Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 84 of 171
Found at i:27880048 original size:30 final size:29
Alignment explanation
Indices: 27880013--27880187 Score: 151
Period size: 30 Copynumber: 5.9 Consensus size: 29
27880003 CCTAGGAGGT
*
27880013 CCTCGAACTTTT-TCAAAATTACATTTTGA
1 CCTCAAACTTTTCT-AAAATTACATTTTGA
* *
27880042 CTCTCGAATTCTTTC-AAAATTACA-TTTGAA
1 C-CTCAAACT-TTTCTAAAATTACATTTTG-A
*
27880072 CCGT-AAACTCTTCTAAAATTACATTTTGA
1 CC-TCAAACTTTTCTAAAATTACATTTTGA
* * * *
27880101 CCTCGAACTTTTCCAAAATTATATTTTAA
1 CCTCAAACTTTTCTAAAATTACATTTTGA
* * *
27880130 CCCTTAAACTTTTCTAAAATTATATTTTAA
1 -CCTCAAACTTTTCTAAAATTACATTTTGA
*
27880160 CCCCTAAACTTTTCTAAAATTACATTTT
1 CCTC-AAACTTTTCTAAAATTACATTTT
27880188 AAACCAAAAT
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
28 4 0.03
29 43 0.36
30 71 0.59
31 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (29 bp):
CCTCAAACTTTTCTAAAATTACATTTTGA
Found at i:27880099 original size:59 final size:59
Alignment explanation
Indices: 27880027--27880186 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 59
27880017 GAACTTTTTC
*
27880027 AAAATTACATTTTGACTCTCGAA-TTCTTTCAAAATTACATTTGAA-CCGTAAACTCTTCT
1 AAAATTACATTTTGAC-CTCGAACTT-TTCCAAAATTACATTTGAACCCGTAAACTCTTCT
* * * *
27880086 AAAATTACATTTTGACCTCGAACTTTTCCAAAATTATATTTTAACCCTTAAACTTTTCT
1 AAAATTACATTTTGACCTCGAACTTTTCCAAAATTACATTTGAACCCGTAAACTCTTCT
* * * * *
27880145 AAAATTATATTTTAACCCCTAAACTTTTCTAAAATTACATTT
1 AAAATTACATTTTGACCTC-GAACTTTTCCAAAATTACATTT
27880187 TAAACCAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
58 22 0.25
59 46 0.53
60 19 0.22
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.41
Consensus pattern (59 bp):
AAAATTACATTTTGACCTCGAACTTTTCCAAAATTACATTTGAACCCGTAAACTCTTCT
Found at i:27880188 original size:30 final size:30
Alignment explanation
Indices: 27880053--27880189 Score: 163
Period size: 30 Copynumber: 4.7 Consensus size: 30
27880043 TCTCGAATTC
* *
27880053 TTTC-AAAATTACATTTGAA-CCGTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
* * * *
27880081 CTTCTAAAATTACATTTTGACCTC-GAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
* * *
27880110 TTTCCAAAATTATATTTTAACCCTTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
*
27880140 TTTCTAAAATTATATTTTAACCCCTAAACT
1 TTTCTAAAATTACATTTTAACCCCTAAACT
27880170 TTTCTAAAATTACATTTTAA
1 TTTCTAAAATTACATTTTAA
27880190 ACCAAAATTC
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
28 3 0.03
29 35 0.39
30 52 0.58
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (30 bp):
TTTCTAAAATTACATTTTAACCCCTAAACT
Found at i:27884340 original size:86 final size:84
Alignment explanation
Indices: 27884191--27884350 Score: 221
Period size: 86 Copynumber: 1.9 Consensus size: 84
27884181 TACATGCATA
* * * *
27884191 AGGTTGAGTTCTCACTCTTAATGAGTTCATATCCCAAGTTGGGTGGTCCTATTGAGACGGACTTA
1 AGGTTGAGTTATCACTCTTAATGAATTCATATCCAAAGTTGGGTGGTCCTATTGAGACAGACTTA
27884256 ATGAATTCATCGACATGAG
66 ATGAATTCATCGACATGAG
* * * *
27884275 AGGTTGAGTTTATTACTCTTAATGAATTCATATCCTAAAGTTTGGTGGTCTTATTGCGACAGACT
1 AGGTTGAG-TTATCACTCTTAATGAATTCATATCC-AAAGTTGGGTGGTCCTATTGAGACAGACT
*
27884340 TGATGAATTCA
64 TAATGAATTCA
27884351 CTGAACTTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 8 0.12
85 23 0.35
86 34 0.52
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (84 bp):
AGGTTGAGTTATCACTCTTAATGAATTCATATCCAAAGTTGGGTGGTCCTATTGAGACAGACTTA
ATGAATTCATCGACATGAG
Found at i:27897318 original size:38 final size:38
Alignment explanation
Indices: 27897275--27897365 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
27897265 CATATAACAA
* *
27897275 GAGAATCTACAACAAGGCTAGATCTCGTTATACTACTT
1 GAGAATCTACAACAAGGCTAGATCCCGTTATACTACTC
* *
27897313 GAGAATCTACAATAAGGCTAGATCCCGTTATATTACTC
1 GAGAATCTACAACAAGGCTAGATCCCGTTATACTACTC
*
27897351 GAGAATCTGCAACAA
1 GAGAATCTACAACAA
27897366 ATACTAGATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (38 bp):
GAGAATCTACAACAAGGCTAGATCCCGTTATACTACTC
Found at i:27905392 original size:15 final size:16
Alignment explanation
Indices: 27905362--27905395 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27905352 GTTCGTTTTA
*
27905362 TTAATTATATATATTT
1 TTAATTATAAATATTT
27905378 TTAATTA-AAATATTT
1 TTAATTATAAATATTT
27905393 TTA
1 TTA
27905396 TATTTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTAATTATAAATATTT
Found at i:27911547 original size:22 final size:23
Alignment explanation
Indices: 27911521--27911566 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
27911511 AGCCGCCACG
*
27911521 TCAGCATC-TACCACCACCGTCA
1 TCAGCAACTTACCACCACCGTCA
*
27911543 TCAGCAACTTGCCACCACCGTCA
1 TCAGCAACTTACCACCACCGTCA
27911566 T
1 T
27911567 TGGCACCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.26, C:0.43, G:0.11, T:0.20
Consensus pattern (23 bp):
TCAGCAACTTACCACCACCGTCA
Found at i:27912999 original size:30 final size:30
Alignment explanation
Indices: 27912905--27913198 Score: 179
Period size: 30 Copynumber: 9.8 Consensus size: 30
27912895 GATCCCTCAA
* **
27912905 TTTTCCAAAAAACATATTTTAACCCTCGAAC
1 TTTTCC-AAAATCATATTTTAACCCTTAAAC
* ** * *
27912936 TTTT-CAAAATTATATTTTCGTCCC-TGAAT
1 TTTTCCAAAATCATATTTT-AACCCTTAAAC
* * * *
27912965 TTTTCTAAAATTACATTTTCACCCTTAAAC
1 TTTTCCAAAATCATATTTTAACCCTTAAAC
**
27912995 TTTTCCAAAATCATATTTTAACCCCAAAAC
1 TTTTCCAAAATCATATTTTAACCCTTAAAC
* ** * **
27913025 -TTCCCAAAATCACGTTTTTACCTCCCAAAC
1 TTTTCCAAAATCATATTTTAACC-CTTAAAC
*
27913055 -TTTCCTAAAATTATATTTTAACCCTTAAAC
1 TTTTCC-AAAATCATATTTTAACCCTTAAAC
* * **
27913085 -TTCCCAAAATCATATTTTGACCCCAAAAAC
1 TTTTCCAAAATCATATTTT-AACCCTTAAAC
*
27913115 TTTTCTAAAATCATATTTTAACCCTTAAAC
1 TTTTCCAAAATCATATTTTAACCCTTAAAC
* * * **
27913145 -TTTCTTAAAATGACATTTTAA-CCTTAATT
1 TTTTC-CAAAATCATATTTTAACCCTTAAAC
* * *
27913174 TTTTCCAAAATTACATTTTGACCCT
1 TTTTCCAAAATCATATTTTAACCCT
27913199 AAGTTCTCCA
Statistics
Matches: 206, Mismatches: 47, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
29 74 0.36
30 99 0.48
31 33 0.16
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTTCCAAAATCATATTTTAACCCTTAAAC
Found at i:27913139 original size:60 final size:60
Alignment explanation
Indices: 27912991--27913146 Score: 215
Period size: 60 Copynumber: 2.6 Consensus size: 60
27912981 TTTCACCCTT
* ** * * *
27912991 AAACTTTTCCAAAATCATATTTTAACCCCAAAACTTCCCAAAATCACGTTTTTACCTCCC
1 AAACTTTTCTAAAATCATATTTTAACCCTTAAACTTCCCAAAATCACATTTTGACCTCCA
* * *
27913051 AAACTTTCCTAAAATTATATTTTAACCCTTAAACTTCCCAAAATCATATTTTGACC-CCAA
1 AAACTTTTCTAAAATCATATTTTAACCCTTAAACTTCCCAAAATCACATTTTGACCTCC-A
27913111 AAACTTTTCTAAAATCATATTTTAACCCTTAAACTT
1 AAACTTTTCTAAAATCATATTTTAACCCTTAAACTT
27913147 TCTTAAAATG
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 2 0.02
60 82 0.98
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.35
Consensus pattern (60 bp):
AAACTTTTCTAAAATCATATTTTAACCCTTAAACTTCCCAAAATCACATTTTGACCTCCA
Found at i:27913182 original size:90 final size:87
Alignment explanation
Indices: 27912966--27913197 Score: 241
Period size: 90 Copynumber: 2.6 Consensus size: 87
27912956 TCCCTGAATT
* *
27912966 TTTCTAAAATTACATTTTCACCCTTAAACTTTTCCAAAATCATATTTTAACCCCAAAACTTCCCA
1 TTTCTAAAATTACATTTT-AACCTTAAA-TTTTCCAAAATCATATTTTGACCCCAAAACTTCCCA
* *
27913031 AAATCACGTTTTTACCTCCCAAAC
64 AAATCACATTTTAACCTCCCAAAC
* * * *
27913055 TTTCCTAAAATTATATTTTAACCCTTAAACTTCCCAAAATCATATTTTGACCCCAAAAACTTTTC
1 TTT-CTAAAATTACATTTTAA-CCTTAAATTTTCCAAAATCATATTTTGACCCC-AAAAC-TTCC
* * **
27913120 TAAAATCATATTTTAACC-CTTAAAC
62 CAAAATCACATTTTAACCTCCCAAAC
* * * *
27913145 TTTCTTAAAATGACATTTTAACCTTAATTTTTTCCAAAATTACATTTTGACCC
1 TTTC-TAAAATTACATTTTAACCTTAA-ATTTTCCAAAATCATATTTTGACCC
27913198 TAAGTTCTCC
Statistics
Matches: 118, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
89 33 0.28
90 68 0.58
91 17 0.14
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (87 bp):
TTTCTAAAATTACATTTTAACCTTAAATTTTCCAAAATCATATTTTGACCCCAAAACTTCCCAAA
ATCACATTTTAACCTCCCAAAC
Found at i:27916172 original size:48 final size:48
Alignment explanation
Indices: 27916070--27916190 Score: 134
Period size: 48 Copynumber: 2.5 Consensus size: 48
27916060 ACTTCAAACC
* * ** *
27916070 CATCTTCCTTATGAGATACAGAGAAATGGGTCAAAGTAATAAAGCGGT
1 CATCTTCCTAATGAGATACAGAGAAATGGATCAAAACAATAAAGCGAT
* * *
27916118 CATCTTCCTAATGAGATACAGAGAAATGGATTAAAACAATGAGGCGAT
1 CATCTTCCTAATGAGATACAGAGAAATGGATCAAAACAATAAAGCGAT
* * * *
27916166 CGTCTTCTTGATAAGATACAGAGAA
1 CATCTTCCTAATGAGATACAGAGAA
27916191 GTAGACCAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (48 bp):
CATCTTCCTAATGAGATACAGAGAAATGGATCAAAACAATAAAGCGAT
Found at i:27916387 original size:85 final size:85
Alignment explanation
Indices: 27916244--27916410 Score: 208
Period size: 85 Copynumber: 2.0 Consensus size: 85
27916234 TAAACCCCCA
* * ** * *
27916244 TCTTCCTTATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCACCTTTCTGATGAGATAC
1 TCTTCCTGATGAGATACAAAGAAGTGAATCAAAACAATAAAGCGATCACCTTCCTGATGAGATAC
*
27916309 AGAGAAGTGGACCAAATCCG
66 AGAGAAGTAGACCAAATCCG
* * * * * *
27916329 TCTTCCTGATGAGATACAAAGAAGTGAATTAAAATAATAAGGCGGTCATCTTCCTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGAATCAAAACAATAAAGCGATCACCTTCCTGATGAGATAC
*
27916394 AGAGAAGTAGATCAAAT
66 AGAGAAGTAGACCAAAT
27916411 TGATGAAGTG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAAAGAAGTGAATCAAAACAATAAAGCGATCACCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCCG
Found at i:27916493 original size:209 final size:209
Alignment explanation
Indices: 27916118--27916563 Score: 601
Period size: 209 Copynumber: 2.1 Consensus size: 209
27916108 ATAAAGCGGT
* * * * *
27916118 CATCTTCCTAATGAGATACAGAGAAATGGATTAAAACAATGAGGCGATCGTCTTCTTGATAAGAT
1 CATCTTCCTAATGAGATACAGAGAAGTGAATTAAAACAATAAGGCGATCATCTTCCTGATAAGAT
*
27916183 ACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTTAAACCCCCATCTT
66 ACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAACCCCCATCTT
* * *
27916248 CCTTATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCACCTT-TCTGATGAGATACAGA
131 CCTTATGAGATACAGAGAAATGGATCAAAGCAATAAAGCGATCACCTTCT-TGAGGAGATACAGA
*
27916312 GAAGTGGACCAAATC
195 GAAGTAGACCAAATC
* * * * * *
27916327 CGTCTTCCTGATGAGATACAAAGAAGTGAATTAAAATAATAAGGCGGTCATCTTCCTGATGAGAT
1 CATCTTCCTAATGAGATACAGAGAAGTGAATTAAAACAATAAGGCGATCATCTTCCTGATAAGAT
* * * * * *
27916392 ATAGAGAAGTAGATCAAATTGATGAAGTGAAGCTCAATGTGAGTGAAACTTCAAACCCTCATCTT
66 ACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAACCCCCATCTT
* * *
27916457 -CTTGATGAGATATAGAGAAATGGATC-AAGACAATAAAGCGGTCATCTTCTTGAGGAGATACAG
131 CCTT-ATGAGATACAGAGAAATGGATCAAAG-CAATAAAGCGATCACCTTCTTGAGGAGATACAG
27916520 AGAAGTAGACCAAATC
194 AGAAGTAGACCAAATC
* *
27916536 CACCTTCCTAATGAGATATAGAGAAGTG
1 CATCTTCCTAATGAGATACAGAGAAGTG
27916564 GACCAAGAGA
Statistics
Matches: 204, Mismatches: 30, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
208 6 0.03
209 197 0.97
210 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.24
Consensus pattern (209 bp):
