Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009586.1 Hibiscus syriacus cultivar Beakdansim tig00116964_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3773412
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 19
Found at i:328162 original size:48 final size:48
Alignment explanation
Indices: 328091--328187 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
328081 AATTCTTGGA
*
328091 TAAATCTTGAACTCTTTCTCTTCCTCTTCTGTGGTCATCTGTTTGATT
1 TAAATCTTGAACTCTTTCTCTTCCTCTTCTGAGGTCATCTGTTTGATT
328139 TAAATCTTGAACTCTTTCTCTTCCTCTTCTGAGGTCATCTGTTTGATT
1 TAAATCTTGAACTCTTTCTCTTCCTCTTCTGAGGTCATCTGTTTGATT
328187 T
1 T
328188 CGACTGGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.49
Consensus pattern (48 bp):
TAAATCTTGAACTCTTTCTCTTCCTCTTCTGAGGTCATCTGTTTGATT
Found at i:330191 original size:2 final size:2
Alignment explanation
Indices: 330184--330209 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
330174 ACATGAAACC
330184 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
330210 TATTTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:331472 original size:5 final size:6
Alignment explanation
Indices: 331455--331549 Score: 86
Period size: 6 Copynumber: 15.2 Consensus size: 6
331445 GGGAGCAGTC
*
331455 TATTTT TATTTT TATTTT CTGTTTGT TCAATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT -TATTT-T T--ATTTT TATTTT TATTTT TATTTT
* * *
331507 TATTTT CAATTT TA-TTT TATTTT GT-TAATT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT -TAT-TTT TATTTT TATTTT T
331550 CTTTGAATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
5 5 0.07
6 54 0.73
7 9 0.12
8 3 0.04
9 3 0.04
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:331960 original size:10 final size:11
Alignment explanation
Indices: 331941--331969 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
331931 TCAAACAGTG
331941 AGAGAAAAAAA
1 AGAGAAAAAAA
331952 AGA-AAAAAAA
1 AGAGAAAAAAA
331962 AGAGAAAA
1 AGAGAAAA
331970 TGATAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AGAGAAAAAAA
Found at i:332874 original size:14 final size:13
Alignment explanation
Indices: 332839--332873 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
332829 TTGTCCCACG
332839 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
332852 AAGAAAAAAGGAA
1 AAGAAAAAAGAAA
*
332865 ATGAAAAAA
1 AAGAAAAAA
332874 ATAGTTTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:334392 original size:16 final size:15
Alignment explanation
Indices: 334367--334407 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
334357 ACCATCCATA
*
334367 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
334382 AATCACAAAATCAAAC
1 AATC-CAAAATCAAAC
*
334398 AATTCAAAAT
1 AATCCAAAAT
334408 GTTGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.17
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:336104 original size:21 final size:21
Alignment explanation
Indices: 336078--336117 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
336068 TAGAACCCCA
*
336078 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
336099 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
336118 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:336152 original size:20 final size:21
Alignment explanation
Indices: 336098--336160 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
336088 GATTCCCCTG
336098 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
336122 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
336142 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
336161 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:339967 original size:22 final size:21
Alignment explanation
Indices: 339925--339964 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
339915 GAGTTTGTTT
*
339925 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
339946 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
339965 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:345954 original size:60 final size:60
Alignment explanation
Indices: 345861--345979 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
345851 TGGGTTGATC
345861 GAGCCAGCATCAATTGAAATCAAATGCTTATATGGCCCGATATCTCTCCTCCCAAAATTG
1 GAGCCAGCATCAATTGAAATCAAATGCTTATATGGCCCGATATCTCTCCTCCCAAAATTG
345921 GAGCCAGCATCAATTGAAATCAAATGCTTATATGGCCCGATATCTCTCCTCCCAAAATT
1 GAGCCAGCATCAATTGAAATCAAATGCTTATATGGCCCGATATCTCTCCTCCCAAAATT
345980 TGAACAAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (60 bp):
GAGCCAGCATCAATTGAAATCAAATGCTTATATGGCCCGATATCTCTCCTCCCAAAATTG
Found at i:349730 original size:13 final size:13
Alignment explanation
Indices: 349698--349746 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
349688 TGAAAATTGA
*
349698 TAATAATCAATAATT
1 TAATAATAAAT-A-T
349713 TAATAATAAATAT
1 TAATAATAAATAT
349726 TAATAATAAATAT
1 TAATAATAAATAT
349739 TAAATAAT
1 T-AATAAT
349747 TGATTATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 15 0.47
14 7 0.22
15 10 0.31
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATAAATAT
Found at i:350335 original size:29 final size:27
Alignment explanation
Indices: 350286--350340 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
350276 ATTAAGTTAG
* *
350286 GTTTTTTTTAAAGTTGGGTTTGGGTCA
1 GTTTTTTTTAAAGGTGGGTTTAGGTCA
*
350313 GTTTTTTTTATAAGGTGATGTTTAGGTC
1 GTTTTTTTTA-AAGGTG-GGTTTAGGTC
350341 GGGTCGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 10 0.43
28 5 0.22
29 8 0.35
ACGTcount: A:0.16, C:0.04, G:0.27, T:0.53
Consensus pattern (27 bp):
GTTTTTTTTAAAGGTGGGTTTAGGTCA
Found at i:351213 original size:23 final size:23
Alignment explanation
Indices: 351187--351234 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
351177 ATAAAGTACA
*
351187 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
351210 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
351233 AT
1 AT
351235 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:351748 original size:23 final size:23
Alignment explanation
Indices: 351718--351776 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
351708 TACAACTACC
351718 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
351741 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
351764 TATTACATCATAT
1 TATTACATTATAT
351777 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:352007 original size:481 final size:481
Alignment explanation
Indices: 351308--353073 Score: 3290
Period size: 481 Copynumber: 3.7 Consensus size: 481
351298 TTATAATATG
351308 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
351373 TCAAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
66 TC-AATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
351438 CAAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
130 CAAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA
351503 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
195 TTAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATA
*
351568 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAATTCAC
260 TATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
* *
351633 TCAAAAGATAACCTTAAATTAATATTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATG
325 TCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
351698 ATAGATACTTTACAACTACCTATTACATTATATAAACGATACATATTACATTATATAAGCGCTAC
390 ATAGATACTTTACAACTACCTATTACATTATATAAACGATAC-TATTACATTATATAAGCGCTAC
351763 CTATTACATCATATTTTTACCTATTATA
454 CTATTACATCATATTTTTACCTATTATA
*
351791 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTGTGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
351856 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
351921 AAAAAAA-TATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
351985 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
*
352050 ATCGTAACGTAAAAAATAAATCATTAGATGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
*
352115 CAAAAGATAATCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
*
352180 TAGATACTTTACAACTACCTATTACATTATATAAACAATACCTATTACATTATATAAGCGCTACC
391 TAGATACTTTACAACTACCTATTACATTATATAAACGATA-CTATTACATTATATAAGCGCTACC
352245 TATTACATCATATTTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
* *
352272 TTGAAAATGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
