGGTAA
1 CGAAGAACATAGGTAA
2163490 CCCTCGACTC
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
30 2 0.03
31 69 0.93
32 3 0.04
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (31 bp):
CGAAGAACATAGGTAATCAGTCCATATGTCC
Found at i:2164677 original size:12 final size:12
Alignment explanation
Indices: 2164660--2164684 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2164650 TGATGACAAG
2164660 TCAAATTTAACT
1 TCAAATTTAACT
2164672 TCAAATTTAACT
1 TCAAATTTAACT
2164684 T
1 T
2164685 ATCAACTCTT
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:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTAACT
Found at i:2168639 original size:13 final size:15
Alignment explanation
Indices: 2168620--2168709 Score: 51
Period size: 15 Copynumber: 5.6 Consensus size: 15
2168610 ATTTTTTTTA
*
2168620 ATAAAATT-ATATAT
1 ATAAAATTAAAATAT
2168634 -TAAAATTAAAATAT
1 ATAAAATTAAAATAT
* *
2168648 ATAAAATTCAATTGAT
1 ATAAAATTAAAAT-AT
2168664 AATAAAAATATAAAAATTAT
1 -AT-AAAAT-T-AAAA-TAT
2168684 ATAAAAATCTAAAACTAT
1 AT-AAAAT-TAAAA-TAT
2168702 -TAAAATTA
1 ATAAAATTA
2168710 CGATCATATC
Statistics
Matches: 61, Mismatches: 7, Indels: 15
0.73 0.08 0.18
Matches are distributed among these distances:
13 7 0.11
14 5 0.08
15 12 0.20
16 7 0.11
17 3 0.05
18 12 0.20
19 10 0.16
20 4 0.07
21 1 0.02
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.34
Consensus pattern (15 bp):
ATAAAATTAAAATAT
Found at i:2168697 original size:18 final size:17
Alignment explanation
Indices: 2168621--2168706 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 17
2168611 TTTTTTTTAA
2168621 TAAAATTATATATTAAAAT
1 TAAAATTATATA--AAAAT
2168640 TAAAA-TATAT-AAAAT
1 TAAAATTATATAAAAAT
*
2168655 T-CAATTGATAATAAAAAT
1 TAAAATT-AT-ATAAAAAT
2168673 ATAAAAATTATATAAAAAT
1 -T-AAAATTATATAAAAAT
*
2168692 CTAAAACTAT-TAAAA
1 -TAAAATTATATAAAA
2168707 TTACGATCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.04
15 7 0.12
16 2 0.04
17 7 0.12
18 17 0.30
19 15 0.27
20 2 0.04
21 4 0.07
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (17 bp):
TAAAATTATATAAAAAT
Found at i:2183841 original size:31 final size:31
Alignment explanation
Indices: 2183803--2183925 Score: 212
Period size: 31 Copynumber: 4.0 Consensus size: 31
2183793 CCCGAAGGAC
* *
2183803 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
2183834 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2183865 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2183896 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
2183926 CCCTCGACCC
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2195135 original size:21 final size:21
Alignment explanation
Indices: 2195104--2195150 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2195094 AACAACTATG
*
2195104 GAAGGGTGAAGGGGGAATAGA
1 GAAGGGGGAAGGGGGAATAGA
*
2195125 TAAGGGGGAAGGGGGAATAGA
1 GAAGGGGGAAGGGGGAATAGA
2195146 GAAGG
1 GAAGG
2195151 AGAGAGGGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.53, T:0.09
Consensus pattern (21 bp):
GAAGGGGGAAGGGGGAATAGA
Done.