CATCTTCCTAATGAGATACAGAGAAGTGAATTAAAACAATAAGGCGATCATCTTCCTGATAAGAT
ACAGAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATGTGAGTAAAACTTCAAACCCCCATCTT
CCTTATGAGATACAGAGAAATGGATCAAAGCAATAAAGCGATCACCTTCTTGAGGAGATACAGAG
AAGTAGACCAAATC
Found at i:27917008 original size:42 final size:43
Alignment explanation
Indices: 27916964--27917045 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
27916954 TAAAAACAAA
* *
27916964 TTTTAAATTTAAATTTATTTTAAATTT-AAAATGTCCAATAAAT
1 TTTTAAATTTAAATTTA-GTTAAATTTAAAAAGGTCCAATAAAT
* *
27917007 TTTTGAGTTTAAATTTAGTTAAATTTAAAAAGGTCCAAT
1 TTTTAAATTTAAATTTAGTTAAATTTAAAAAGGTCCAAT
27917046 TACATGACCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 8 0.24
43 26 0.76
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTTAAATTTAAATTTAGTTAAATTTAAAAAGGTCCAATAAAT
Found at i:27918433 original size:59 final size:59
Alignment explanation
Indices: 27918335--27918669 Score: 345
Period size: 59 Copynumber: 5.6 Consensus size: 59
27918325 GTCCTTAAAC
* * * *
27918335 TTTCCAAAAATCATATTTTAACTCTCAAACTTTTCTAAAATTACATTTTCACCTCTAAATT
1 TTTCC-AAAATCATATTTTAACCCT-AAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
* * * *
27918396 TTTCCAAAATTATATTTTCACCCTAAACTTTTTTAAAATCACATTTTAACC-CTAAAAC
1 TTTCCAAAATCATATTTTAACCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
* * * * *
27918454 TTTCCAAAATCATATTTTCACCCCTAAACTTTTCCAAAATCATATTTTAACCCCTAAACT
1 TTTCCAAAATCATATTTT-AACCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
* * * * * * *
27918514 TTTCCAAAATCATATTTTGACTCCTAAAC-TTCCCAAAATCATATTTTGACCTCAAAAAC
1 TTTCCAAAATCATATTTTAAC-CCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
* * * *
27918573 TTTCCTAAAATCATATTTTAACCCCTAAACTTTTCTAAAATTACACTTTGACCT-TAAATT
1 TTTCC-AAAATCATATTTTAA-CCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
* * *
27918633 TTTCCAAAATTACATTTTAACCCTAAA-TTCTCTAAAA
1 TTTCCAAAATCATATTTTAACCCTAAACTTTTCTAAAA
27918670 CTTCATTTTT
Statistics
Matches: 232, Mismatches: 36, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
57 9 0.04
58 29 0.12
59 95 0.41
60 75 0.32
61 24 0.10
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.39
Consensus pattern (59 bp):
TTTCCAAAATCATATTTTAACCCTAAACTTTTCTAAAATCACATTTTAACCTCTAAAAT
Found at i:27918661 original size:29 final size:29
Alignment explanation
Indices: 27918330--27918659 Score: 308
Period size: 30 Copynumber: 11.1 Consensus size: 29
27918320 AAAAGGTCCT
*
27918330 TAAAC-TTTCCAAAAATCATATTTTAACTC
1 TAAACTTTTCC-AAAATCATATTTTAACCC
* * * *
27918359 TCAAACTTTTCTAAAATTACATTTTCACCTC
1 T-AAACTTTTCCAAAATCATATTTTAACC-C
* * *
27918390 TAAATTTTTCCAAAATTATATTTTCACCC
1 TAAACTTTTCCAAAATCATATTTTAACCC
** *
27918419 TAAACTTTTTTAAAATCACATTTTAACCC
1 TAAACTTTTCCAAAATCATATTTTAACCC
*
27918448 TAAAAC-TTTCCAAAATCATATTTTCACCCC
1 T-AAACTTTTCCAAAATCATATTTT-AACCC
27918478 TAAACTTTTCCAAAATCATATTTTAACCCC
1 TAAACTTTTCCAAAATCATATTTTAA-CCC
*
27918508 TAAACTTTTCCAAAATCATATTTTGACTCC
1 TAAACTTTTCCAAAATCATATTTTAAC-CC
* *
27918538 TAAAC-TTCCCAAAATCATATTTTGACCTC
1 TAAACTTTTCCAAAATCATATTTTAACC-C
*
27918567 AAAAAC-TTTCCTAAAATCATATTTTAACCCC
1 -TAAACTTTTCC-AAAATCATATTTTAA-CCC
* * * * * *
27918598 TAAACTTTTCTAAAATTACACTTTGACCT
1 TAAACTTTTCCAAAATCATATTTTAACCC
* * *
27918627 TAAATTTTTCCAAAATTACATTTTAACCC
1 TAAACTTTTCCAAAATCATATTTTAACCC
27918656 TAAA
1 TAAA
27918660 TTCTCTAAAA
Statistics
Matches: 252, Mismatches: 36, Indels: 26
0.80 0.11 0.08
Matches are distributed among these distances:
28 1 0.00
29 98 0.39
30 126 0.50
31 25 0.10
32 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.38
Consensus pattern (29 bp):
TAAACTTTTCCAAAATCATATTTTAACCC
Found at i:27920274 original size:12 final size:12
Alignment explanation
Indices: 27920257--27920291 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
27920247 TTTATGAACA
27920257 ACTCGTTTATTG
1 ACTCGTTTATTG
27920269 ACTCGTTTATTG
1 ACTCGTTTATTG
* *
27920281 AGTCATTTATT
1 ACTCGTTTATT
27920292 TATTAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (12 bp):
ACTCGTTTATTG
Found at i:27920371 original size:55 final size:55
Alignment explanation
Indices: 27920288--27920409 Score: 210
Period size: 55 Copynumber: 2.2 Consensus size: 55
27920278 TTGAGTCATT
* *
27920288 TATTTA-TTAATGATATTTTCCTATAAAAATATTAAAATAATATTTGTGTGTATG
1 TATTTATTTATTGATATTTTCCTATAAAAATATTAAAATAATATCTGTGTGTATG
*
27920342 TATTTATTTATTGATATTTTCTTATAAAAATATTAAAATAATATCTGTGTGTATG
1 TATTTATTTATTGATATTTTCCTATAAAAATATTAAAATAATATCTGTGTGTATG
27920397 TATTTATTTATTG
1 TATTTATTTATTG
27920410 TTTGTTTGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
54 6 0.09
55 58 0.91
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (55 bp):
TATTTATTTATTGATATTTTCCTATAAAAATATTAAAATAATATCTGTGTGTATG
Found at i:27920432 original size:55 final size:54
Alignment explanation
Indices: 27920317--27920480 Score: 208
Period size: 55 Copynumber: 3.0 Consensus size: 54
27920307 CCTATAAAAA
* * ** *
27920317 TATTAAAATAATATTTGTGTGTATGTATTTATTTATTGATAT-TTTCTTATAAAAA
1 TATTAAAATAATATTTGTGTGTATGTATTTATTTATTG-TTTGTTTGTT-TATTAT
*
27920372 TATTAAAATAATATCTGTGTGTATGTATTTATTTATTGTTTGTTTGTTTATTAT
1 TATTAAAATAATATTTGTGTGTATGTATTTATTTATTGTTTGTTTGTTTATTAT
* *
27920426 TCATTAACAT--TGTTTGTGTGTATGTATTTATTTATTGTTTGTTTGTTTATTAT
1 T-ATTAAAATAATATTTGTGTGTATGTATTTATTTATTGTTTGTTTGTTTATTAT
27920479 TA
1 TA
27920481 AAAGAAAGGG
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
52 1 0.01
53 42 0.43
54 6 0.06
55 49 0.50
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (54 bp):
TATTAAAATAATATTTGTGTGTATGTATTTATTTATTGTTTGTTTGTTTATTAT
Found at i:27920785 original size:12 final size:12
Alignment explanation
Indices: 27920768--27920820 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
27920758 AAAAAAAATT
27920768 TGTTCATGAACA
1 TGTTCATGAACA
* *
27920780 TGTTCAAT-TATA
1 TGTTC-ATGAACA
*
27920792 TGTTTATGAACA
1 TGTTCATGAACA
*
27920804 TGTTCGTGAACA
1 TGTTCATGAACA
27920816 TGTTC
1 TGTTC
27920821 GATTAAGTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (12 bp):
TGTTCATGAACA
Found at i:27920843 original size:35 final size:36
Alignment explanation
Indices: 27920768--27920851 Score: 118
Period size: 35 Copynumber: 2.4 Consensus size: 36
27920758 AAAAAAAATT
* *
27920768 TGTTCATGAACATGTTCAATTATATGTTTATGAACA
1 TGTTCGTGAACATGTTCAATTATATGTTAATGAACA
*
27920804 TGTTCGTGAACATGTTCGATTA-A-GTTAAATGAACA
1 TGTTCGTGAACATGTTCAATTATATGTT-AATGAACA
27920839 TGTTCGTGAACAT
1 TGTTCGTGAACAT
27920852 TAATCAAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.07
35 21 0.48
36 20 0.45
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (36 bp):
TGTTCGTGAACATGTTCAATTATATGTTAATGAACA
Found at i:27920854 original size:23 final size:23
Alignment explanation
Indices: 27920810--27920854 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
27920800 AACATGTTCG
* *
27920810 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
27920833 TGAACATGTTCG-TGAACATTAA
1 TGAACATGTTCGATGAA-ATTAA
27920855 TCAAATGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:27921531 original size:27 final size:28
Alignment explanation
Indices: 27921501--27921555 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
27921491 CGCACATATC
*
27921501 AGTTCCAATAGAA-AAAAGATATGTCTA
1 AGTTCCAATAGAATAAAAGATACGTCTA
27921528 AGTTCCAATAGAATAAAAGATACGTCTA
1 AGTTCCAATAGAATAAAAGATACGTCTA
27921556 CCCATACAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.25
Consensus pattern (28 bp):
AGTTCCAATAGAATAAAAGATACGTCTA
Found at i:27924540 original size:29 final size:28
Alignment explanation
Indices: 27924508--27924763 Score: 131
Period size: 29 Copynumber: 8.8 Consensus size: 28
27924498 TGGATACCCG
27924508 GGGGTAAAATGGTAATTTTTGGTGAAATC
1 GGGGTAAAATGGTAATTTTTGG-GAAATC
* * *
27924537 GGGGTTGAAAA-CG-AGACTTTT-GGATACTC
1 GGGG-T-AAAATGGTA-ATTTTTGGGA-AATC
*
27924566 GGGGGCAAAATGGTAA-TTTTGGTGAAATC
1 -GGGGTAAAATGGTAATTTTTGG-GAAATC
* **
27924595 GGGATTAAAATGG-AATTTTTGAGG-GTTC
1 GGG-GTAAAATGGTAATTTTTG-GGAAATC
* * *
27924623 GGGGGTAAAATGATATTTTTTGATGAAATC
1 -GGGGTAAAATGGTAATTTTTG-GGAAATC
27924653 GGGGTTAAAAATGG-AA-TTTT-GGAAAGTTC
1 GGGG-T-AAAATGGTAATTTTTGGGAAA--TC
27924682 GGGGGTAAAATGGTAATTTTTGGTGAAATC
1 -GGGGTAAAATGGTAATTTTTGG-GAAATC
*
27924712 GGGGTTAAAAATGG-AA-TTTT-GGAAAGTTAG
1 GGGG-T-AAAATGGTAATTTTTGGGAAA--T-C
27924742 GGGGTAAAATGGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
27924764 AAGTTTTGGG
Statistics
Matches: 175, Mismatches: 20, Indels: 62
0.68 0.08 0.24
Matches are distributed among these distances:
27 8 0.05
28 39 0.22
29 65 0.37
30 40 0.23
31 19 0.11
32 4 0.02
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.32
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTTGGGAAATC
Found at i:27924644 original size:58 final size:59
Alignment explanation
Indices: 27924471--27924819 Score: 370
Period size: 59 Copynumber: 5.9 Consensus size: 59
27924461 TAAGAAACGA
** * * **
27924471 TGAAATCGGGGTTGAAAACGGGACTTTTGGATA-CCCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * * * *
27924530 TGAAATCGGGGTTGAAAACGAGACTTTTGGATA-CTCGGGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTTAAAAATG-GAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * ** * * *
27924588 TGAAATCGGGATT-AAAATGGAATTTTTGAGGGTTCGGGGGTAAAATGATATTTTTTGA
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
27924646 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
*
27924705 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTAGGGGGTAAAATGGTAATTTTT-G
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * * * * *
27924763 -GAAGTTTTGGGGTTAAAAATAGAATTTT-AAAAGGTTTGAGGGTAAAATGGTAATTTT
1 TGAA--ATCGGGGTTAAAAATGGAATTTTGGAAA-GTTCGGGGGTAAAATGGTAATTTT
27924820 GGAAGTTTCG
Statistics
Matches: 253, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
56 8 0.03
57 23 0.09
58 43 0.17
59 179 0.71
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:27924767 original size:29 final size:27
Alignment explanation
Indices: 27924564--27924832 Score: 132
Period size: 29 Copynumber: 9.2 Consensus size: 27
27924554 TTTTGGATAC
* *
27924564 TCGGGGGCAAAATGGTAATTTTGGTGAA-A
1 TCGGGGGTAAAATGG-AATTTT-G-GAAGT
** * *
27924593 TCGGGATTAAAATGGAATTTTTGAGGGT
1 TCGGGGGTAAAATGGAATTTTGGA-AGT
*
27924621 TCGGGGGTAAAAT-GATATTTTTTGATGAA-A
1 TCGGGGGTAAAATGGA-A--TTTTG--GAAGT
*
27924651 TCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGT-AAAATGGAATTTTGG-AAGT
*
27924680 TCGGGGGTAAAATGGTAATTTTTGGTGAA-A
1 TCGGGGGTAAAATGG-AA-TTTT-G-GAAGT
*
27924710 TCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGT-AAAATGGAATTTTGG-AAGT
*
27924739 TAGGGGGTAAAATGGTAATTTTTGGAAGTT
1 TCGGGGGTAAAATGG-AA-TTTTGGAAG-T
* * * **
27924769 TTGGGGTTAAAAATAGAATTTTAAAAGGT
1 TCGGGGGT-AAAATGGAATTTTGGAA-GT
* *
27924798 TTGAGGGTAAAATGGTAATTTTGGAAGTT
1 TCGGGGGTAAAATGG-AATTTTGGAAG-T
27924827 TCGGGG
1 TCGGGG
27924833 ACCTATAAAC
Statistics
Matches: 184, Mismatches: 31, Indels: 50
0.69 0.12 0.19
Matches are distributed among these distances:
26 2 0.01
27 4 0.02
28 44 0.24
29 67 0.36
30 40 0.22
31 22 0.12
32 5 0.03
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (27 bp):
TCGGGGGTAAAATGGAATTTTGGAAGT
Found at i:27925998 original size:15 final size:15
Alignment explanation
Indices: 27925978--27926013 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27925968 AAACTGCCCT
27925978 TTATTATTAATACCA
1 TTATTATTAATACCA
* *
27925993 TTATTATTATTAGCA
1 TTATTATTAATACCA
27926008 TTATTA
1 TTATTA
27926014 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATTATTAATACCA
Found at i:27926611 original size:17 final size:17
Alignment explanation
Indices: 27926591--27926655 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
27926581 TTAATATTAT
* *
27926591 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
27926608 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
27926625 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
27926639 TTTAAGATAAATTTAAA
1 TTTAAAATAAATTTAAA
27926656 AATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:27926618 original size:11 final size:11
Alignment explanation
Indices: 27926604--27926674 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
27926594 AAATTAAGTT
27926604 TAAATTTAAAA
1 TAAATTTAAAA
27926615 TAAATTT-AAA
1 TAAATTTAAAA
* *
27926625 T-AA-GTAAATT
1 TAAATTTAAA-A
*
27926635 TAAATTTAAGA
1 TAAATTTAAAA
27926646 TAAATTTAAAAA
1 TAAATTT-AAAA
*
27926658 TGAATTTAAAA
1 TAAATTTAAAA
*
27926669 TCAATT
1 TAAATT
27926675 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 25 0.53
12 12 0.26
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:27926640 original size:31 final size:29
Alignment explanation
Indices: 27926602--27926667 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 29
27926592 TTAAATTAAG
27926602 TTTAAATTTAAAATAAATTTAAATAAGTAAA
1 TTTAAATTTAAAATAAATTTAAA-AA-TAAA
* *
27926633 TTTAAATTTAAGATAAATTTAAAAATGAA
1 TTTAAATTTAAAATAAATTTAAAAATAAA
27926662 TTTAAA
1 TTTAAA
27926668 ATCAATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 9 0.27
30 2 0.06
31 22 0.67
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTAAATTTAAAATAAATTTAAAAATAAA
Found at i:27927242 original size:28 final size:26
Alignment explanation
Indices: 27927210--27927280 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 26
27927200 ATACCAAAAA
* *
27927210 CATTTTTAGAATTTAGTTTTTATATTTT
1 CATTTTTAAAATTTA-TTTCTAT-TTTT
27927238 CATTTTTAAAAATTTATTTCTATTTTT
1 CATTTTT-AAAATTTATTTCTATTTTT
*
27927265 TAGTTTTTAAAATTTA
1 CA-TTTTTAAAATTTA
27927281 AGTCCTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 13 0.34
28 18 0.47
29 7 0.18
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (26 bp):
CATTTTTAAAATTTATTTCTATTTTT
Found at i:27932984 original size:156 final size:156
Alignment explanation
Indices: 27932698--27932985 Score: 486
Period size: 156 Copynumber: 1.8 Consensus size: 156
27932688 TTCTCATTTG
* *
27932698 ATACTCACGATGACACATAGTCATTAAACCTCATAATCCGAAAAGGATTCATATGCTCACGATGA
1 ATACTCACGATGACACATAGTCATTAAACCTCATAATCCGAAAAGGATTCATATACCCACGATGA
* * *
27932763 CATATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACGATGACACATAGTCATCG
66 CACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACAATGACACATAATCATCG
27932828 GAACTCATAATCTGTAAAAGATTCAT
131 GAACTCATAATCTGTAAAAGATTCAT
* *
27932854 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCATATACCCACGATGA
1 ATACTCACGATGACACATAGTCATTAAACCTCATAATCCGAAAAGGATTCATATACCCACGATGA
* * *
27932919 CACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATATACTCACAATGACACATAATTATCG
66 CACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACAATGACACATAATCATCG
27932984 GA
131 GA
27932986 CCTTTTGCAT
Statistics
Matches: 122, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
156 122 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.26
Consensus pattern (156 bp):
ATACTCACGATGACACATAGTCATTAAACCTCATAATCCGAAAAGGATTCATATACCCACGATGA
CACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACAATGACACATAATCATCG
GAACTCATAATCTGTAAAAGATTCAT
Found at i:27932989 original size:52 final size:52
Alignment explanation
Indices: 27932698--27932988 Score: 429
Period size: 52 Copynumber: 5.6 Consensus size: 52
27932688 TTCTCATTTG
*** *
27932698 ATACTCACGATGACACATAGTCATTAAACCTCATAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
27932750 ATGCTCACGATGACATATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
27932802 ATACTCACGATGACACATAGTCATCGGAACTCATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
27932854 ATACTCACGATGACACATAGTCATTGAACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
27932906 ATACCCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
27932958 ATACTCACAATGACACATAATTATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
27932989 TTTGCATTTA
Statistics
Matches: 213, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 213 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:27933560 original size:18 final size:16
Alignment explanation
Indices: 27933529--27933564 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
27933519 CATCAATATC
27933529 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
27933545 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
27933563 AT
1 AT
27933565 ATTTACAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:27937345 original size:31 final size:31
Alignment explanation
Indices: 27937309--27937377 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
27937299 GCAATTAATG
* *
27937309 CTTTTCCCGTATAACTCCGATCTCATCTTTC
1 CTTTTCCCATATAACCCCGATCTCATCTTTC
27937340 CTTTTCCCATATAACCCCGATCTCATCTTTC
1 CTTTTCCCATATAACCCCGATCTCATCTTTC
27937371 CTTTTCC
1 CTTTTCC
27937378 TGTTCACTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.16, C:0.38, G:0.04, T:0.42
Consensus pattern (31 bp):
CTTTTCCCATATAACCCCGATCTCATCTTTC
Found at i:27938208 original size:30 final size:29
Alignment explanation
Indices: 27938164--27938221 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
27938154 AAAATGCAAT
27938164 TTTTAAAGGATTAAA-TCAAAATTTTATCA
1 TTTTAAAGGATTAAAGT-AAAATTTTATCA
* *
27938193 TTTTAAAGGGGTTAAAGTACAATTTTATC
1 TTTTAAA-GGATTAAAGTAAAATTTTATC
27938222 TCTACTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 17 0.68
31 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (29 bp):
TTTTAAAGGATTAAAGTAAAATTTTATCA
Found at i:27948081 original size:19 final size:20
Alignment explanation
Indices: 27948054--27948098 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
27948044 GTTTAATATA
* *
27948054 TAATGTTATATAT-AAATTT
1 TAATTTTATAAATAAAATTT
27948073 TAATTTTATAAATAAAATTT
1 TAATTTTATAAATAAAATTT
27948093 TAATTT
1 TAATTT
27948099 GATTTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATTTTATAAATAAAATTT
Found at i:27951013 original size:16 final size:15
Alignment explanation
Indices: 27950992--27951030 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
27950982 TTTGAACTAT
* *
27950992 TTATATTTTATATAA
1 TTATATATTATAAAA
27951007 TTGATATATTATAAAA
1 TT-ATATATTATAAAA
27951023 TTATATAT
1 TTATATAT
27951031 GATTTAGAAA
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:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTATATATTATAAAA
Found at i:27952514 original size:8 final size:8
Alignment explanation
Indices: 27952496--27952550 Score: 56
Period size: 8 Copynumber: 6.5 Consensus size: 8
27952486 ATTAAATAAT
27952496 TTTTTATAA
1 TTTTTA-AA
27952505 TTTTTAAA
1 TTTTTAAA
27952513 TTTTTAAA
1 TTTTTAAA
* *
27952521 ATATTAAA
1 TTTTTAAA
*
27952529 TATTTTGAAT
1 T-TTTT-AAA
27952539 TTTTTAAA
1 TTTTTAAA
27952547 TTTT
1 TTTT
27952551 AAAAAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 22 0.58
9 13 0.34
10 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TTTTTAAA
Found at i:27952534 original size:25 final size:25
Alignment explanation
Indices: 27952506--27952553 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27952496 TTTTTATAAT
27952506 TTTTAAATTTTTAAAATATTAAATA
1 TTTTAAATTTTTAAAATATTAAATA
* * *
27952531 TTTTGAATTTTTTAAATTTTAAA
1 TTTTAAATTTTTAAAATATTAAA
27952554 AAATAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTAAATTTTTAAAATATTAAATA
Found at i:27952548 original size:9 final size:9
Alignment explanation
Indices: 27952493--27952550 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
27952483 AATATTAAAT
27952493 AATTTTTTA
1 AATTTTTTA
27952502 TAA-TTTTTA
1 -AATTTTTTA
27952511 AA-TTTTTA
1 AATTTTTTA
* *
27952519 AA-ATATTA
1 AATTTTTTA
* *
27952527 AATATTTTG
1 AATTTTTTA
27952536 AATTTTTTA
1 AATTTTTTA
27952545 AATTTT
1 AATTTT
27952551 AAAAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 16 0.39
9 23 0.56
10 2 0.05
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (9 bp):
AATTTTTTA
Found at i:27955157 original size:3 final size:3
Alignment explanation
Indices: 27955149--27955173 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
27955139 ATATATTCAA
27955149 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
27955174 GAGTGGCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27955835 original size:28 final size:27
Alignment explanation
Indices: 27955774--27955837 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
27955764 GGGGTCACCC
* **
27955774 CTTTTTAATTAATTTTTTAATTTATTA
1 CTTTTTATTTAATTTTTTAAAATATTA
*
27955801 TTATTTTATTTAATTTTATTAAAATATTA
1 CT-TTTTATTTAATTTT-TTAAAATATTA
27955830 CTTTTTAT
1 CTTTTTAT
27955838 GAGTGATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 1 0.03
28 19 0.63
29 10 0.33
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
CTTTTTATTTAATTTTTTAAAATATTA
Found at i:27956996 original size:22 final size:22
Alignment explanation
Indices: 27956971--27957014 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27956961 AATGATCAAC
27956971 TGAGCTGGCAGCGTAATGGTAA
1 TGAGCTGGCAGCGTAATGGTAA
27956993 TGAGCTGGCAGCGTAATGGTAA
1 TGAGCTGGCAGCGTAATGGTAA
27957015 AAAGCTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.36, T:0.23
Consensus pattern (22 bp):
TGAGCTGGCAGCGTAATGGTAA
Found at i:27957020 original size:22 final size:22
Alignment explanation
Indices: 27956973--27957020 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
27956963 TGATCAACTG
**
27956973 AGCTGGCAGCGTAATGGTAATG
1 AGCTGGCAGCGTAATGGTAAAA
27956995 AGCTGGCAGCGTAATGGTAAAA
1 AGCTGGCAGCGTAATGGTAAAA
27957017 AGCT
1 AGCT
27957021 TAAAAGAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (22 bp):
AGCTGGCAGCGTAATGGTAAAA
Found at i:27966963 original size:29 final size:29
Alignment explanation
Indices: 27966931--27966997 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
27966921 TGGGAATTTG
* *
27966931 GGGGTAAAACGGTAATTTTTGGATGTTTA
1 GGGGTAAAACGGTAAATTTTAGATGTTTA
* * *
27966960 GGGGTATAATGGTAAATTTTAGATTTTTA
1 GGGGTAAAACGGTAAATTTTAGATGTTTA
*
27966989 GGGGCAAAA
1 GGGGTAAAA
27966998 TCATAATTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (29 bp):
GGGGTAAAACGGTAAATTTTAGATGTTTA