352337 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTATAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
352402 -AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
352466 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTG---TT--TTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
352526 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
352591 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
326 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
352656 TAGATACTTTACAACTACCTATTACATTATATAAACGATATCTATTACATTATATAAGCGCTACC
391 TAGATACTTTACAACTACCTATTACATTATATAAACGATA-CTATTACATTATATAAGCGCTACC
*
352721 TATTAAATCATATTTTTACCTATTATA
455 TATTACATCATATTTTTACCTATTATA
352748 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
352813 TCAA-TTTTTT-ATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
352876 AAAAAAATTATTTGATTGTTTTGATA-TTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
131 AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
352940 TAACCAAAG---A-AATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
196 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
353001 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
261 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
353066 CAAAAGAT
326 CAAAAGAT
353074 GTATATACCT
Statistics
Matches: 1255, Mismatches: 20, Indels: 24
0.97 0.02 0.02
Matches are distributed among these distances:
470 28 0.02
471 1 0.00
473 2 0.00
474 99 0.08
475 120 0.10
476 300 0.24
478 2 0.00
480 6 0.00
481 561 0.45
482 70 0.06
483 66 0.05
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (481 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGA
TAGATACTTTACAACTACCTATTACATTATATAAACGATACTATTACATTATATAAGCGCTACCT
ATTACATCATATTTTTACCTATTATA
Found at i:352221 original size:23 final size:23
Alignment explanation
Indices: 352190--352257 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
352180 TAGATACTTT
352190 ACAACTACCTATTACATTATATAA
1 ACAA-TACCTATTACATTATATAA
352214 ACAATACCTATTACATTATATAA
1 ACAATACCTATTACATTATATAA
* ** *
352237 GCGCTACCTATTACATCATAT
1 ACAATACCTATTACATTATAT
352258 TTTTACCTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 36 0.90
24 4 0.10
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ACAATACCTATTACATTATATAA
Found at i:352300 original size:21 final size:22
Alignment explanation
Indices: 352275--352319 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
352265 TATTATATTG
352275 AAAATG-TCCATACTTTTTATA
1 AAAATGATCCATACTTTTTATA
* *
352296 AAAATGATCGATACTTTTTTTA
1 AAAATGATCCATACTTTTTATA
352318 AA
1 AA
352320 GTTATGTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (22 bp):
AAAATGATCCATACTTTTTATA
Found at i:352733 original size:23 final size:23
Alignment explanation
Indices: 352670--352725 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
352660 TACTTTACAA
352670 CTACCTATTACATTATATAAACG
1 CTACCTATTACATTATATAAACG
* * *
352693 ATATCTATTACATTATATAAGCG
1 CTACCTATTACATTATATAAACG
352716 CTACCTATTA
1 CTACCTATTA
352726 AATCATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:353101 original size:25 final size:25
Alignment explanation
Indices: 353073--353137 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
353063 ACTCAAAAGA
*
353073 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
353098 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
353123 TGTACATACCTAAAT
1 TGTACATACCTAAAT
353138 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:355448 original size:3 final size:3
Alignment explanation
Indices: 355440--355511 Score: 63
Period size: 3 Copynumber: 24.0 Consensus size: 3
355430 ACTTGTTTGG
* * * * *
355440 ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * *
355488 GTC ATC ATA ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
355512 GTCAGCTTCA
Statistics
Matches: 51, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.25, C:0.32, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:355494 original size:36 final size:36
Alignment explanation
Indices: 355447--355528 Score: 119
Period size: 36 Copynumber: 2.3 Consensus size: 36
355437 TGGATCATCA
**
355447 TCATCATCATCATCGTCATCATCTTCATCGTCAGCT
1 TCATCATCATCATAATCATCATCTTCATCGTCAGCT
* *
355483 TCATCGTCATCATAATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATAATCATCATCTTCATCGTCAGCT
*
355519 TCATCTTCAT
1 TCATCATCAT
355529 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.22, C:0.32, G:0.09, T:0.38
Consensus pattern (36 bp):
TCATCATCATCATAATCATCATCTTCATCGTCAGCT
Found at i:355512 original size:12 final size:12
Alignment explanation
Indices: 355441--355528 Score: 86
Period size: 12 Copynumber: 7.3 Consensus size: 12
355431 CTTGTTTGGA
* *
355441 TCATCATCATCA
1 TCATCTTCATCG
* * *
355453 TCATCATCGTCA
1 TCATCTTCATCG
355465 TCATCTTCATCG
1 TCATCTTCATCG
*
355477 TCAGCTTCATCG
1 TCATCTTCATCG
* *
355489 TCATCATAATCG
1 TCATCTTCATCG
355501 TCATCTTCATCG
1 TCATCTTCATCG
* *
355513 TCAGCTTCATCT
1 TCATCTTCATCG
355525 TCAT
1 TCAT
355529 TGACCGCTTG
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:355537 original size:18 final size:18
Alignment explanation
Indices: 355465--355528 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
355455 ATCATCGTCA
*
355465 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
* * * *
355483 TCATCGTCATC-ATAATCG
1 TCATCTTCATCGA-CAGCT
*
355501 TCATCTTCATCGTCAGCT
1 TCATCTTCATCGACAGCT
355519 TCATCTTCAT
1 TCATCTTCAT
355529 TGACCGCTTG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCGACAGCT
Found at i:358060 original size:200 final size:200
Alignment explanation
Indices: 357002--358534 Score: 2571
Period size: 200 Copynumber: 7.8 Consensus size: 200
356992 AACATTAAAC
* * * *
357002 AGTGTCGATACA-TATTATATACAAATTCTCTCATAAAACCTGTAAACTTGTACCGGTTAGATTG
1 AGTGTCGACACATTATT-TAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTG
*
357066 AAAAATTACATATTACATTATACTTTTGATTTTCGATGTTTTTGGGATCGACACTTTTTATATAT
65 AAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATAT
* *
357131 GGAGCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
357196 TAAAAA
195 TAAAAA
*
357202 A--GTCGA-AAATTA-TTAGACA-ATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
* *
357262 AAAATTACATATTACATTATACTTTTGGATTTCGATATTTTTGGGATCGACACTTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
*
357327 GATCGACACTTTATGGTTGGACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
357392 AAAAA
196 AAAAA
357397 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
357462 AAAATTACATATTAC---ATACTTTTGG-TTTCGATGTTTTTGGGATCGACAC-TTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
* * *
357522 GATCAACACTTTATGGTTGGACCCTATTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
357587 AAAAA
196 AAAAA
*
357592 AGTGTCG--ACATTATTTAGACATA-T-TCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
357653 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGG---GATCACTTTTT-TATAT
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGA-CACTTTTTATATAT
357714 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC-AAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
357778 TAAAAA
195 TAAAAA
* *
357784 AGTGTCGACATA-TATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
* *
357848 AAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
*
357913 GATCGACACTTTATGGTTGCACCATGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
357978 AAAAA
196 AAAAA
*
357983 AGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
*
358048 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACAATTTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
358113 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
358178 AAAAA
196 AAAAA
* *
358183 AGTGTCGACGCATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
* *
358248 AAAAGTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTTTATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
*
358313 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAAGATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
358378 AAAAA
196 AAAAA
* *
358383 CGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATACTTGTACCGGTTAGATTG-
1 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