Found at i:27967044 original size:29 final size:29
Alignment explanation
Indices: 27966985--27967189 Score: 189
Period size: 30 Copynumber: 7.0 Consensus size: 29
27966975 ATTTTAGATT
* * *
27966985 TTTAGGGGCAAAATCATAATTTTGGAGAAG
1 TTTAGGGTCAAAAT-GTAATTTTGGAAAAG
* *
27967015 TTTAGGCTCAAAATGTGATTTTGGAAAAG
1 TTTAGGGTCAAAATGTAATTTTGGAAAAG
** * * *
27967044 TTCGGGGTTAAAATATAATTTTGGAGAAG
1 TTTAGGGTCAAAATGTAATTTTGGAAAAG
* *
27967073 TTTAAGGGTTAAAATGTAATTTTAGAAAAG
1 TTT-AGGGTCAAAATGTAATTTTGGAAAAG
* * *
27967103 TTCAAGGTCAAAATGTGATTTTTGGAAAAG
1 TTTAGGGTCAAAATGT-AATTTTGGAAAAG
*
27967133 TTT--GGTGCAAAATGTAATTTTGGAGAAG
1 TTTAGGGT-CAAAATGTAATTTTGGAAAAG
* *
27967161 TTTAGGGGTCAAAATGTGATTTTGAAAAA
1 TTTA-GGGTCAAAATGTAATTTTGGAAAA
27967190 AATAGGGGCC
Statistics
Matches: 141, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
28 17 0.12
29 55 0.39
30 66 0.47
31 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
TTTAGGGTCAAAATGTAATTTTGGAAAAG
Found at i:27967114 original size:88 final size:87
Alignment explanation
Indices: 27967022--27967188 Score: 246
Period size: 88 Copynumber: 1.9 Consensus size: 87
27967012 AAGTTTAGGC
* *
27967022 TCAAAATGTGA-TTTTGGAAAAGTTCGGGGTTAAAATATAATTTTGGAGAAGTTTAAGGGTTAAA
1 TCAAAATGTGATTTTTGGAAAAGTTCGGGG-CAAAATATAATTTTGGAGAAGTTTAAGGGTCAAA
27967086 ATGTAATTTTAGAAAAGTTCAAGG
65 ATGTAATTTT-GAAAAGTTCAAGG
* * * *
27967110 TCAAAATGTGATTTTTGGAAAAGTTTGGTGCAAAATGTAATTTTGGAGAAGTTTAGGGGTCAAAA
1 TCAAAATGTGATTTTTGGAAAAGTTCGGGGCAAAATATAATTTTGGAGAAGTTTAAGGGTCAAAA
*
27967175 TGTGATTTTGAAAA
66 TGTAATTTTGAAAA
27967189 AAATAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
87 5 0.07
88 50 0.70
89 16 0.23
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (87 bp):
TCAAAATGTGATTTTTGGAAAAGTTCGGGGCAAAATATAATTTTGGAGAAGTTTAAGGGTCAAAA
TGTAATTTTGAAAAGTTCAAGG
Found at i:27968930 original size:39 final size:38
Alignment explanation
Indices: 27968887--27969210 Score: 119
Period size: 39 Copynumber: 8.4 Consensus size: 38
27968877 TCTTAAGCTT
* * *
27968887 GGGGTTAAAGATTGAATGGCTGCAATCTATCCCAGGCTC
1 GGGGTAAAAGATCGAATGGCTACAATCTA-CCCAGGCTC
* ** *** *
27968926 GGGGTAAAAGATTGGCTGG-TGGTGATTTACTCCAGGCTC
1 GGGGTAAAAGATCGAATGGCT-ACAATCTAC-CCAGGCTC
* * * * *
27968965 GGGGTAAAAGATCGGATGGCTAAAATTTGCCCCAGGCTT
1 GGGGTAAAAGATCGAATGGCTACAATCT-ACCCAGGCTC
27969004 GGGGTAAAAGATCGAATGGCTACAATCTA--C--GCTC
1 GGGGTAAAAGATCGAATGGCTACAATCTACCCAGGCTC
* * * * * *
27969038 GGGGGTAAGAGATTGGTTGATGG-T--GATCTGCCCTCGGCTC
1 -GGGGTAAAAGA-TCG--AATGGCTACAATCTACCC-AGGCTC
* * ** * *
27969078 GGGGTAAAAGATTGAATGACTGTAATTTCCCCAGGCTC
1 GGGGTAAAAGATCGAATGGCTACAATCTACCCAGGCTC
* * * ** ** * *
27969116 GGAGTAAGAGATTGGCTGG-TGATGATC-CCCTCATGCTC
1 GGGGTAAAAGATCGAATGGCT-ACAATCTACC-CAGGCTC
*
27969154 GGGGTAAAAGATCGAATGGCTACAATCTGACCTAGGCTC
1 GGGGTAAAAGATCGAATGGCTACAATCT-ACCCAGGCTC
*
27969193 GGGGTAAGAGATCAGAAT
1 GGGGTAAAAGATC-GAAT
27969211 CTTCAATTTG
Statistics
Matches: 212, Mismatches: 51, Indels: 43
0.69 0.17 0.14
Matches are distributed among these distances:
34 3 0.01
35 14 0.07
36 6 0.03
37 7 0.03
38 54 0.25
39 116 0.55
40 12 0.06
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.24
Consensus pattern (38 bp):
GGGGTAAAAGATCGAATGGCTACAATCTACCCAGGCTC
Found at i:27968969 original size:78 final size:78
Alignment explanation
Indices: 27968843--27969015 Score: 186
Period size: 78 Copynumber: 2.2 Consensus size: 78
27968833 ATCTGCCCTT
* * * * * *
27968843 GGCTCGGGGTAAGAGATTGGATGATGGTGATTTGTCTTAAGCTTGGGGTTAAAGATTGAATGGCT
1 GGCTCGGGGTAAAAGATTGGATGATGGTGATTTCTCTCAAGCTCGGGGTAAAAGATCGAATGGCT
** *
27968908 GCAATCTATCCCA
66 AAAATCTACCCCA
* * * *
27968921 GGCTCGGGGTAAAAGATTGGCTGGTGGTGATTTACTC-CAGGCTCGGGGTAAAAGATCGGATGGC
1 GGCTCGGGGTAAAAGATTGGATGATGGTGATTT-CTCTCAAGCTCGGGGTAAAAGATCGAATGGC
* *
27968985 TAAAATTTGCCCCA
65 TAAAATCTACCCCA
*
27968999 GGCTTGGGGTAAAAGAT
1 GGCTCGGGGTAAAAGAT
27969016 CGAATGGCTA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 76 0.97
79 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (78 bp):
GGCTCGGGGTAAAAGATTGGATGATGGTGATTTCTCTCAAGCTCGGGGTAAAAGATCGAATGGCT
AAAATCTACCCCA
Found at i:27969082 original size:74 final size:72
Alignment explanation
Indices: 27968997--27969181 Score: 192
Period size: 74 Copynumber: 2.5 Consensus size: 72
27968987 AAATTTGCCC
* * * *
27968997 CAGGCTTGGGGTAAAAGATCGAATGGCTACAATCTACGCTCGGGGGTAAGAGATTGGTTGATGGT
1 CAGGCTCGGGGTAAAAGATCGAATGGCTACAATCTACGCTC-GGAGTAAGAGATTGGCTGATGAT
27969062 GATCTGCCCT
65 GATC--CCCT
* * ** * * *
27969072 C-GGCTCGGGGTAAAAGATTGAATGACTGTAATTTCCCCAGGCTCGGAGTAAGAGATTGGCTGGT
1 CAGGCTCGGGGTAAAAGATCGAATGGCTACAA--T--CTACGCTCGGAGTAAGAGATTGGCTGAT
27969136 GATGATCCCCT
62 GATGATCCCCT
*
27969147 CATGCTCGGGGTAAAAGATCGAATGGCTACAATCT
1 CAGGCTCGGGGTAAAAGATCGAATGGCTACAATCT
27969182 GACCTAGGCT
Statistics
Matches: 88, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
72 1 0.01
74 26 0.30
75 6 0.07
76 26 0.30
77 23 0.26
78 6 0.07
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (72 bp):
CAGGCTCGGGGTAAAAGATCGAATGGCTACAATCTACGCTCGGAGTAAGAGATTGGCTGATGATG
ATCCCCT
Found at i:27969191 original size:77 final size:75
Alignment explanation
Indices: 27968999--27969204 Score: 222
Period size: 77 Copynumber: 2.7 Consensus size: 75
27968989 ATTTGCCCCA
* * *
27968999 GGCTTGGGGTAAAAGATCGAATGGCTACAATCTA-C--GCTCGGGGGTAAGAGATTGGTTGATGG
1 GGCTCGGGGTAAAAGATCGAATGGCTACAATCTACCAGGCTC-GGGGTAAGAGATTGGCTGATGA
27969061 TGATCTGCCCTC
65 TGATC-GCCCTC
* * ** * * * *
27969073 GGCTCGGGGTAAAAGATTGAATGACTGTAATTTCCCCAGGCTCGGAGTAAGAGATTGGCTGGTGA
1 GGCTCGGGGTAAAAGATCGAATGGCTACAATCT-ACCAGGCTCGGGGTAAGAGATTGGCTGATGA
27969138 TGATC-CCCTC
65 TGATCGCCCTC
*
27969148 ATGCTCGGGGTAAAAGATCGAATGGCTACAATCTGACCTAGGCTCGGGGTAAGAGAT
1 -GGCTCGGGGTAAAAGATCGAATGGCTACAATCT-ACC-AGGCTCGGGGTAAGAGAT
27969205 CAGAATCTTC
Statistics
Matches: 106, Mismatches: 20, Indels: 9
0.79 0.15 0.07
Matches are distributed among these distances:
74 27 0.25
75 5 0.05
76 30 0.28
77 40 0.38
78 4 0.04
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.24
Consensus pattern (75 bp):
GGCTCGGGGTAAAAGATCGAATGGCTACAATCTACCAGGCTCGGGGTAAGAGATTGGCTGATGAT
GATCGCCCTC
Found at i:27969573 original size:49 final size:49
Alignment explanation
Indices: 27969520--27969615 Score: 111
Period size: 49 Copynumber: 2.0 Consensus size: 49
27969510 TTAAGGTGTC
**
27969520 GGGTTCACCATTGCAGCCTAAACCTTTCCCTTCAAATCTTCATGGTATT
1 GGGTTCACCATTGCAGCCTAAACCTTTCCAATCAAATCTTCATGGTATT
* * * * * **
27969569 GGGTTTACCGTTGCTGCCTCAACTTTTCCAATCGCATCTTCATGGTA
1 GGGTTCACCATTGCAGCCTAAACCTTTCCAATCAAATCTTCATGGTA
27969616 CCGGATTTTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (49 bp):
GGGTTCACCATTGCAGCCTAAACCTTTCCAATCAAATCTTCATGGTATT
Found at i:27976164 original size:29 final size:28
Alignment explanation
Indices: 27976124--27976223 Score: 87
Period size: 29 Copynumber: 3.5 Consensus size: 28
27976114 TTTGAGGTTG
*
27976124 AAAATG-TGATTTTTGGGAATTTGGGGGC
1 AAAATGATAATTTTT-GGAATTTGGGGGC
27976152 AAAATGATAATTTTTGG-ATGTTCGGGGGC
1 AAAATGATAATTTTTGGAAT-TT-GGGGGC
* * * * *
27976181 ATAATGGTAGTTTTTGGATGTTTGAGGGC
1 AAAATGATAATTTTTGGA-ATTTGGGGGC
*
27976210 AAAATCATAATTTT
1 AAAATGATAATTTT
27976224 GGAGAAGTTC
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.04
28 10 0.18
29 42 0.74
30 2 0.04
31 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.38
Consensus pattern (28 bp):
AAAATGATAATTTTTGGAATTTGGGGGC
Found at i:27976312 original size:59 final size:59
Alignment explanation
Indices: 27976237--27976404 Score: 232
Period size: 59 Copynumber: 2.8 Consensus size: 59
27976227 GAAGTTCGGG
* * * *
27976237 GGTGAAAATATAATTTTGAAAAAGTTTAGGGGTCAAAATGTCATTTTAGAAAAGTTT-G
1 GGTGAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTAGAAAAGTTTAA
* * *
27976295 GCGTGAAAATGTGATTTTGGAAAAG-TTCGAGGTCAAAATGTGATTTTTAGAAAAGTTTAA
1 G-GTGAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTGA-TTTTAGAAAAGTTTAA
*
27976355 GGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTAGA
1 GGTGAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTAGA
27976405 GAAAATAGGG
Statistics
Matches: 95, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
58 16 0.17
59 62 0.65
60 17 0.18
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (59 bp):
GGTGAAAATGTAATTTTGGAAAAGTTTAGGGGTCAAAATGTGATTTTAGAAAAGTTTAA
Found at i:27976317 original size:29 final size:30
Alignment explanation
Indices: 27976219--27976401 Score: 192
Period size: 30 Copynumber: 6.2 Consensus size: 30
27976209 CAAAATCATA
* ** * * *
27976219 ATTTTGGAGAAGTTCGGGGGTGAAAATATA
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* *
27976249 ATTTTGAAAAAGTTTAGGGGTCAAAATGTC
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* * *
27976279 ATTTTAGAAAAGTTT-GGCGTGAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* *
27976308 ATTTTGGAAAAG-TTCGAGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
* * *
27976337 ATTTTTAGAAAAGTTTA-AGGTCAAAATGTA
1 A-TTTTGGAAAAGTTTAGGGGTCAAAATGTG
27976367 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
1 ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
27976397 ATTTT
1 ATTTT
27976402 AGAGAAAATA
Statistics
Matches: 127, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
28 2 0.02
29 48 0.38
30 75 0.59
31 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTAGGGGTCAAAATGTG
Found at i:27978263 original size:27 final size:27
Alignment explanation
Indices: 27978233--27978310 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
27978223 CACCTGAAAC
*
27978233 AATGAATACTCTTAATCATCAGGCAAT
1 AATGAACACTCTTAATCATCAGGCAAT
27978260 AATGAACACTCTTAATCATCAGGCAAT
1 AATGAACACTCTTAATCATCAGGCAAT
*
27978287 AATGAACACTCTTAATAATCAGGC
1 AATGAACACTCTTAATCATCAGGC
27978311 CAATCACGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.27
Consensus pattern (27 bp):
AATGAACACTCTTAATCATCAGGCAAT
Found at i:27982384 original size:19 final size:21
Alignment explanation
Indices: 27982347--27982389 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
27982337 TGAGATTCTG
27982347 TTTTGTTCTTATATTCC-TTC
1 TTTTGTTCTTATATTCCTTTC
27982367 TTTTGTTTCTT-T-TTCCTTTC
1 TTTTG-TTCTTATATTCCTTTC
27982387 TTT
1 TTT
27982390 ATTCTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 12 0.57
21 5 0.24
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTGTTCTTATATTCCTTTC
Found at i:28002831 original size:29 final size:30
Alignment explanation
Indices: 28002790--28002866 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
28002780 AAGTTTTGAA
*
28002790 TTTAGTCCATATA-TTTT-AATT-TGATCAAT
1 TTTAGTCCTTATACTTTTGAATTAT--TCAAT
28002819 TTTAGTCCTTATACTTTTTGAATTATTCAAT
1 TTTAGTCCTTATAC-TTTTGAATTATTCAAT
28002850 TTTAGT-CTTATACTTTT
1 TTTAGTCCTTATACTTTT
28002867 TTTAATTTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
29 16 0.37
30 7 0.16
31 15 0.35
32 4 0.09
33 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (30 bp):
TTTAGTCCTTATACTTTTGAATTATTCAAT