*
358446 AAAATTAC--ATTACATTATAC-TTTGGTTTTCGAAGTTTTTGGGATCGACAC-TTTTATATATG
66 AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
* *
358507 GTTCGACACTTTATAGTTGCACCCTGTT
131 GATCGACACTTTATGGTTGCACCCTGTT
358535 GGCCATATTG
Statistics
Matches: 1270, Mismatches: 41, Indels: 50
0.93 0.03 0.04
Matches are distributed among these distances:
191 51 0.04
192 33 0.03
193 80 0.06
194 53 0.04
195 382 0.30
196 40 0.03
197 25 0.02
198 72 0.06
199 66 0.05
200 468 0.37
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTAGATTGA
AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAACT
AAAAA
Found at i:358687 original size:19 final size:19
Alignment explanation
Indices: 358653--358700 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
358643 TTATATTCAC
358653 ATACAAAATT-TAAATCGT
1 ATACAAAATTATAAATCGT
*
358671 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
358690 ATACAAAATTA
1 ATACAAAATTA
358701 ACCCTACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:359289 original size:4 final size:4
Alignment explanation
Indices: 359280--359316 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
359270 AATGTCATTT
359280 CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA C
359317 CAATCTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:360543 original size:32 final size:32
Alignment explanation
Indices: 360507--360570 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
360497 CATCTTAATA
360507 TCACCCCTTAAAC-CCCAACTTCTTTCACCACT
1 TCACCCC-TAAACACCCAACTTCTTTCACCACT
* * *
360539 TCACCCCTCAACACTCTACTTCTTTCACCACT
1 TCACCCCTAAACACCCAACTTCTTTCACCACT
360571 CCATCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (32 bp):
TCACCCCTAAACACCCAACTTCTTTCACCACT
Found at i:362950 original size:20 final size:20
Alignment explanation
Indices: 362918--362974 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
362908 ATCCGGTATC
*
362918 ATTT-TACCGGTTTTATCAT
1 ATTTATACCTGTTTTATCAT
362937 -TTTGATACCTGTTTTATCAT
1 ATTT-ATACCTGTTTTATCAT
* *
362957 ATTTTTACCTGTTATATC
1 ATTTATACCTGTTTTATC
362975 GTTGTGGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (20 bp):
ATTTATACCTGTTTTATCAT
Found at i:363127 original size:20 final size:20
Alignment explanation
Indices: 363100--363146 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
363090 TCCGGTAACG
363100 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
363119 TTCTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
363140 TTTTACC
1 TTTTACC
363147 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.19, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:363301 original size:183 final size:181
Alignment explanation
Indices: 362888--363359 Score: 625
Period size: 183 Copynumber: 2.6 Consensus size: 181
362878 CGTACTTACG
* * * *
362888 AAAGTATCGACACTTTCAA-TATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCTGTTTT
1 AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACCGGTTTT
* **
362952 ATCATATTTTTACCTGTTATATCGTTGTGGATCGAT--ATTTTTTTTAAGTATCGACACATATAG
66 ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATATAG
*
363015 GCGCTAAAACTACTTCTCTTTTAAATTCACAAAGGTCGATCCTTCCTTATAT
131 GCGCTAAAACTACTTCTCTTTTAAATTCACAAAGGTCGATCCTT-CATATAT
*
363067 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCTTACCGGTTT
1 AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACCGGTTT
* *
363132 TATCATATTTTTACCTGGTATATCGTTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTA
65 TATCATATTTTTACCTGTTATATCG-TTTTGGATCGATACATTTTTTAAAAGTATCGACAC-ATA
* * *
363197 TAGGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTT-ATAT-T
128 TAGG-CGCTAAAACTACTTCTCTTTTAAATTCACAAAG-GTCGATCCTTCATATAT
* * * * *
363250 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCA-TTTCAATACTGGTT
1 AAAGTATCGACACTTTCAAT-TATCCGGTAACGTTTTACCGGTTTTATCATTTTC-ATACCGGTT
* * *
363314 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
64 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
363360 AATTTGGATC
Statistics
Matches: 259, Mismatches: 25, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
179 19 0.07
181 63 0.24
182 34 0.13
183 76 0.29
184 22 0.08
185 34 0.13
186 11 0.04
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATTATCCGGTAACGTTTTACCGGTTTTATCATTTTCATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATATAG
GCGCTAAAACTACTTCTCTTTTAAATTCACAAAGGTCGATCCTTCATATAT
Found at i:372856 original size:31 final size:31
Alignment explanation
Indices: 372821--372884 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
372811 CACGATGAGA
372821 CAAGCCTTCTTCTGCAATAGATATCCAAAAC
1 CAAGCCTTCTTCTGCAATAGATATCCAAAAC
372852 CAAGCCTTCTTCTGCAATAGATATCCAAAAC
1 CAAGCCTTCTTCTGCAATAGATATCCAAAAC
372883 CA
1 CA
372885 GTGGTCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (31 bp):
CAAGCCTTCTTCTGCAATAGATATCCAAAAC
Found at i:376915 original size:16 final size:16
Alignment explanation
Indices: 376885--376915 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
376875 TAATATTGAA
*
376885 ACTTGAACTCGAAAAG
1 ACTTGAACTCAAAAAG
376901 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
376916 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:377497 original size:18 final size:18
Alignment explanation
Indices: 377474--377509 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
377464 CTTAACTCTC
377474 TTCTAAAACACCCATCTT
1 TTCTAAAACACCCATCTT
*
377492 TTCTAAAACTCCCATCTT
1 TTCTAAAACACCCATCTT
377510 CCCCTCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
TTCTAAAACACCCATCTT
Found at i:383947 original size:182 final size:181
Alignment explanation
Indices: 383639--384113 Score: 605
Period size: 182 Copynumber: 2.6 Consensus size: 181
383629 CGATCCAAAT
* * *** * *
383639 TAAAAATGTATCGATCCATATTAATATAACAGGTAAAAATATCGATAGAACCGGTTAT-GAAA-G
1 TAAAAATATATCGATCCACAACGATATAACAGGTAAAAATAT-GA-AAAATCGG-TATCGAAATG
* * ** * *
383702 ACAATACCGGTAAA-TCCTTACCGGATATATTGAACGTGTCGATACTTTAATATAAGGATCGACA
63 ATAAAACCGGTAAAGAGC-TACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACA
*
383766 CTTTGTGAATTTAAAAGAGAAGCATTTTTAACGCCTATAAAGTGTCAATACTTTA
127 CTTTGTGAATTTAAAAGAGAAGCAATTTTAACGCCTATAAAGTGTCAATACTTTA
*
383821 TAAAAATATATTGATCCACAACGATATAACAGGTAAAAATATGACAAAATCGGTATCGAAATGAT
1 TAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGA-AAAATCGGTATCGAAATGAT
* * * *
383886 AAAACCGGTAAAGAGCTACCAGATATATTTAAAGTGTCGGTACTTTAATATAAGTATCGACATTT
65 AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* * *
383951 TGTGAATTTAAAAGAGAAGTAATTTTAGCGCCTATAAAGTGTCGATACTTTA
130 TGTGAATTTAAAAGAGAAGCAATTTTAACGCCTATAAAGTGTCAATACTTTA
* * * * *
384003 TAAAAATGTATCGATCCACAATGATATAACAGATAAAAATATGATAAATCCGGTATCAAAATGAT
1 TAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGAAAAAT-CGGTATCGAAATGAT
* * *
384068 AAAATCGATAAAGCGCTACCGGATATATTTAAAGTGTCGATACTTT
65 AAAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTT
384114 CATAAGTACG
Statistics
Matches: 255, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
180 3 0.01
181 16 0.06
182 235 0.92
183 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.29
Consensus pattern (181 bp):
TAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGAAAAATCGGTATCGAAATGATA
AAACCGGTAAAGAGCTACCGGATATATTTAAAGTGTCGATACTTTAATATAAGGATCGACACTTT
GTGAATTTAAAAGAGAAGCAATTTTAACGCCTATAAAGTGTCAATACTTTA
Found at i:386229 original size:201 final size:201
Alignment explanation
Indices: 385872--386296 Score: 631
Period size: 201 Copynumber: 2.1 Consensus size: 201
385862 AACTTTTTGT
* *
385872 GTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACACATAAAGT
1 GTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTCAACACATAAAGT
* * *
385937 GTCGATACATTTTCAAAAAGTGTCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATATG
66 GTCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCAAAACCCATAAGTATAATGTAATAGG
*
386002 TAAATTTTCAATATAACCGGTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTAT
131 TAAATTTTCAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTAT
*
386067 CAACAT
196 CAACAC
* * *
386073 TTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAATGGTTCAA-TCATAAAG
1 GTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAA-GGGTCAACACATAAAG
* * *
386137 TGTCGATACATTTAT-AAAAAGTATCGATCCCAGAAACAT-ATACATCCATAAGTATAATGTAAT
65 TGTCGATACATTT-TCAAAAAGTATCGATCCCAAAAACATCA-AAACCCATAAGTATAATGTAAT
* ** * *
386200 AGGTAAATTTTCAATGTAATTGATATAAATATACCGGTTTTATGAGAGAATATGTCTACAACATG
128 AGGTAAATTTTCAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATG
*
386265 TATCGACAC
193 TATCAACAC
386274 GTTTTTAATTTTGTGTCGATACT
1 GTTTTTAATTTTGTGTCGATACT
386297 AATTTAAATA
Statistics
Matches: 201, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
200 1 0.00
201 194 0.97
202 6 0.03
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (201 bp):
GTTTTTAATTTTGTGTCGATACTTTTGGTCCAGAATGAATGCCAAAAAGGGTCAACACATAAAGT
GTCGATACATTTTCAAAAAGTATCGATCCCAAAAACATCAAAACCCATAAGTATAATGTAATAGG
TAAATTTTCAATATAACCGATATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTAT
CAACAC
Found at i:389540 original size:250 final size:250
Alignment explanation
Indices: 389094--389545 Score: 642
Period size: 250 Copynumber: 1.8 Consensus size: 250
389084 AACAACCCCA
*
389094 AAAACATCGAAACCCATAATTATAATGTAATGGGTAATTTTTCAATATAACCGATATAAATATAC
1 AAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGATATAAATATAC
* * * * * * *
389159 CGGTTTTATGAAAAATATGTCTGCAACATTTATCGACACTTATTAGTATTGTGTCGATACTTTTT
66 CGATTTTATGAAAAATAGGTCTACAACATGTATCGACACTTATTAATATAGTGTCGATAATTTTT
* * * **
389224 GTCCGGAATGGATGCCAAAAAGGGTGAACCTACAAAGTGTCGATACATTTTCATAGAGTTTCGAT
131 ATCCAGAATGGATGCCAAAAAGGGTGAACCTACAAAGTGTCGATACATTTTCATAAAGCGTCGAT
389289 -CCAAAAGGGTTGCACACATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCT
196 CCCAAAAGGGTTGCACACATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCT
* * * *
389343 AAAATATCGAAACCCATAATTATAGTGTAATAGGTAATTTTGT-AATATAACCGGTATACATATA
1 AAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TCAATATAACCGATATAAATATA
* * *
389407 TCGATTTTATGAGAAAATAGGTCTATAATATGTATCGACACTTATTAATATAGTGTCGATAATTT
65 CCGATTTTATGA-AAAATAGGTCTACAACATGTATCGACACTTATTAATATAGTGTCGATAATTT
* *
389472 TTATCCATAATGGATGCCAAAAAGGGTGAACGC-ATAAAGTGTCGATACATTTTCGA-AAAGCGT
129 TTATCCAGAATGGATGCCAAAAAGGGTGAAC-CTACAAAGTGTCGATACATTTTC-ATAAAGCGT
389535 CGATCCCAAAA
192 CGATCCCAAAA
389546 ATATCGAAAC
Statistics
Matches: 176, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
249 67 0.38
250 101 0.57
251 8 0.05
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (250 bp):
AAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTCAATATAACCGATATAAATATAC
CGATTTTATGAAAAATAGGTCTACAACATGTATCGACACTTATTAATATAGTGTCGATAATTTTT
ATCCAGAATGGATGCCAAAAAGGGTGAACCTACAAAGTGTCGATACATTTTCATAAAGCGTCGAT
CCCAAAAGGGTTGCACACATAAAGTGTCGATACATTTATTAAAAGTGTCGATCCT
Found at i:392636 original size:198 final size:197
Alignment explanation
Indices: 392169--392898 Score: 746
Period size: 198 Copynumber: 3.6 Consensus size: 197
392159 ACCTAAATAT
* * * * *
392169 GTGTCGATATATTT-TATACAAGTATCGACCCAAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTATA-AAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAAT
* * * * * * *
392233 AGGTAAATTAACAATGTAACCGGTATAAATATACCTG-TTAATTAGAAAACAGGTTAACATAATG
65 AGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATG
* * * * *
392297 TATCGACACTTGTGCAATTTGTGTCGATACTTATTGTCCAGGACGAATGCACAAACGAGGTGC-A
130 TATCGACACTTGT-AAATTTGTGTCGATACTT-TTGTCCAGAATGAATCCA-AAAAG-GGTGCAA
392361 CGCATAAA
191 C-CATAAA
* ** * *
392369 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAACCAATAATTATAATGTATTA
1 GTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATA
*
392434 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGATAAAATAGGTCAACATCAA-G
66 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACAT-AATG
392498 TATC-A-ACTTGCTAAATTTGTGTCGATACTTTTGGTCCAGAATGAATACCAAAAAGGGTGCAAC
130 TATCGACACTTG-TAAATTTGTGTCGATACTTTT-GTCCAGAATGAAT-CCAAAAAGGGTGCAAC
392561 CATAAA
192 CATAAA
* * * *
392567 GTGTCGATACATTTATAAAAAATATCGATCTGAGAAACATCGAAA-CACATAAGTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCA-ATAATTATAATGTAAT
* *
392631 AGGTAAATTTTCAATGTAACC-AGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAA-ATAA
65 AGGTAAATTTACAATGTAACCGA-TATAAATATACCGGTTTTATGAGAAAATAGGTC-AACATAA
* * * **
392694 TGTATCGACACATTGTTAGTTTGTGTCGATACTTTTTTCCAAAATGAAATATGAATGCCCAACCA
128 TGTATCGACAC-TTGTAAATTTGTGTCGATACTTTTGTCC---A-G--A-ATGAAT--CCAAAAA
*
392759 -GGTGCAAGCATAAA
183 GGGTGCAACCATAAA
** * *
392773 GTGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGAAACCGATAATAATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATA
** * * ** *
392837 GGTAAATTTGTAATGTTACCGTTATAAATATACCGG-TTTACTTCGAAAATAGGTCAATATAA
66 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTA-TGAGAAAATAGGTCAACATAA
392899 GAGCTACCTA
Statistics
Matches: 450, Mismatches: 54, Indels: 47
0.82 0.10 0.09
Matches are distributed among these distances:
197 5 0.01
198 124 0.28
199 45 0.10
200 113 0.25
201 27 0.06
202 3 0.01
203 1 0.00
204 6 0.01
205 86 0.19
206 35 0.08
207 5 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCTAAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAATGT
ATCGACACTTGTAAATTTGTGTCGATACTTTTGTCCAGAATGAATCCAAAAAGGGTGCAACCATA
AA
Found at i:393002 original size:23 final size:23
Alignment explanation
Indices: 392969--393018 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
392959 TGGTTAAATG
* *
392969 CCTATTTCATTATATAAGCGCTA
1 CCTATTACATTATATAAACGCTA
392992 CCTATTACATTATATAAACGCTA
1 CCTATTACATTATATAAACGCTA
393015 CCTA
1 CCTA
393019 ATATGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (23 bp):
CCTATTACATTATATAAACGCTA
Found at i:394164 original size:17 final size:17
Alignment explanation
Indices: 394142--394176 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
394132 AAAATTAATT
*
394142 AAAAAATTCAAACTTAA
1 AAAAAATCCAAACTTAA
*
394159 AAAAAATCCAAATTTAA
1 AAAAAATCCAAACTTAA
394176 A
1 A
394177 GAGTTAATTG
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:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAATCCAAACTTAA
Found at i:395240 original size:43 final size:43
Alignment explanation
Indices: 395162--395243 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
395152 TGATTTTTTT
* *
395162 ATTCTGCTTGGGATCCTTTATGGAGGGCGATATCCCCATTCTA
1 ATTCTGCTTGGGATCCTTTATGAAGGGCGACATCCCCATTCTA
* **
395205 ATTCTGAC-TGGGATCCTTTGTGAAGGGTTACATCCCCAT
1 ATTCTG-CTTGGGATCCTTTATGAAGGGCGACATCCCCAT
395244 CCTGATATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 32 0.97
44 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (43 bp):
ATTCTGCTTGGGATCCTTTATGAAGGGCGACATCCCCATTCTA
Found at i:398262 original size:20 final size:21
Alignment explanation
Indices: 398223--398263 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
398213 CGATCTTTGT
* *
398223 TTTTATTTTGTAATTATAATA
1 TTTTATTTTGAAAATATAATA
398244 TTTTATTTT-AAAATATAATA
1 TTTTATTTTGAAAATATAATA
398264 ACTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTTTGAAAATATAATA
Found at i:398994 original size:20 final size:19
Alignment explanation
Indices: 398958--398998 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
398948 CACGATATGT
*
398958 TTTTTTAAAATAAATATTA
1 TTTTTCAAAATAAATATTA
398977 TTTTTCAAAAT-AATA-TA
1 TTTTTCAAAATAAATATTA
398994 TTTTT
1 TTTTT
398999 AGTGTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 4 0.19
19 10 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTTCAAAATAAATATTA
Found at i:399458 original size:50 final size:50
Alignment explanation
Indices: 399395--399496 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
399385 TTTATCCTAT
399395 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
399445 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
399495 TT
1 TT
399497 CAATAATTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.25, C:0.02, G:0.16, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
Found at i:400112 original size:30 final size:30
Alignment explanation
Indices: 400073--400176 Score: 190
Period size: 30 Copynumber: 3.5 Consensus size: 30
400063 TTCCATGGAT
*
400073 CACCTGGCGACCTTCATTGGTCGCCCAGAA
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
400103 CACCCGGCGACCTTCATTGGTCGCCCAGAA
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
*
400133 CACCCGGCGACCTTCATTGGTCGCCCAGAC
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