Found at i:28002882 original size:31 final size:31
Alignment explanation
Indices: 28002803--28002889 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
28002793 AGTCCATATA
28002803 TTTTAA-TTTGATCAATTTTAGTCCTTATACTT
1 TTTTAATTTTGA--AATTTTAGTCCTTATACTT
* *
28002835 TTTGAATTATT-CAATTTTAGT-CTTATACTTT
1 TTTTAATT-TTGAAATTTTAGTCCTTATAC-TT
*
28002866 TTTTAATTTTGAAATTTTAATCCT
1 TTTTAATTTTGAAATTTTAGTCCT
28002890 GACTAGTCTT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
30 9 0.20
31 26 0.58
32 7 0.16
33 1 0.02
34 2 0.04
ACGTcount: A:0.26, C:0.10, G:0.06, T:0.57
Consensus pattern (31 bp):
TTTTAATTTTGAAATTTTAGTCCTTATACTT
Found at i:28004011 original size:31 final size:30
Alignment explanation
Indices: 28003943--28004030 Score: 142
Period size: 29 Copynumber: 2.9 Consensus size: 30
28003933 GTTATTGAAC
* *
28003943 TATTTAAAAGTTTTTATTTAAGTCACTATA
1 TATTTGAAAGTTTTTATTTAAGTTACTATA
28003973 -ATTTGAAAGTTTTTATTTAAGTTACTATA
1 TATTTGAAAGTTTTTATTTAAGTTACTATA
28004002 TTATTTGAAAGTTTTTATTTAAGTTACTA
1 -TATTTGAAAGTTTTTATTTAAGTTACTA
28004031 GTTGTTAAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
29 27 0.50
31 27 0.50
ACGTcount: A:0.34, C:0.05, G:0.09, T:0.52
Consensus pattern (30 bp):
TATTTGAAAGTTTTTATTTAAGTTACTATA
Found at i:28005353 original size:50 final size:50
Alignment explanation
Indices: 28005299--28005395 Score: 124
Period size: 50 Copynumber: 1.9 Consensus size: 50
28005289 AAAAAACTAA
* * *
28005299 TCACGCCAATTACATTAGCACCACTAGAA-AAAAAATCAATTTTTTTAGGG
1 TCACGCCAATTACAGTAGCACAACCA-AATAAAAAATCAATTTTTTTAGGG
* * *
28005349 TCACGCGAATTACAGTCGCAGAACCAAATAAAAAATCAATTTTTTTA
1 TCACGCCAATTACAGTAGCACAACCAAATAAAAAATCAATTTTTTTA
28005396 AAAATCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
49 2 0.05
50 38 0.95
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (50 bp):
TCACGCCAATTACAGTAGCACAACCAAATAAAAAATCAATTTTTTTAGGG
Found at i:28012423 original size:16 final size:16
Alignment explanation
Indices: 28012402--28012436 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28012392 TTTGGAAACC
*
28012402 AATATTTGAGCTTATT
1 AATATTTGAGCTTACT
28012418 AATATTTGAGCTTACT
1 AATATTTGAGCTTACT
28012434 AAT
1 AAT
28012437 TTTAGCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (16 bp):
AATATTTGAGCTTACT
Found at i:28022957 original size:22 final size:22
Alignment explanation
Indices: 28022931--28022973 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
28022921 ATAATTCATT
28022931 TAAATA-TAATTATCAAAATACA
1 TAAATATTAA-TATCAAAATACA
*
28022953 TAAATATTAATATTAAAATAC
1 TAAATATTAATATCAAAATAC
28022974 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAATATTAATATCAAAATACA
Found at i:28023428 original size:16 final size:18
Alignment explanation
Indices: 28023389--28023422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28023379 TAAGTTTATA
28023389 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28023406 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28023423 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28026008 original size:27 final size:26
Alignment explanation
Indices: 28025964--28026025 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
28025954 TAAGATGAAT
*
28025964 ATATATAAATTTTCAATAGATAAAA-AA
1 ATATA-AAATTTTAAATA-ATAAAATAA
*
28025991 ATATAAAATTATTAAATATTAAAATAA
1 ATATAAAATT-TTAAATAATAAAATAA
28026018 A-ATAAAAT
1 ATATAAAAT
28026026 AAATATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 17 0.55
27 14 0.45
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (26 bp):
ATATAAAATTTTAAATAATAAAATAA
Found at i:28027722 original size:40 final size:40
Alignment explanation
Indices: 28027663--28027742 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
28027653 ATACTTTTAT
* *
28027663 TATTCCTTTTTAAACTAAACAGTCTATTTAATTTAGGAAA
1 TATTCCTTCTTAAACTAAACAGTCCATTTAATTTAGGAAA
* * *
28027703 TATTCCTTCTTAAATTAAACCGTCCATTTATTTTAGGAAA
1 TATTCCTTCTTAAACTAAACAGTCCATTTAATTTAGGAAA
28027743 ATGTTGATGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (40 bp):
TATTCCTTCTTAAACTAAACAGTCCATTTAATTTAGGAAA
Found at i:28052017 original size:23 final size:20
Alignment explanation
Indices: 28051977--28052019 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
28051967 GAATTCATGG
28051977 TTATATTTTGAGCTTGAGTA
1 TTATATTTTGAGCTTGAGTA
28051997 TTATGATTTTGAATGCTTGAGTA
1 TTAT-ATTTTG-A-GCTTGAGTA
28052020 AGAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 6 0.30
22 1 0.05
23 9 0.45
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (20 bp):
TTATATTTTGAGCTTGAGTA
Found at i:28054948 original size:15 final size:16
Alignment explanation
Indices: 28054912--28054950 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28054902 TACTTATATT
*
28054912 ATAATAATATTATTAA
1 ATAATTATATTATTAA
*
28054928 AAAATTATATT-TTAA
1 ATAATTATATTATTAA
28054943 ATAATTAT
1 ATAATTAT
28054951 TAAATAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTATATTATTAA
Found at i:28054968 original size:23 final size:25
Alignment explanation
Indices: 28054916--28054969 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
28054906 TATATTATAA
*
28054916 TAAT-ATTATTAAAAAATTATATTT
1 TAATAATTATTAAAAAATTATACTT
*
28054940 TAAATAATTATTAAATAA-TA-ACTT
1 T-AATAATTATTAAAAAATTATACTT
28054964 TAATAA
1 TAATAA
28054970 AAAAAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 5 0.19
26 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TAATAATTATTAAAAAATTATACTT
Found at i:28058293 original size:21 final size:22
Alignment explanation
Indices: 28058257--28058300 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
28058247 ATGTCAAAAA
*
28058257 AATAAATATGATTAAAATATAT
1 AATAAATATGATTAAAAAATAT
*
28058279 AATAAA-ATTATTAAAAAATAT
1 AATAAATATGATTAAAAAATAT
28058300 A
1 A
28058301 TATAGCTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
AATAAATATGATTAAAAAATAT
Found at i:28058656 original size:30 final size:29
Alignment explanation
Indices: 28058587--28058657 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
28058577 TTTAATAATC
*
28058587 TATATTTTTATAATTTTTAAAAGATTAAA
1 TATAATTTTATAATTTTTAAAAGATTAAA
* * *
28058616 TCA-AATTTTTATTATTTTTAAGAGGTTAAAA
1 T-ATAA-TTTTATAATTTTTAAAAGATT-AAA
28058647 TATAATTTTAT
1 TATAATTTTAT
28058658 CATTACTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
29 2 0.06
30 26 0.76
31 6 0.18
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (29 bp):
TATAATTTTATAATTTTTAAAAGATTAAA
Found at i:28058716 original size:84 final size:83
Alignment explanation
Indices: 28058559--28058717 Score: 178
Period size: 84 Copynumber: 1.9 Consensus size: 83
28058549 TATGATAGTA
* * * ** *
28058559 AAAATATAATTTTATTATTTTAATAATCTATATTTTTATAATTTTTAAAAGATTAAATCAAATTT
1 AAAATATAATTTTATCA-TTTAATAATCTAAAGTTTTATAAACTATAAAAGATTAAATCAAATTT
*
28058624 TTATTATTTTTAAGAGGTT
65 TTACTATTTTTAAGAGGTT
* * *
28058643 AAAATATAATTTTATCA-TTACTAATTTAAAGTTTTATAAACTATAAAAGGATCTAAATGAAGAT
1 AAAATATAATTTTATCATTTAATAATCTAAAGTTTTATAAACTATAAAA-GAT-TAAATCAA-AT
28058707 TTTT-CTATTTT
63 TTTTACTATTTT
28058718 AAGGAAATCA
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
82 24 0.39
83 3 0.05
84 29 0.47
85 6 0.10
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (83 bp):
AAAATATAATTTTATCATTTAATAATCTAAAGTTTTATAAACTATAAAAGATTAAATCAAATTTT
TACTATTTTTAAGAGGTT
Found at i:28060319 original size:31 final size:31
Alignment explanation
Indices: 28060284--28060352 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
28060274 TACAAAATAG
*
28060284 TCATTGATTTATTT-AAAAGTTTTTATTTAAA
1 TCATTGAATTATTTGAAAA-TTTTTATTTAAA
* *
28060315 TCATTAAATTATTTGAAAATTTTTATTTAAG
1 TCATTGAATTATTTGAAAATTTTTATTTAAA
28060346 TCATTGA
1 TCATTGA
28060353 GTTGTTAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (31 bp):
TCATTGAATTATTTGAAAATTTTTATTTAAA
Found at i:28060886 original size:12 final size:12
Alignment explanation
Indices: 28060865--28060896 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
28060855 AAGTACAAAG
*
28060865 ATATATATATAT
1 ATATAAATATAT
28060877 ATATAAATATAT
1 ATATAAATATAT
28060889 ATATAAAT
1 ATATAAAT
28060897 TTTTTTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATAAATATAT
Found at i:28062326 original size:27 final size:29
Alignment explanation
Indices: 28062277--28062345 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 29
28062267 AGTCTCGATT
**
28062277 GAATCTAAATTTTCAAATCTAAAAAGTA-A-
1 GAAT-TAAATTTTCAAAAATAAAAA-TACAG
*
28062306 G-ATTAAATTTTTAAAAATAAAAATACAG
1 GAATTAAATTTTCAAAAATAAAAATACAG
28062334 GAATTAAATTTT
1 GAATTAAATTTT
28062346 AAATTTACAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 2 0.06
27 18 0.53
28 3 0.09
29 11 0.32
ACGTcount: A:0.52, C:0.06, G:0.07, T:0.35
Consensus pattern (29 bp):
GAATTAAATTTTCAAAAATAAAAATACAG
Found at i:28064408 original size:3 final size:3
Alignment explanation
Indices: 28064400--28064444 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
28064390 AGACTATGTT
28064400 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28064445 AGACATCACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28068334 original size:19 final size:19
Alignment explanation
Indices: 28068312--28068356 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28068302 TTATATTAGG
28068312 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
28068331 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
28068350 ATTTAAT
1 ATTTAAT
28068357 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:28069421 original size:7 final size:7
Alignment explanation
Indices: 28069409--28069436 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
28069399 ATTGTTAATC
28069409 CCCTTCT
1 CCCTTCT
28069416 CCCTTCT
1 CCCTTCT
28069423 CCCTTCT
1 CCCTTCT
28069430 CCCTTCT
1 CCCTTCT
28069437 TGGTCTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (7 bp):
CCCTTCT
Found at i:28071109 original size:43 final size:43
Alignment explanation
Indices: 28071054--28071323 Score: 366
Period size: 43 Copynumber: 6.3 Consensus size: 43
28071044 GTTTATTAGA
* *
28071054 AAAAACGCCGCTATAGAACATGGTTTTTAGCGGCGCTTTTCAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
*
28071097 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* * *
28071139 AAAAACGCCGCTAAAGAACATTGTCTTTAGCGACGCTTTTTAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* * *
28071182 ACAAACGCCGCTAAAGAACATGATCTTCAGCGGCGCTTTTCAC
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* * * * *
28071225 ACAAACGCCACTAAAGAACATTG-CTTTTAGCGGCGCTTTCCCC
1 AAAAACGCCGCTAAAGAACATGGTC-TTTAGCGGCGCTTTTCAC
28071268 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTC-C
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
* *
28071310 ACAAACACCGCTAA
1 AAAAACGCCGCTAA
28071324 CATTAATAAA
Statistics
Matches: 199, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
42 53 0.27
43 145 0.73
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCAC
Found at i:28071188 original size:85 final size:85
Alignment explanation