400163 CACCCGGCGACCTT
1 CACCCGGCGACCTT
400177 TATTCGAACT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.17
Consensus pattern (30 bp):
CACCCGGCGACCTTCATTGGTCGCCCAGAA
Found at i:402987 original size:20 final size:20
Alignment explanation
Indices: 402962--403010 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
402952 AAGCTTAGGG
*
402962 TATCGATACTGCATGACCAA
1 TATCGATACTGCATGAACAA
* *
402982 TATCGATATTGCATGAACAG
1 TATCGATACTGCATGAACAA
403002 TATCGATAC
1 TATCGATAC
403011 CATAAGGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
TATCGATACTGCATGAACAA
Found at i:404273 original size:15 final size:16
Alignment explanation
Indices: 404242--404275 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
404232 AGTACTGTTT
404242 ATGATAAAATGAATTA
1 ATGATAAAATGAATTA
*
404258 ATGATAATAT-AATTA
1 ATGATAAAATGAATTA
404273 ATG
1 ATG
404276 TTTAGCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (16 bp):
ATGATAAAATGAATTA
Found at i:405134 original size:35 final size:36
Alignment explanation
Indices: 405076--405146 Score: 126
Period size: 35 Copynumber: 2.0 Consensus size: 36
405066 GTATGTACAG
*
405076 GGGAATAGATTCCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
405112 GGGAACAGATT-CCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
405147 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 24 0.71
36 10 0.29
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCTGGGGGGTATCGATTCCCC
Found at i:405455 original size:27 final size:25
Alignment explanation
Indices: 405406--405474 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
405396 ATGACCAATG
* *
405406 TGAAATGAAAT-AAGTATGTAATATA
1 TGAAATGATATGAA-TATGCAATATA
*
405431 TGAAATGACATATGAATATGCAATATG
1 TGAAATG--ATATGAATATGCAATATA
*
405458 TGATATGATATGAATAT
1 TGAAATGATATGAATAT
405475 ATGGTTACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 17 0.46
27 18 0.49
28 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.33
Consensus pattern (25 bp):
TGAAATGATATGAATATGCAATATA
Found at i:405476 original size:20 final size:20
Alignment explanation
Indices: 405440--405477 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
405430 ATGAAATGAC
*
405440 ATATGAATATGCAATATGTG
1 ATATGAATATGAAATATGTG
405460 ATATG-ATATGAATATATG
1 ATATGAATATGAA-ATATG
405478 GTTACACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (20 bp):
ATATGAATATGAAATATGTG
Found at i:409649 original size:18 final size:19
Alignment explanation
Indices: 409620--409656 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
409610 TTCCCCTTCA
409620 AAGGGGGAATCGATTCCTC
1 AAGGGGGAATCGATTCCTC
409639 AAGGGGG-ATCGATTCCTC
1 AAGGGGGAATCGATTCCTC
409657 TGCACAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.22, G:0.32, T:0.22
Consensus pattern (19 bp):
AAGGGGGAATCGATTCCTC
Found at i:417124 original size:4 final size:4
Alignment explanation
Indices: 417115--417140 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
417105 AAATGATGAC
417115 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
417141 ATAATGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:417356 original size:31 final size:30
Alignment explanation
Indices: 417318--417413 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
417308 GTCAAAGAGC
417318 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
417348 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
417380 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
417410 TACC
1 TACC
417414 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:417430 original size:30 final size:30
Alignment explanation
Indices: 417396--417588 Score: 359
Period size: 30 Copynumber: 6.4 Consensus size: 30
417386 GGTTCTTCGG
* *
417396 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
417426 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
417456 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
417486 GATCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
417516 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
417546 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
417576 GACCTCTGGATAG
1 GACCTCTGGATAG
417589 GTCCTTCGGA
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 159 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:421512 original size:30 final size:30
Alignment explanation
Indices: 421478--421670 Score: 359
Period size: 30 Copynumber: 6.4 Consensus size: 30
421468 GGTTCTTCGG
* *
421478 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
421508 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
421538 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
421568 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
421598 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
421628 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
421658 GACCTCTGGATAG
1 GACCTCTGGATAG
421671 GTCCTTCGGA
Statistics
Matches: 159, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 159 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:426823 original size:34 final size:35
Alignment explanation
Indices: 426768--426836 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
426758 TATGTGCAGG
426768 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
426803 GGGAACAGATT-CCCCTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
426837 CCTAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 23 0.68
35 11 0.32
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.20
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:427269 original size:22 final size:20
Alignment explanation
Indices: 427244--427285 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
427234 CCAATGTGAA
427244 ATGAAATAAGCTATATGAATAT
1 ATGAAATAA-C-ATATGAATAT
*
427266 ATGAAATGACATATGAATAT
1 ATGAAATAACATATGAATAT
427286 GTAATATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
ATGAAATAACATATGAATAT
Found at i:452602 original size:160 final size:163
Alignment explanation
Indices: 452327--452625 Score: 498
Period size: 160 Copynumber: 1.8 Consensus size: 163
452317 TATATCCTTT
* * *
452327 CTTTGGTTTCTTTGGTTATTATATGCTTTTGTTTGTTTTAAAGGTCTTGGTGAGTTGGTGTCAGC
1 CTTTGCTTTCTTTGGTTATCATATGC--TTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGC
452392 GTTGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGC
64 GTTGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGC
452457 ACTCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
129 ACTCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
*
452492 CTTTGCTTTCTTTGGTTATCATATGC-T-TTTGTTTTAAAGGCCTTGGTGAGTT-GTGTCAGTGT
1 CTTTGCTTTCTTTGGTTATCATATGCTTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGCGT
452554 TGCTCCTTGGTTACTTGTTTGTGTCC-TGCTTTATGCGCTGTACATTATGGACATTCATGGTGCA
66 TGCTCCTTGGTTACTTGTTTGTG-CCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGCA
*
452618 TTCTTTTT
130 CTCTTTTT
452626 TCTTAAGTAG
Statistics
Matches: 128, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
160 77 0.60
161 26 0.20
162 1 0.01
165 24 0.19
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (163 bp):
CTTTGCTTTCTTTGGTTATCATATGCTTGTTTGTTTTAAAGGCCTTGGTGAGTTGGTGTCAGCGT
TGCTCCTTGGTTACTTGTTTGTGCCATGCTTTATGCGCTGTACATTATGGACATTCATGGTGCAC
TCTTTTTCCTCAAATTTCCTTCTCCTTAGAATG
Found at i:454012 original size:42 final size:44
Alignment explanation
Indices: 453948--454044 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
453938 AAAATTATAA
* *
453948 AAAAAATTAAAAAATATCAT-AAA-TAAAAATATTATAAAAAT-T
1 AAAAAA-TAAAAAATAACATAAAATTAAAAATATCATAAAAATAT
* * *
453990 AAAAAATAAAGAATAACTATAAAATTCAAAATATCATAAAACTAT
1 AAAAAATAAAAAATAAC-ATAAAATTAAAAATATCATAAAAATAT
*
454035 AAATAATAAA
1 AAAAAATAAA
454045 TTATAAATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
41 9 0.20
42 8 0.18
43 3 0.07
44 15 0.33
45 10 0.22
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (44 bp):
AAAAAATAAAAAATAACATAAAATTAAAAATATCATAAAAATAT
Found at i:454020 original size:26 final size:25
Alignment explanation
Indices: 453957--454037 Score: 67
Period size: 26 Copynumber: 3.1 Consensus size: 25
453947 AAAAAAATTA
* *
453957 AAAAATATCATAAATAAAAATATTAT
1 AAAAAT-TCAAAAATAAAAATACTAT
*
453983 AAAAATTAAAAAATAAAGAATAACTAT
1 AAAAATTCAAAAATAAA-AAT-ACTAT
*
454010 -AAAATTCAAAATATCATAAA-ACTAT
1 AAAAATTCAAAA-AT-AAAAATACTAT
454035 AAA
1 AAA
454038 TAATAAATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
25 14 0.31
26 21 0.47
27 8 0.18
28 2 0.04
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (25 bp):
AAAAATTCAAAAATAAAAATACTAT
Found at i:454058 original size:45 final size:44
Alignment explanation
Indices: 453973--454058 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
453963 ATCATAAATA
* *
453973 AAAATATTATAAAAATTAAAAAATAAAGAATAACTATAAAATTC
1 AAAATATCATAAAAATTAAAAAATAAAGAATAAATATAAAATTC
* * **
454017 AAAATATCATAAAACTATAAATAATAAATTATAAATATAAAA
1 AAAATATCATAAAAAT-TAAAAAATAAAGAATAAATATAAAA
454059 ACATATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 14 0.40
45 21 0.60
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.28
Consensus pattern (44 bp):
AAAATATCATAAAAATTAAAAAATAAAGAATAAATATAAAATTC
Found at i:463603 original size:3 final size:3
Alignment explanation
Indices: 463595--463624 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
463585 CAATTTGGTT
*
463595 GAA GAA GAA GAA TAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
463625 CGGGTTGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
GAA
Found at i:468365 original size:285 final size:285
Alignment explanation
Indices: 467855--468426 Score: 1135
Period size: 285 Copynumber: 2.0 Consensus size: 285
467845 AAAAAATATG
467855 TATGTATTTGACATTATTTCGCATTGAACGTAAACGTTAAACACTTGTTTAATTATAAATGGTAT
1 TATGTATTTGACATTATTTCGCATTGAACGTAAACGTTAAACACTTGTTTAATTATAAATGGTAT
467920 ACGAGTTATCAATATTACATTGACTAGTCCTTTTCCTATGTGCAGGAGCTTTTATTAATGCTATG
66 ACGAGTTATCAATATTACATTGACTAGTCCTTTTCCTATGTGCAGGAGCTTTTATTAATGCTATG
467985 TTCGTTAATCGATAAAATATCAAAAATGGTTATCAAAGTAGAGTACATGTGTCAGTAGAATCTCG
131 TTCGTTAATCGATAAAATATCAAAAATGGTTATCAAAGTAGAGTACATGTGTCAGTAGAATCTCG
*
468050 TCTTGATAATGACAACCATTTCGGAGTCCTTATCTAACTTGCAAAACGTGCAATTTGTAGTTTAC
196 TCTTGATAAAGACAACCATTTCGGAGTCCTTATCTAACTTGCAAAACGTGCAATTTGTAGTTTAC
468115 TTGTTAGTCTTCAGACATTAAGGCC
261 TTGTTAGTCTTCAGACATTAAGGCC
468140 TATGTATTTGACATTATTTCGCATTGAACGTAAACGTTAAACACTTGTTTAATTATAAATGGTAT
1 TATGTATTTGACATTATTTCGCATTGAACGTAAACGTTAAACACTTGTTTAATTATAAATGGTAT
468205 ACGAGTTATCAATATTACATTGACTAGTCCTTTTCCTATGTGCAGGAGCTTTTATTAATGCTATG
66 ACGAGTTATCAATATTACATTGACTAGTCCTTTTCCTATGTGCAGGAGCTTTTATTAATGCTATG
468270 TTCGTTAATCGATAAAATATCAAAAATGGTTATCAAAGTAGAGTACATGTGTCAGTAGAATCTCG
131 TTCGTTAATCGATAAAATATCAAAAATGGTTATCAAAGTAGAGTACATGTGTCAGTAGAATCTCG
468335 TCTTGATAAAGACAACCATTTCGGAGTCCTTATCTAACTTGCAAAACGTGCAATTTGTAGTTTAC
196 TCTTGATAAAGACAACCATTTCGGAGTCCTTATCTAACTTGCAAAACGTGCAATTTGTAGTTTAC
468400 TTGTTAGTCTTCAGACATTAAGGCC
261 TTGTTAGTCTTCAGACATTAAGGCC
468425 TA
1 TA
468427 CATCTTCTGG
Statistics
Matches: 286, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
285 286 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.37
Consensus pattern (285 bp):
TATGTATTTGACATTATTTCGCATTGAACGTAAACGTTAAACACTTGTTTAATTATAAATGGTAT
ACGAGTTATCAATATTACATTGACTAGTCCTTTTCCTATGTGCAGGAGCTTTTATTAATGCTATG
TTCGTTAATCGATAAAATATCAAAAATGGTTATCAAAGTAGAGTACATGTGTCAGTAGAATCTCG
TCTTGATAAAGACAACCATTTCGGAGTCCTTATCTAACTTGCAAAACGTGCAATTTGTAGTTTAC
TTGTTAGTCTTCAGACATTAAGGCC
Found at i:490433 original size:17 final size:16
Alignment explanation
Indices: 490402--490435 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
490392 CACGTGAGGA
490402 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
490418 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
490435 T
1 T
490436 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:491175 original size:13 final size:13
Alignment explanation
Indices: 491157--491182 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
491147 GTTGCACATT
491157 TCAACATGTTCAA
1 TCAACATGTTCAA
491170 TCAACATGTTCAA
1 TCAACATGTTCAA
491183 CATGTTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TCAACATGTTCAA
Found at i:491182 original size:22 final size:21
Alignment explanation
Indices: 491152--491192 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
491142 TTCAAGTTGC
491152 ACATTTCAACATGTTCAATCA
1 ACATTTCAACATGTTCAATCA
491173 ACATGTTCAACATGTTCAAT
1 ACAT-TTCAACATGTTCAAT
491193 TCCATTGGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (21 bp):
ACATTTCAACATGTTCAATCA
Found at i:500686 original size:17 final size:16
Alignment explanation
Indices: 500655--500688 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
500645 CACGTGAGGA
500655 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
500671 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
500688 T
1 T
500689 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:504447 original size:21 final size:21
Alignment explanation
Indices: 504421--504464 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
504411 TACGAAAGTT
*
504421 ACTGTAGTAGTGCATCGATGC
1 ACTGTAGTAATGCATCGATGC
504442 ACTGTAGTAATGCATCGATGC
1 ACTGTAGTAATGCATCGATGC
504463 AC
1 AC
504465 AATTCTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (21 bp):
ACTGTAGTAATGCATCGATGC
Found at i:510672 original size:12 final size:12
Alignment explanation
Indices: 510637--510666 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
510627 ATAATAGAAA
510637 TAGAGAGAAATT
1 TAGAGAGAAATT
510649 TAGAGAGAAATT
1 TAGAGAGAAATT
510661 TAGAGA
1 TAGAGA
510667 AGAATTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (12 bp):
TAGAGAGAAATT
Found at i:524988 original size:30 final size:31
Alignment explanation
Indices: 524918--524989 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
524908 ATTTATAATT
* *
524918 AAATCAAAATT-TTATATATTTAATTGAATA
1 AAATCAAAATTCTCATATATATAATTGAATA
**
524948 AAATTTAAATTCTCATATATATAA-T-ACATA
1 AAATCAAAATTCTCATATATATAATTGA-ATA
524978 AAATCAAAATTC
1 AAATCAAAATTC
524990 ATATATCGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.03
30 23 0.68
31 10 0.29
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.39
Consensus pattern (31 bp):
AAATCAAAATTCTCATATATATAATTGAATA
Found at i:527673 original size:26 final size:26
Alignment explanation
Indices: 527637--527692 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
527627 AAAAAAAAAT
527637 GAAATTATGCCTTTCTTTTAGTATAA
1 GAAATTATGCCTTTCTTTTAGTATAA
527663 GAAATTATGCCTTTCTTTTAGTATAA
1 GAAATTATGCCTTTCTTTTAGTATAA
527689 GAAA
1 GAAA
527693 ATAATGATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (26 bp):
GAAATTATGCCTTTCTTTTAGTATAA
Found at i:528327 original size:14 final size:14
Alignment explanation
Indices: 528308--528338 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
528298 GAATATATAT
528308 GTGATCCTTATGGA
1 GTGATCCTTATGGA
528322 GTGATCCTTATGGA
1 GTGATCCTTATGGA
528336 GTG
1 GTG
528339 GTCTTTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.13, G:0.32, T:0.35
Consensus pattern (14 bp):
GTGATCCTTATGGA
Found at i:531338 original size:3 final size:3
Alignment explanation
Indices: 531330--531358 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
531320 AGTTCTTAGG
531330 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
531359 TTGAAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:532032 original size:47 final size:47
Alignment explanation
Indices: 531934--532032 Score: 110
Period size: 47 Copynumber: 2.1 Consensus size: 47
531924 TCGAATAAAT
* * **
531934 GCATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTCGAACAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAACAA
* * * *
531981 GCATGCGAATTAGATATCATGCGGTTAGGATT-TTTGTGAATAACAA
1 GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAACAA
532027 GGCATG
1 -GCATG
532033 GGGTAGATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 9 0.21
47 34 0.79
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (47 bp):
GCATGCGAACTAGAAATCATGCGGTTAGGATTATTTGTCAAGAACAA
Found at i:538840 original size:42 final size:41
Alignment explanation
Indices: 538767--538845 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 41
538757 ACAATTTAAG
* **
538767 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGTAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAAAGCAT-ATGATGTAA
* *
538809 TCCTTCGGGTCATCTGTAAGCCTTTAAAGCATATGAT
1 TCCTTCGGGCCATCAGTAAGCCTTTAAAGCATATGAT