Indices: 28071054--28071323 Score: 371
Period size: 85 Copynumber: 3.2 Consensus size: 85
28071044 GTTTATTAGA
* * *
28071054 AAAAACGCCGCTATAGAACATGGTTTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATTGTCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACATG
28071119 GTCTTTAGCGGCGCTTTCCC
66 GTCTTTAGCGGCGCTTTCCC
* * *
28071139 AAAAACGCCGCTAAAGAACATTGTCTTTAGCGACGCTTTTTACACAAACGCCGCTAAAGAACATG
1 AAAAACGCCGCTAAAGAACATTGTCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACATG
* * *
28071204 ATCTTCAGCGGCGCTTTTCAC
66 GTCTTTAGCGGCGC-TTTCCC
* * * *
28071225 ACAAACGCCACTAAAGAACATTG-CTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACAT
1 AAAAACGCCGCTAAAGAACATTGTC-TTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACAT
*
28071289 GGTCTTTAGCGGCGCTTTTCC
65 GGTCTTTAGCGGCGCTTTCCC
* *
28071310 ACAAACACCGCTAA
1 AAAAACGCCGCTAA
28071324 CATTAATAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
85 88 0.55
86 73 0.45
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (85 bp):
AAAAACGCCGCTAAAGAACATTGTCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACATG
GTCTTTAGCGGCGCTTTCCC
Found at i:28071200 original size:128 final size:128
Alignment explanation
Indices: 28071056--28071323 Score: 405
Period size: 128 Copynumber: 2.1 Consensus size: 128
28071046 TTATTAGAAA
* * * * *
28071056 AAACGCCGCTATAGAACATGGTTTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGAACATGG-
1 AAACGCCGCTAAAGAACATGATCTTCAGCGGCGCTTTTCACAAAAACGCCACTAAAGAACATGGC
*
28071120 TCTTTAGCGGCGCTTT-CCCAAAAACGCCGCTAAAGAACATTGTCTTTAGCGACGCTTTTTACAC
66 T-TTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGC-TTTTACAC
* *
28071184 AAACGCCGCTAAAGAACATGATCTTCAGCGGCGCTTTTCACACAAACGCCACTAAAGAACATTGC
1 AAACGCCGCTAAAGAACATGATCTTCAGCGGCGCTTTTCACAAAAACGCCACTAAAGAACATGGC
* *
28071249 TTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAC
66 TTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTACAC
*
28071312 AAACACCGCTAA
1 AAACGCCGCTAA
28071324 CATTAATAAA
Statistics
Matches: 127, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
128 89 0.70
129 38 0.30
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATGATCTTCAGCGGCGCTTTTCACAAAAACGCCACTAAAGAACATGGC
TTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAGAACATGGTCTTTAGCGACGCTTTTACAC
Found at i:28073868 original size:41 final size:41
Alignment explanation
Indices: 28073820--28074195 Score: 431
Period size: 41 Copynumber: 9.0 Consensus size: 41
28073810 TTCTGCTTTA
*
28073820 ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTATG
1 ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTG
* * * *
28073861 ACATTTAGCGGCGCTT-TTCCATAAGCGTCGCTATTGGTCTG
1 ACCTTTAGCGGCGCTTGCT-CATAAGCGCCGCTATTGCTCTG
*
28073902 ACCTTTAGCGGCGCTTGAC-CATAAGCGCCGCTATTGCTTTG
1 ACCTTTAGCGGCGCTTG-CTCATAAGCGCCGCTATTGCTCTG
28073943 ACCTTTAGCGGCGCTTGAC-CATAAGCGCCGCTATTGCTCTG
1 ACCTTTAGCGGCGCTTG-CTCATAAGCGCCGCTATTGCTCTG
* **
28073984 ACTTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTAATCTG
1 ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTG
*
28074025 ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGATCTG
1 ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTG
* *
28074066 ACCTTTAGCGGCGCTTTTCCATCTTGACCATAAGCGTCGCTATTGCTCTG
1 ACCTTTAGCGGCGC--TT---GC-T---CATAAGCGCCGCTATTGCTCTG
* * *
28074116 ACCTTTAGCGACGCTTTAC-CATAAGCGCCGCTATTGCTC-C
1 ACCTTTAGCGGCGC-TTGCTCATAAGCGCCGCTATTGCTCTG
* *
28074156 ACTTTTAGCGGCGCTT-TTCTATAAGCGCCGCTATTGCTCT
1 ACCTTTAGCGGCGCTTGCTC-ATAAGCGCCGCTATTGCTCT
28074196 AGTTTTTGTG
Statistics
Matches: 293, Mismatches: 26, Indels: 32
0.83 0.07 0.09
Matches are distributed among these distances:
39 3 0.01
40 33 0.11
41 216 0.74
43 2 0.01
46 2 0.01
47 1 0.00
49 3 0.01
50 33 0.11
ACGTcount: A:0.17, C:0.29, G:0.22, T:0.31
Consensus pattern (41 bp):
ACCTTTAGCGGCGCTTGCTCATAAGCGCCGCTATTGCTCTG
Found at i:28073945 original size:24 final size:24
Alignment explanation
Indices: 28073916--28073985 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
28073906 TTAGCGGCGC
28073916 TTGACCATAAGCGCCGCTATTGCT
1 TTGACCATAAGCGCCGCTATTGCT
* *
28073940 TTGACCTTTAGCG--GC----GC-
1 TTGACCATAAGCGCCGCTATTGCT
28073957 TTGACCATAAGCGCCGCTATTGCT
1 TTGACCATAAGCGCCGCTATTGCT
*
28073981 CTGAC
1 TTGAC
28073986 TTTTAGCGGC
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 2 0.06
22 2 0.06
23 2 0.06
24 15 0.44
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.29
Consensus pattern (24 bp):
TTGACCATAAGCGCCGCTATTGCT
Found at i:28074080 original size:24 final size:24
Alignment explanation
Indices: 28074048--28074130 Score: 76
Period size: 24 Copynumber: 3.4 Consensus size: 24
28074038 CTTGCTCATA
*
28074048 AGCGCCGCTATTGATCTGACCTTT
1 AGCGACGCTATTGATCTGACCTTT
* * * * *
28074072 AGCGGCGCTTTTCCATCTTGACCATA
1 AGCGACGCTATT-GATC-TGACCTTT
* *
28074098 AGCGTCGCTATTGCTCTGACCTTT
1 AGCGACGCTATTGATCTGACCTTT
28074122 AGCGACGCT
1 AGCGACGCT
28074131 TTACCATAAG
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
24 24 0.53
25 5 0.11
26 16 0.36
ACGTcount: A:0.17, C:0.30, G:0.22, T:0.31
Consensus pattern (24 bp):
AGCGACGCTATTGATCTGACCTTT
Found at i:28074180 original size:40 final size:40
Alignment explanation
Indices: 28074093--28074214 Score: 145
Period size: 40 Copynumber: 3.0 Consensus size: 40
28074083 TCCATCTTGA
* * * * *
28074093 CCATAAGCGTCGCTATTGCTCTGACCTTTAGCGACGCTTTA
1 CCATAAGCGCCGCTATTGCTC-CACTTTTAGCGGCGCTTTT
28074134 CCATAAGCGCCGCTATTGCTCCACTTTTAGCGGCGCTTTT
1 CCATAAGCGCCGCTATTGCTCCACTTTTAGCGGCGCTTTT
* * * * *
28074174 CTATAAGCGCCGCTATTGCTCTAGTTTTTGTGGCGCTTTT
1 CCATAAGCGCCGCTATTGCTCCACTTTTAGCGGCGCTTTT
28074214 C
1 C
28074215 ATCCAAACGC
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 51 0.72
41 20 0.28
ACGTcount: A:0.16, C:0.29, G:0.20, T:0.35
Consensus pattern (40 bp):
CCATAAGCGCCGCTATTGCTCCACTTTTAGCGGCGCTTTT
Found at i:28075769 original size:31 final size:29
Alignment explanation
Indices: 28075714--28075784 Score: 97
Period size: 31 Copynumber: 2.4 Consensus size: 29
28075704 AATGTTTGAA
*
28075714 TTAATTTTAAATTCATTTTTAAATTTATC
1 TTAAATTTAAATTCATTTTTAAATTTATC
* *
28075743 TTAAATTTAAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTCA-TT-TTTAAATTTATC
28075774 TTAAATTTAAA
1 TTAAATTTAAA
28075785 CTTAATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 13 0.35
30 2 0.05
31 22 0.59
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTTAAATTCATTTTTAAATTTATC
Found at i:28075781 original size:11 final size:11
Alignment explanation
Indices: 28075712--28075782 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
28075702 TTAATGTTTG
*
28075712 AATTAATTTTA
1 AATTTATTTTA
*
28075723 AATTCATTTTTA
1 AATTTA-TTTTA
*
28075735 AATTTATCTTA
1 AATTTATTTTA
*
28075746 AATTTAAATTT-
1 AATTT-ATTTTA
*
28075757 -ACTTA-TTTA
1 AATTTATTTTA
28075766 AATTTATTTTA
1 AATTTATTTTA
28075777 AATTTA
1 AATTTA
28075783 AACTTAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.15
11 24 0.50
12 13 0.27
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTATTTTA
Found at i:28075793 original size:17 final size:17
Alignment explanation
Indices: 28075761--28075795 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28075751 AAATTTACTT
* *
28075761 ATTTAAATTTATTTTAA
1 ATTTAAACTTAATTTAA
28075778 ATTTAAACTTAATTTAA
1 ATTTAAACTTAATTTAA
28075795 A
1 A
28075796 ATAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAACTTAATTTAA
Found at i:28077596 original size:162 final size:162
Alignment explanation
Indices: 28077420--28077894 Score: 880
Period size: 162 Copynumber: 2.9 Consensus size: 162
28077410 TCTTTCCAAT
28077420 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
28077485 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
28077550 AATTAGTCCAAGAATTTTTCATGGTTTATAAA
131 AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
* *
28077582 TTAGTCCATTGACTGTTTGGCTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
28077647 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
28077712 AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
131 AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
28077744 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
* *
28077809 TTTAGTCCTTTTTATTTTTAATATGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
28077874 AATT-GCCCCAAGAATTTTTCA
131 AATTAG-TCCAAGAATTTTTCA
28077895 AGATATACAA
Statistics
Matches: 304, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
161 1 0.00
162 303 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
Found at i:28078054 original size:29 final size:28
Alignment explanation
Indices: 28078022--28078159 Score: 104
Period size: 29 Copynumber: 4.8 Consensus size: 28
28078012 AAAAGTTTTG
28078022 AAAATTACCATTTTACCCCCGAACTTT-CC
1 AAAATTACCATTTTACCCCCG-A-TTTACC
* *
28078051 AAAATT-CCATTTTTAACCCTGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTT-ACC
**
28078080 GAAAATTACCATTTTACCCCCGTATCTT-TT
1 -AAAATTACCATTTTACCCCCG-AT-TTACC
*
28078110 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTT-ACC
* *
28078139 AAAATCACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
28078160 GGTATCCACA
Statistics
Matches: 86, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
27 5 0.06
28 9 0.10
29 47 0.55
30 18 0.21
31 5 0.06
32 2 0.02
ACGTcount: A:0.30, C:0.31, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGATTTACC
Found at i:28078089 original size:59 final size:59
Alignment explanation
Indices: 28078021--28078159 Score: 210
Period size: 59 Copynumber: 2.4 Consensus size: 59
28078011 CAAAAGTTTT
*
28078021 GAAAATTACCATTTTACCCCCG-AACTTTCCAAAATTCCATTTTTAACCCTGATTTCACC
1 GAAAATTACCATTTTACCCCCGTAACTTT-CAAAATTCCATTTTTAACCCCGATTTCACC
* *
28078080 GAAAATTACCATTTTACCCCCGTATCTTTTAAAATTCCATTTTTAACCCCGATTTCACC
1 GAAAATTACCATTTTACCCCCGTAACTTTCAAAATTCCATTTTTAACCCCGATTTCACC
* *
28078139 -AAAATCACCATTTTGCCCCCG
1 GAAAATTACCATTTTACCCCCG
28078160 GGTATCCACA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
58 19 0.26
59 50 0.68
60 5 0.07
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (59 bp):
GAAAATTACCATTTTACCCCCGTAACTTTCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:28090334 original size:68 final size:69
Alignment explanation
Indices: 28090221--28090699 Score: 515
Period size: 68 Copynumber: 6.8 Consensus size: 69
28090211 ATCATTTCCT
* * * * * *
28090221 ATCCTCTTGAAATTAAAGTAAAGCTGGATATCAAGTCTTCATCTCTGAAATTGAAGTAAAAGCGA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
28090286 CGTT
66 CGTC
* *
28090290 ATCCTCTTGAAGA-TGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAGC
1 ATCCCCTTGAA-ATTGAAGTAGAGCTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGC
28090352 AACGTC
64 AACGTC
* *
28090358 ATCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTACCTCTGAAATTGAAGTAAGAGCA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
28090421 ACGTC
65 ACGTC
*
28090426 ATCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
28090489 ACGTC
65 ACGTC