538846 AAGTCCTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 5 0.16
42 27 0.84
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAAAGCATATGATGTAA
Found at i:539044 original size:42 final size:42
Alignment explanation
Indices: 538981--539204 Score: 164
Period size: 42 Copynumber: 5.1 Consensus size: 42
538971 ACTTAGTAAG
* *
538981 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
* * * *
539023 TCCTTAGGGCTATCAGTAAGTCTATAGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
** ** * * * *
539065 TCCTTAGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGC--AAA
1 TCCTTAGGGCCATCAGTAAGTCTT-TC----GAGCA-TGATGCTTAAA
* * * *
539111 TCCATCAGTAAGTGCCATCAATAAGTCTTTCGAGTATGATTCTTAAA
1 TCC-T---T-AGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
*
539158 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
539200 TCCTT
1 TCCTT
539205 CGGGTAATTT
Statistics
Matches: 137, Mismatches: 32, Indels: 26
0.70 0.16 0.13
Matches are distributed among these distances:
42 91 0.66
43 1 0.01
45 4 0.03
46 12 0.09
47 11 0.08
48 4 0.03
50 2 0.01
51 12 0.09
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (42 bp):
TCCTTAGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
Found at i:539232 original size:135 final size:135
Alignment explanation
Indices: 538989--539258 Score: 477
Period size: 135 Copynumber: 2.0 Consensus size: 135
538979 AGTCCTTCGG
*
538989 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCTATCAGTAAGTCTATAGAGCA
1 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTATAGAGCA
*
539054 TGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCCATCAG
66 TGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
539119 TAAGT
131 TAAGT
* * * *
539124 GCCATCAATAAGTCTTTCGAGTATGATTCTTAAATCCTTAGGGCCATCAGTAAGTCTTTCGAGCA
1 GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTATAGAGCA
*
539189 TGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
66 TGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
539254 TAAGT
131 TAAGT
539259 CTTTCGAGCT
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
135 128 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (135 bp):
GCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTAGGGCCATCAGTAAGTCTATAGAGCA
TGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAG
TAAGT
Found at i:539300 original size:80 final size:80
Alignment explanation
Indices: 539167--539379 Score: 390
Period size: 80 Copynumber: 2.7 Consensus size: 80
539157 ATCCTTAGGG
539167 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
539232 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAT
*
539247 CCATCAGTAAGTCTTTCGAGCTTGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
*
539312 AGTAGTGAATCAAAT
66 AGTAGTGAAGCAAAT
* *
539327 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
539380 TCTTTCAAGC
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 128 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.31
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAG
AGTAGTGAAGCAAAT
Found at i:539396 original size:42 final size:41
Alignment explanation
Indices: 539333--539419 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
539323 AAATCCATCA
* * *
539333 GTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTT
1 GTAAGTCTTTCAAGCAAGATGAT-AAATCCTTCGGGCCATTT
*
539375 GTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATTT
1 GTAAGTCTTTCAAGCAAGATGATAAATCCTTCGGGCCATTT
539416 -TAAG
1 GTAAG
539420 CCTTATCGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 4 0.10
41 16 0.39
42 21 0.51
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (41 bp):
GTAAGTCTTTCAAGCAAGATGATAAATCCTTCGGGCCATTT
Found at i:539968 original size:50 final size:52
Alignment explanation
Indices: 539789--540088 Score: 380
Period size: 50 Copynumber: 5.8 Consensus size: 52
539779 AGAATCACAC
*
539789 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAG
* *
539841 ACAGAAGATTGTTCGAGTTCTACTCCCTGAAACAAGAGGG-GTGAACCCGTAGG
1 -CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTA-G
*
539894 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGG-GTGAACCCGTAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAG
539944 CAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTA-
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAG
* * * * ** **
539994 -AGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGATCAAACCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAG
* * *
540045 TAGAAGATTATTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCG
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCG
540089 GGACCATCAT
Statistics
Matches: 224, Mismatches: 16, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
49 20 0.09
50 61 0.27
51 36 0.16
52 49 0.22
53 48 0.21
54 10 0.04
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (52 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAG
Found at i:539989 original size:102 final size:103
Alignment explanation
Indices: 539789--540032 Score: 372
Period size: 102 Copynumber: 2.4 Consensus size: 103
539779 AGAATCACAC
539789 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAGACAGAAGATTGTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAGACAGAAGATTGTT
*
539854 CGAGTTCTACTCCCTGAAACAAGAGGGGTGAACCCGTA
66 CGAGTTCTACTCCCTGAAACAAGAGGGGCGAACCCGTA
* *
539892 GGCAGAAGATTGTTCGAGTTCTAC-CCCTGAAGCAAGAGGG-GTGAACCCGTAG-CAGAAGATTG
1 --CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAGACAGAAGATTG
*
539954 TTCGAGTTCTAC-CCCTGAAGCAAGAGGGAGCGAACCCGTA
64 TTCGAGTTCTACTCCCTGAAACAAGAGGG-GCGAACCCGTA
* *
539994 -AGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGA
540033 TCAAACCATT
Statistics
Matches: 130, Mismatches: 6, Indels: 10
0.89 0.04 0.07
Matches are distributed among these distances:
99 20 0.15
100 15 0.12
101 15 0.12
102 32 0.25
103 11 0.08
104 15 0.12
105 22 0.17
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.20
Consensus pattern (103 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGCGAACCCGTAGACAGAAGATTGTT
CGAGTTCTACTCCCTGAAACAAGAGGGGCGAACCCGTA
Found at i:541381 original size:13 final size:13
Alignment explanation
Indices: 541363--541391 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
541353 AGTTTAGGTC
541363 TAGGTTTTTTATT
1 TAGGTTTTTTATT
541376 TAGGTTTTTTATT
1 TAGGTTTTTTATT
541389 TAG
1 TAG
541392 ACATTTGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (13 bp):
TAGGTTTTTTATT
Found at i:541726 original size:3 final size:3
Alignment explanation
Indices: 541718--541842 Score: 232
Period size: 3 Copynumber: 41.0 Consensus size: 3
541708 AGTCCTTAGG
541718 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
541766 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA
541812 TTA TTA TATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
541843 CATGATAATA
Statistics
Matches: 120, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
3 114 0.95
4 6 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:541860 original size:25 final size:22
Alignment explanation
Indices: 541718--541867 Score: 218
Period size: 21 Copynumber: 6.8 Consensus size: 22
541708 AGTCCTTAGG
541718 TTATTATTATTATTATT-ATTA
1 TTATTATTATTATTATTAATTA
541739 TTATTATTATTATTATT-ATTA
1 TTATTATTATTATTATTAATTA
541760 TTATTATTATTATTATT-ATTA
1 TTATTATTATTATTATTAATTA
541781 TTATTATTATTATTATTAATTA
1 TTATTATTATTATTATTAATTA
541803 TTATTATTATTATTA-TATATTA
1 TTATTATTATTATTATTA-ATTA
*
541825 TTATTATTATTATTATTACATGA
1 TTATTATTATTATTATTA-ATTA
*
541848 TAATATATGTATTATTATTA
1 TTAT-TAT-TATTATTATTA
541868 GTGTTTAATT
Statistics
Matches: 121, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
21 61 0.50
22 38 0.31
23 8 0.07
24 3 0.02
25 11 0.09
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (22 bp):
TTATTATTATTATTATTAATTA
Found at i:542573 original size:15 final size:15
Alignment explanation
Indices: 542553--542588 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
542543 AAATCAAATT
542553 AAGTTCGAATTTGTA
1 AAGTTCGAATTTGTA
542568 AAGTTCGAATTTGTA
1 AAGTTCGAATTTGTA
542583 AAGTTC
1 AAGTTC
542589 ATTGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (15 bp):
AAGTTCGAATTTGTA
Found at i:543184 original size:52 final size:52