* * * * *
28090494 ATCCCCTTGAAATTAAAGTAAAGCTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
28090559 -GATC
66 CG-TC
* *
28090563 ATTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTA
1 A--T--C--CC-CTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTA
28090628 AGAGCAACGTC
59 AGAGCAACGTC
** * * *
28090639 ATTTCCTATCCGTTCGAAATTGAAGTAGAATTGGGTATCAAGTTTTTATCTCCGAAATTGA
1 A--TCC---CC-TT-GAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGA
28090700 GCAAGACAAA
Statistics
Matches: 367, Mismatches: 24, Indels: 31
0.87 0.06 0.07
Matches are distributed among these distances:
67 1 0.00
68 192 0.52
69 58 0.16
70 1 0.00
71 1 0.00
72 1 0.00
73 1 0.00
74 2 0.01
75 5 0.01
76 104 0.28
77 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.30
Consensus pattern (69 bp):
ATCCCCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
CGTC
Found at i:28090344 original size:37 final size:37
Alignment explanation
Indices: 28090303--28090482 Score: 168
Period size: 37 Copynumber: 5.2 Consensus size: 37
28090293 CTCTTGAAGA
*
28090303 TGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAAT
1 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
** * **
28090340 TGAAGTA-A---GAGCA-ACGTCATCCCCT-TGAAAT
1 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
28090371 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
1 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
** * **
28090408 TGAAGTA-A---GAGCA-ACGTCATCCCCT-TGAAAT
1 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
*
28090439 TGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAAT
1 TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
28090476 TGAAGTA
1 TGAAGTA
28090483 AGAGCAACGT
Statistics
Matches: 109, Mismatches: 22, Indels: 24
0.70 0.14 0.15
Matches are distributed among these distances:
31 26 0.24
32 19 0.17
33 6 0.06
35 6 0.06
36 19 0.17
37 33 0.30
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (37 bp):
TGAAGTAGAGTGGATAATACGTCTTTACCTCTGAAAT
Found at i:28090369 original size:31 final size:31
Alignment explanation
Indices: 28090334--28090514 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
28090324 TCTTTATCTC
28090334 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
** * **
28090365 TGAAATTGAAGTAGAGTGGATAATACGTCTTTACCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT
28090401 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
** * ***
28090433 TGAAATTGAAGTAGAGTGGATAATACGTCTTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCCCT
28090469 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCCCT
*
28090501 TGAAATTAAAGTAA
1 TGAAATTGAAGTAA
28090515 AGCTGGATAT
Statistics
Matches: 115, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
31 39 0.34
32 19 0.17
33 6 0.05
35 6 0.05
36 19 0.17
37 26 0.23
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCCCT
Found at i:28090619 original size:76 final size:76
Alignment explanation
Indices: 28090493--28090695 Score: 284
Period size: 76 Copynumber: 2.7 Consensus size: 76
28090483 AGAGCAACGT
* * * *
28090493 CATCCCCTTGAAATTAAAGTAAAGCTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCA
1 CATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCA
28090558 A-GATCATTTCC
66 ACG-TCATTTCC
* *
28090569 CATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCCGAAATTGAAGTAAGAGCA
1 CATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCA
28090634 ACGTCATTTCC
66 ACGTCATTTCC
* * * *
28090645 TATCCGT-TCGAAATTGAAGTAGAATTGGGTATCAAGTTTTTATCTCCGAAA
1 CATCC-TCTTGAAATTGAAGTAGAGTTGGATATCAAGTTTTTATCTCCGAAA
28090696 TTGAGCAAGA
Statistics
Matches: 114, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
76 112 0.98
77 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (76 bp):
CATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTTTTTATCTCCGAAAATGAAGTAAGAGCA
ACGTCATTTCC
Found at i:28091069 original size:16 final size:17
Alignment explanation
Indices: 28091038--28091071 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28091028 CCAAATTAAA
28091038 GGCCCGATTACAAAAAG
1 GGCCCGATTACAAAAAG
28091055 GGCCCGATTACAAAAAG
1 GGCCCGATTACAAAAAG
28091072 CACAATTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.12
Consensus pattern (17 bp):
GGCCCGATTACAAAAAG
Found at i:28092800 original size:162 final size:162
Alignment explanation
Indices: 28092624--28093098 Score: 862
Period size: 162 Copynumber: 2.9 Consensus size: 162
28092614 TCTTTCCAAT
28092624 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
28092689 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
28092754 AATTAGTCCAAGAATTTTTCATGGTTTATAAA
131 AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
* * *
28092786 TTAGTCCATTGACTGTTTGGCTGCACTAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
28092851 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
28092916 AATTAGTCTAAGAATTTTTCAGGGTTTATAAA
131 AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
28092948 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
1 TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
* *
28093013 TTTAGTCCTTTTTATTTTTAATATGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACAA
66 TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
*
28093078 AATT-GCCCCAAGAATTTTTCA
131 AATTAG-TCCAAGAATTTTTCA
28093099 AGATTTACAA
Statistics
Matches: 300, Mismatches: 12, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
161 1 0.00
162 299 1.00
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (162 bp):
TTAGTCCTTTGACTGTTTGACTGCACCAGGGGCTGCCACGTGTCATTTTTTGGATTATTTATGCA
TTTAGTCCTTTTTATTTTTAATTTGTTTTAATTTAATCCCCAAATCAACTTTTATTTAATTACGA
AATTAGTCCAAGAATTTTTCAGGGTTTATAAA
Found at i:28093258 original size:29 final size:27
Alignment explanation
Indices: 28093226--28093481 Score: 178
Period size: 29 Copynumber: 8.8 Consensus size: 27
28093216 AAAAGTTTTG
28093226 AAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTACCATTTTACCCCCG-A-TTTCC
* *
28093255 AAAATT-CCATTTTTAACCCTGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTT--CC
**
28093284 GAAAATTACCATTTTACCCCCGAATCTTTT
1 -AAAATTACCATTTTACCCCCG-AT-TTCC
*
28093314 AAAATT-CCATTTTTAACCCCGATTTCAC
1 AAAATTACCA-TTTTACCCCCGATTTC-C
28093342 AAAAAATTACCATTTTACCCCCGAGCTTTCC
1 --AAAATTACCATTTTACCCCCGA--TTTCC
*
28093373 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTT--CC
**
28093402 AAAAATTACCATTTTACCCCCGCATATTTT
1 -AAAATTACCATTTTACCCCCG-AT-TTCC
*
28093432 AAAATT-CCATTTTTAACCCCGATTTCATC
1 AAAATTACCA-TTTTACCCCCGATTTC--C
* *
28093461 AAAATCACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
28093482 GGTATCCATA
Statistics
Matches: 182, Mismatches: 20, Indels: 50
0.72 0.08 0.20
Matches are distributed among these distances:
27 10 0.05
28 17 0.09
29 82 0.45
30 51 0.28
31 14 0.08
32 8 0.04
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (27 bp):
AAAATTACCATTTTACCCCCGATTTCC
Found at i:28093293 original size:59 final size:58
Alignment explanation
Indices: 28093226--28093481 Score: 372
Period size: 59 Copynumber: 4.4 Consensus size: 58
28093216 AAAAGTTTTG
* *
28093226 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCG
1 AAAATTACCATTTTACCCCCGAACTTT-CAAAATTCCATTTTTAACCCCGATTTCACCA
* *
28093285 AAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCACAA
1 AAAATTACCATTTTACCCCCGAA-CTTTCAAAATTCCATTTTTAACCCCGATTTCACCA
*
28093344 AAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTT-CAAAATTCCATTTTTAACCCCGATTTCACCA
* *
28093403 AAAATTACCATTTTACCCCCGCATA-TTTTAAAATTCCATTTTTAACCCCGATTTCATC-
1 AAAATTACCATTTTACCCCCG-A-ACTTTCAAAATTCCATTTTTAACCCCGATTTCACCA
* *
28093461 AAAATCACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
28093482 GGTATCCATA
Statistics
Matches: 181, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
58 23 0.13
59 150 0.83
60 8 0.04
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTTCAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:28093419 original size:118 final size:117
Alignment explanation
Indices: 28093226--28093516 Score: 433
Period size: 118 Copynumber: 2.5 Consensus size: 117
28093216 AAAAGTTTTG
* * *
28093226 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCGAAAATT
1 AAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
*
28093291 ACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA-C
66 ACCATTTTACCCCCGAATATTTTAAAATTCCATTTTTAACCCCGATTTCATC
28093342 AAAAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
1 --AAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAA
*
28093407 TTACCATTTTACCCCCGCATATTTTAAAATTCCATTTTTAACCCCGATTTCATC
64 TTACCATTTTACCCCCGAATATTTTAAAATTCCATTTTTAACCCCGATTTCATC
* * * * * * *
28093461 AAAATCACCATTTTGCCCCCG-GGTATCCATAAATCCCGTTTTTCACCCCGATTTCA
1 AAAATTACCATTTTACCCCCGAGCTTTCCA-AAATTCCATTTTTAACCCCGATTTCA
28093517 TCATTTATCA
Statistics
Matches: 159, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
116 6 0.04
117 42 0.26
118 110 0.69
119 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.34
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCGAGCTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCCCGAATATTTTAAAATTCCATTTTTAACCCCGATTTCATC
Found at i:28093503 original size:58 final size:59
Alignment explanation
Indices: 28093226--28093519 Score: 314
Period size: 59 Copynumber: 5.0 Consensus size: 59
28093216 AAAAGTTTTG
* * * * *
28093226 AAAATTACCATTTTACCCCCGAACTTTCCA-AAATTCCATTTTTAACCCTGATTTCACCG
1 AAAATTACCATTTTACCCCCGGA-TATCCATAAATTCCATTTTTAACCCCGATTTCATCA
**
28093285 AAAATTACCATTTTACCCCC-GA-ATCTTTTAAAATTCCATTTTTAACCCCGATTTCA-CAA
1 AAAATTACCATTTTACCCCCGGATATC-CAT-AAATTCCATTTTTAACCCCGATTTCATC-A
* * *
28093344 AAAATTACCATTTTACCCCCGAGCTTTCCA-AAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTACCCCCG-GATATCCATAAATTCCATTTTTAACCCCGATTTCATCA
* **
28093403 AAAATTACCATTTTACCCCCGCATAT-TTTAAAATTCCATTTTTAACCCCGATTTCATC-
1 AAAATTACCATTTTACCCCCGGATATCCAT-AAATTCCATTTTTAACCCCGATTTCATCA
* * * * * *
28093461 AAAATCACCATTTTGCCCCCGGGTATCCATAAATCCCGTTTTTCACCCCGATTTCATCA
1 AAAATTACCATTTTACCCCCGGATATCCATAAATTCCATTTTTAACCCCGATTTCATCA
28093520 TTTATCAATG
Statistics
Matches: 198, Mismatches: 25, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
56 2 0.01
58 51 0.26
59 141 0.71
60 1 0.01
61 1 0.01
62 2 0.01
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGGATATCCATAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:28096300 original size:30 final size:30
Alignment explanation
Indices: 28096264--28096323 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
28096254 ATTGAGTGTG
28096264 TTTTTCGCTGAGGAGCTTAATTGATTTTTT
1 TTTTTCGCTGAGGAGCTTAATTGATTTTTT
*
28096294 TTTTTCGCTGAGGGGCTTAATTGATTTTTT
1 TTTTTCGCTGAGGAGCTTAATTGATTTTTT
28096324 AGCCCAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.15, C:0.10, G:0.22, T:0.53
Consensus pattern (30 bp):
TTTTTCGCTGAGGAGCTTAATTGATTTTTT
Found at i:28102750 original size:36 final size:36
Alignment explanation
Indices: 28102710--28102810 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
28102700 TGGTAACAGG
* *
28102710 CATGACCTTTAGGACAATAGGGAGTAAAATGAGCAA
1 CATGACCTTCAGGACAACAGGGAGTAAAATGAGCAA
* *
28102746 CATGACCTTCGGGTCAACAGGGAGTAAAATGAGCAA
1 CATGACCTTCAGGACAACAGGGAGTAAAATGAGCAA
** * *
28102782 CATGACCCACGGGTCAACAGGGAGTAAAA
1 CATGACCTTCAGGACAACAGGGAGTAAAA
28102811 CGAATAACAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.39, C:0.19, G:0.27, T:0.16
Consensus pattern (36 bp):
CATGACCTTCAGGACAACAGGGAGTAAAATGAGCAA
Found at i:28113811 original size:18 final size:19
Alignment explanation
Indices: 28113784--28113822 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28113774 CTTAGATTGA
* *
28113784 AAAAATAATTGAATTAATT
1 AAAAATAATTAAATGAATT
28113803 AAAAA-AATTAAATGAATT
1 AAAAATAATTAAATGAATT
28113821 AA
1 AA
28113823 TTTAAAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAATAATTAAATGAATT
Found at i:28113831 original size:21 final size:22
Alignment explanation
Indices: 28113783--28113830 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
28113773 ACTTAGATTG
*
28113783 AAAAAA-TAATTGAATTAATTA
1 AAAAAATTAAATGAATTAATTA
*
28113804 AAAAAATTAAATGAATTAATTT
1 AAAAAATTAAATGAATTAATTA
28113826 AAAAA
1 AAAAA
28113831 TCAAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAAAATTAAATGAATTAATTA
Found at i:28114134 original size:29 final size:30
Alignment explanation
Indices: 28114096--28114154 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
28114086 AAGTCTAAAC
* * *
28114096 TAAAAAAAATCTTATTTTCTTTAAAATAAT
1 TAAAAAAATTCTTATTTGCTTCAAAATAAT
*
28114126 TAAAAAAATTTTTATTTGCTTCAAAATAA
1 TAAAAAAATTCTTATTTGCTTCAAAATAA
28114155 AAATAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
TAAAAAAATTCTTATTTGCTTCAAAATAAT
Found at i:28114196 original size:6 final size:6
Alignment explanation
Indices: 28114185--28114220 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28114175 ATTTATGTTA
28114185 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG
28114221 AGTCTCCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
GAGTTG
Found at i:28119137 original size:12 final size:11
Alignment explanation
Indices: 28119084--28119180 Score: 61
Period size: 11 Copynumber: 8.5 Consensus size: 11
28119074 GACTCTTGAG
* *
28119084 TTAAATTGATT
1 TTAAATTAAAT
*
28119095 TTAAATT-TAT
1 TTAAATTAAAT
*
28119105 TTAAATTTAGAT
1 TTAAA-TTAAAT
**
28119117 TTATTTTAAATT
1 TTAAATTAAA-T
28119129 TTAAATTAAATAT
1 TTAAATT-AA-AT
*
28119142 TTAAATTTAAT
1 TTAAATTAAAT
28119153 TTAAATTTAAAT
1 TTAAA-TTAAAT
* *
28119165 TTAAATAAAAA
1 TTAAATTAAAT
28119176 TTAAA
1 TTAAA
28119181 ATATTAAATT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.09
11 29 0.43
12 22 0.32
13 10 0.15
14 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:28119148 original size:37 final size:34
Alignment explanation
Indices: 28119102--28119193 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 34
28119092 ATTTTAAATT
*
28119102 TATTTAAATTTAGATTTATTTTAAATTTTAAATTAAA
1 TATTTAAATTTA-ATTTAATTTAAA-TTTAAA-TAAA
28119139 TATTTAAATTTAATTTAAATTTAAATTTAAATAAA
1 TATTTAAATTTAATTT-AATTTAAATTTAAATAAA
* *
28119174 AATTAAAATATTAAATTTAA
1 TATTTAAAT-TT-AATTTAA
28119194 CATTTAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
35 11 0.22
36 14 0.29
37 24 0.49
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
TATTTAAATTTAATTTAATTTAAATTTAAATAAA
Found at i:28119150 original size:31 final size:30
Alignment explanation
Indices: 28119084--28119171 Score: 101
Period size: 31 Copynumber: 3.0 Consensus size: 30
28119074 GACTCTTGAG
* *
28119084 TTAAATTGATTTTAAATTT--ATTTAA-AT
1 TTAAATTTATTTTAAATTTAAATTAAATAT
*
28119111 TTAGATTTATTTTAAATTTTAAATTAAATAT
1 TTAAATTTATTTTAAA-TTTAAATTAAATAT
*
28119142 TTAAATTTAATTTAAATTTAAATTTAAATA
1 TTAAATTTATTTTAAATTTAAA-TTAAATA
28119172 AAAATTAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 14 0.27
28 3 0.06
30 11 0.22
31 23 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTAAATTTATTTTAAATTTAAATTAAATAT
Found at i:28119156 original size:11 final size:11
Alignment explanation
Indices: 28119084--28119170 Score: 70
Period size: 11 Copynumber: 7.5 Consensus size: 11
28119074 GACTCTTGAG
* *
28119084 TTAAATTGATT
1 TTAAATTTAAT
28119095 TTAAATTT-AT
1 TTAAATTTAAT
28119105 TTAAATTTAGAT
1 TTAAATTTA-AT
*
28119117 TT-ATTTTAAATT
1 TTAAATTT-AA-T
*
28119129 TTAAATTAAATAT
1 TTAAATT-TA-AT
28119142 TTAAATTTAAT
1 TTAAATTTAAT
28119153 TTAAATTTAAAT
1 TTAAATTT-AAT
28119165 TTAAAT
1 TTAAAT
28119171 AAAAATTAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
10 9 0.15
11 22 0.35
12 18 0.29
13 12 0.19
14 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:28119198 original size:7 final size:6
Alignment explanation
Indices: 28119094--28119201 Score: 98
Period size: 6 Copynumber: 18.0 Consensus size: 6
28119084 TTAAATTGAT
* * *
28119094 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTTAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAA-A
** *
28119141 TTTAAA TTT-AA TTTAAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
28119189 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
28119202 AGTCCAAATG
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 50 0.60
7 22 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:28119254 original size:14 final size:14
Alignment explanation
Indices: 28119237--28119275 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
28119227 CATGGCCCAG
28119237 GGCCCAATTACAAA
1 GGCCCAATTACAAA
*
28119251 GGCCCAATT--AAG
1 GGCCCAATTACAAA
28119263 GGCCCAATTACAA
1 GGCCCAATTACAA
28119276 TAGTCCAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.15
Consensus pattern (14 bp):
GGCCCAATTACAAA
Found at i:28119344 original size:20 final size:21
Alignment explanation
Indices: 28119319--28119358 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
28119309 GTGCCTACTG
*
28119319 CTGCTGGCCACC-AGCTCCAT
1 CTGCTGACCACCAAGCTCCAT
28119339 CTGCTGACCACCAAGCTCCA
1 CTGCTGACCACCAAGCTCCA
28119359 CCATGCCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.20, C:0.45, G:0.17, T:0.17
Consensus pattern (21 bp):
CTGCTGACCACCAAGCTCCAT
Found at i:28120903 original size:29 final size:30
Alignment explanation
Indices: 28120777--28120977 Score: 309
Period size: 30 Copynumber: 6.7 Consensus size: 30
28120767 CTCTAAATTG
* *
28120777 TCCAGAAATTATATTTTGACCTCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
28120808 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28120838 CCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28120868 CCCAAAATTACATTTTGACCCC-AAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
28120897 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
28120927 TCCAAAATTACATTTTGACCCCAAAA-TTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
28120956 TCAAAAATTACAATTTT-ACCCC
1 TCCAAAATTAC-ATTTTGACCCC
28120978 CCGAATCTTT
Statistics
Matches: 163, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
29 46 0.28
30 113 0.69
31 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:28120904 original size:59 final size:59
Alignment explanation
Indices: 28120777--28120977 Score: 305
Period size: 59 Copynumber: 3.4 Consensus size: 59
28120767 CTCTAAATTG
* * *
28120777 TCCAGAAATTATATTTTGACCTCAAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCC-AAACTTT
* *
28120838 CCCAAAATTACATTTTGACCCCAAAACTTTCCCAAAATTACATTTTGACCCCAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAACTTT
*
28120897 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAATTT
1 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAACTTT
*
28120956 TCAAAAATTACAATTTT-ACCCC
1 TCCAAAATTAC-ATTTTGACCCC
28120978 CCGAATCTTT
Statistics
Matches: 130, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
59 78 0.60
60 49 0.38
61 3 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAACTTT
Found at i:28120993 original size:59 final size:57
Alignment explanation
Indices: 28120771--28121001 Score: 257
Period size: 59 Copynumber: 3.9 Consensus size: 57
28120761 GTAAGCCTCT
* * * *
28120771 AAATTGTCCAGAAATTATATTTTGACCTCAAAACTTTTCCAAAATTATATTTTGACCCCA
1 AAATTTTCCA-AAATTACATTTTGACCCCAAAACTTTT--AAAATTACATTTTGACCCCA
* *
28120831 AAACTTTCCCAAAATTACATTTTGACCCCAAAACTTTCCCAAAATTACATTTTGACCCCA
1 AAA-TTTTCCAAAATTACATTTTGACCCCAAAACTTT--TAAAATTACATTTTGACCCCA
*
28120891 AACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCA
1 AAATTTTCCAAAATTACATTTTGACCCCAAAACTTTT--AAAATTACATTTTGACCCCA
* * * *
28120950 AAATTTTCAAAAATTACAATTTT-ACCCCCCGAATCTTTTAAAATTCCATTTT
1 AAATTTTCCAAAATTAC-ATTTTGA--CCCCAAAACTTTTAAAATTACATTTT
28121002 TAACCTCGAT
Statistics
Matches: 149, Mismatches: 14, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
59 80 0.54
60 53 0.36
61 16 0.11
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (57 bp):
AAATTTTCCAAAATTACATTTTGACCCCAAAACTTTTAAAATTACATTTTGACCCCA
Found at i:28121023 original size:30 final size:31
Alignment explanation
Indices: 28120989--28121208 Score: 106
Period size: 30 Copynumber: 7.5 Consensus size: 31
28120979 CGAATCTTTT
*
28120989 AAAATT-CCATTTTTAACCTCGATTTCAACA
1 AAAATTACCATTTTTAACCCCGATTTCAACA
* *
28121019 AAAATTACCA-TTTTACCCCCGAAACTT--AC-
1 AAAATTACCATTTTTAACCCCG--ATTTCAACA
* * *
28121048 AGAATT-CCGTTTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTTAACCCCGATTTCAACA
* ** ** *
28121078 AAAATTACCA-TTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTTAACCCCGATTTCAACA
* * *
28121107 AAAATT-TCATTTTTAACCTCGATTTCACCA
1 AAAATTACCATTTTTAACCCCGATTTCAACA
* * ** ****
28121137 AAAATTGCCA-TTTT-ACCCCTAAATCTTTT
1 AAAATTACCATTTTTAACCCCGATTTCAACA
* *
28121166 AAAATT-CCATTTTTAACCCCGATTAC-ACC
1 AAAATTACCATTTTTAACCCCGATTTCAACA
28121195 AAAATTACCATTTT
1 AAAATTACCATTTT
28121209 ACCCCCGGGT
Statistics
Matches: 136, Mismatches: 40, Indels: 28
0.67 0.20 0.14
Matches are distributed among these distances:
27 3 0.02
28 7 0.05
29 57 0.42
30 59 0.43
31 7 0.05
32 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (31 bp):
AAAATTACCATTTTTAACCCCGATTTCAACA
Found at i:28121040 original size:59 final size:59
Alignment explanation
Indices: 28120957--28121215 Score: 340
Period size: 59 Copynumber: 4.4 Consensus size: 59
28120947 CCAAAATTTT
* *
28120957 CAAAAATTACAATTTTACCCCCCGAATCTTTTAAAATTCCATTTTTAACCTCGATTTCAA
1 CAAAAATTACCATTTTA-CCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAA
* ** * * *
28121017 CAAAAATTACCATTTTACCCCCGAAACTTACAGAATTCCGTTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAA
* * * * *
28121076 CAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAA
* ** *
28121135 CAAAAATTGCCATTTTACCCCTAAATCTTTTAAAATTCCATTTTTAACCCCGATTAC-A
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAA
*
28121193 CCAAAATTACCATTTTACCCCCG
1 CAAAAATTACCATTTTACCCCCG
28121216 GGTATCCATA
Statistics
Matches: 171, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
58 19 0.11
59 136 0.80
60 16 0.09
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCAA
Done.