Alignment explanation
Indices: 543115--543229 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 52
543105 ATTCTTCAAT
*
543115 GTTCACATTAGGATAGGATT-AATTTTCGATTTTATTCGGATATTATTAATCA
1 GTTCACATTAGGATAGGATTAAATTTT-GATTTTATTCGGATACTATTAATCA
*
543167 GTTCACATT-GGACTAGGATTAAATTTTGGTTTTATTCGGATACTATTAATCA
1 GTTCACATTAGGA-TAGGATTAAATTTTGATTTTATTCGGATACTATTAATCA
543219 GTTCACATTAG
1 GTTCACATTAG
543230 AAATTAATTA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
51 3 0.05
52 48 0.83
53 7 0.12
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (52 bp):
GTTCACATTAGGATAGGATTAAATTTTGATTTTATTCGGATACTATTAATCA
Found at i:543240 original size:52 final size:52
Alignment explanation
Indices: 543131--543272 Score: 155
Period size: 52 Copynumber: 2.7 Consensus size: 52
543121 ATTAGGATAG
* *
543131 GATT-AATTTTCGATTTTATTCGGATATTATTAATCAGTTCACATTGGACTA
1 GATTAAATTTTCGATTTTATTCGGATACTATTAATCAGTTCACATTGAACTA
* *
543182 GGATTAAATTTT-GGTTTTATTCGGATACTATTAATCAGTTCACATTAGAAATTA
1 -GATTAAATTTTCGATTTTATTCGGATACTATTAATCAGTTCACATT-G-AACTA
* *
543236 -ATTAATTATTTTCGATTTTGTTCGGATGCTAATTAAT
1 GATTAA--ATTTTCGATTTTATTCGGATACT-ATTAAT
543273 TGTCTTTGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
52 41 0.54
53 7 0.09
54 8 0.11
55 14 0.18
56 6 0.08
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (52 bp):
GATTAAATTTTCGATTTTATTCGGATACTATTAATCAGTTCACATTGAACTA
Found at i:544391 original size:2 final size:2
Alignment explanation
Indices: 544384--544449 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
544374 AAATACATAC
544384 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
544426 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
544450 TGAAATAAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:544651 original size:30 final size:30
Alignment explanation
Indices: 544611--544673 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
544601 TGTTTATAAA
* * *
544611 ATTGGCATAATTATATATTTGGTTCTTAAT
1 ATTGGAATAATTATACATTTGGTCCTTAAT
544641 ATTGGAATAATTATACATTTGGTCCTTAAT
1 ATTGGAATAATTATACATTTGGTCCTTAAT
544671 ATT
1 ATT
544674 TACATATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (30 bp):
ATTGGAATAATTATACATTTGGTCCTTAAT
Found at i:545032 original size:16 final size:16
Alignment explanation
Indices: 545007--545040 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
544997 GTTAAAACAA
545007 TTAAACAAATTATTTT
1 TTAAACAAATTATTTT
*
545023 TTAAATAAATTATTTT
1 TTAAACAAATTATTTT
545039 TT
1 TT
545041 CTTTAACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAACAAATTATTTT
Found at i:545098 original size:26 final size:26
Alignment explanation
Indices: 545046--545096 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
545036 TTTTTCTTTA
*
545046 ACTGGTAATCGAACTAAAATTATTTG
1 ACTGGTAATCGAACGAAAATTATTTG
* *
545072 ACTGTTAATCGAACCGAAATTTATT
1 ACTGGTAATCGAA-CGAAAATTATT
545097 GAAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (26 bp):
ACTGGTAATCGAACGAAAATTATTTG
Found at i:545302 original size:91 final size:93
Alignment explanation
Indices: 545193--545370 Score: 297
Period size: 91 Copynumber: 1.9 Consensus size: 93
545183 AATAATTATT
* * *
545193 AACCGAATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAATT
1 AACCGAATTTTTTCTTTAACCATTAATCAAAACAAAATTATTTGACCGTTAATCGAACCCAAATT
545258 TATTT-AAAATTATTAACCGAACAAATC
66 TATTTGAAAATTATTAACCGAACAAATC
*
545285 AACCG-ATTTTTTTTTTAACCATTAATCAAAACAAAATTATTTGACCGTTAATCGAACCCAAATT
1 AACCGAATTTTTTCTTTAACCATTAATCAAAACAAAATTATTTGACCGTTAATCGAACCCAAATT
*
545349 TATTTGAAAATTATTAATCGAA
66 TATTTGAAAATTATTAACCGAA
545371 TTAACCAAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
91 60 0.75
92 20 0.25
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.35
Consensus pattern (93 bp):
AACCGAATTTTTTCTTTAACCATTAATCAAAACAAAATTATTTGACCGTTAATCGAACCCAAATT
TATTTGAAAATTATTAACCGAACAAATC
Found at i:545578 original size:90 final size:93
Alignment explanation
Indices: 545402--545585 Score: 234
Period size: 91 Copynumber: 2.0 Consensus size: 93
545392 TTTTTCTTTA
* *
545402 ACCGTTAATCAAATCAAAATTTATTTGAAAATTATTAACCAAACAAATCAACCGATTTTTTTCTT
1 ACCGTTAATCAAATCAAAATTTATTTGAAAATTATTAACCAAACAAATCAAACGATTTTTTCCTT
545467 AACCATTAATCGAACCAAAA-TTATTTG
66 AACCATTAATCGAACCAAAATTTATTTG
* * **
545494 ACCG-TAATCGAATCGAAAA-TTATTTGAAAATTATTACCCAATA-AAAT-AAATTATTTTTTCC
1 ACCGTTAATCAAATC-AAAATTTATTTGAAAATTATTAACCAA-ACAAATCAAACGATTTTTTCC
* * *
545555 TTAACCGTTGATCGATCCAAAATTTATTTG
64 TTAACCATTAATCGAACCAAAATTTATTTG
545585 A
1 A
545586 AAATTATTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
90 29 0.36
91 42 0.52
92 9 0.11
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (93 bp):
ACCGTTAATCAAATCAAAATTTATTTGAAAATTATTAACCAAACAAATCAAACGATTTTTTCCTT
AACCATTAATCGAACCAAAATTTATTTG
Found at i:546618 original size:21 final size:21
Alignment explanation
Indices: 546592--546636 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
546582 TCAATTTTGT
*
546592 TAAAAATATTAATATTTTAGA
1 TAAAAATAATAATATTTTAGA
*
546613 TAAAAATAATAATTTTTTAGA
1 TAAAAATAATAATATTTTAGA
546634 TAA
1 TAA
546637 TTTTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAGA
Found at i:547503 original size:18 final size:19
Alignment explanation
Indices: 547468--547504 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
547458 CACGGAATGT
547468 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
547488 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
547505 GGATTACTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:551986 original size:21 final size:21
Alignment explanation
Indices: 551962--552004 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
551952 AATGGCTTCT
*
551962 GAAG-AGCTGCGCAAAGCAAAG
1 GAAGAAGCAGCGC-AAGCAAAG
551983 GAAGAAGCAGCGCAAGCAAAG
1 GAAGAAGCAGCGCAAGCAAAG
552004 G
1 G
552005 CTGGAGCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.44, C:0.19, G:0.35, T:0.02
Consensus pattern (21 bp):
GAAGAAGCAGCGCAAGCAAAG
Found at i:562400 original size:21 final size:21
Alignment explanation
Indices: 562375--562435 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
562365 ATATGTGAAC
562375 ATGTGAATTATATGAAAAGTG
1 ATGTGAATTATATGAAAAGTG
562396 ATGTGAATTATATGAAAAGTG
1 ATGTGAATTATATGAAAAGTG
* * *
562417 ATATGAATTACATAAAAAG
1 ATGTGAATTATATGAAAAG
562436 AAGTTATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (21 bp):
ATGTGAATTATATGAAAAGTG
Found at i:563086 original size:31 final size:31
Alignment explanation
Indices: 563051--563109 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
563041 TGCTATGATG
563051 GCAGTAATTGTTCAAGCATGATTACAAGATA
1 GCAGTAATTGTTCAAGCATGATTACAAGATA
563082 GCAGTAATTGTTCAAGCATGATTACAAG
1 GCAGTAATTGTTCAAGCATGATTACAAG
563110 TTATAGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (31 bp):
GCAGTAATTGTTCAAGCATGATTACAAGATA
Found at i:566032 original size:19 final size:19
Alignment explanation
Indices: 566008--566059 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
565998 GAATGCAATT
566008 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
566027 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
*
566046 AGTACATCGATGCA
1 AGTGCATCGATGCA
566060 CCTGCTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:567274 original size:615 final size:615
Alignment explanation
Indices: 566327--567557 Score: 2354
Period size: 615 Copynumber: 2.0 Consensus size: 615
566317 AACAAGGCGA
566327 ATGTGAGTGCATATGATTATAGTATATGATTATATGGAAATTAGACTTGCGATGAGTCTATTTCC
1 ATGTGAGTGCATATGATTATAGTATATGATTATATGGAAATTAGACTTGCGATGAGTCTATTTCC
566392 ATGTTTTGATTTTATGAATGCATGAAAATAAGTATAGTTGGTAGTCGTTAGTATGTGGATATGTA
66 ATGTTTTGATTTTATGAATGCATGAAAATAAGTATAGTTGGTAGTCGTTAGTATGTGGATATGTA
566457 TTGTTATGTTCTTTTCTATGTGATATGATTTATGTGATGATGTGACTCTGTGATATAAGTTATAT
131 TTGTTATGTTCTTTTCTATGTGATATGATTTATGTGATGATGTGACTCTGTGATATAAGTTATAT
*
566522 GATCATAAATTATGTAAATAATAATGACTTATGTAATGACAAGAGAAAGTGATATAAGCTATGTG
196 GATCATAAATTATGTAAATAATAATGACTTATGTAATGACAAGAGAAAGTGATATAAGATATGTG
* *
566587 GTATAGATATAAATGATTATATGAACATGTAATATAAGTTATGTGATGAGGATCTATGTTTTTTA
261 GTATAGATATAAATGATTATATGAACATGTAATATAAATTATGTGATGAAGATCTATGTTTTTTA
*
566652 TATGTCTATGAGAAGTATGTGTTATGTGATGTATATATGAGTTATGTGATCCTATGAGATTATGA
326 TATGTCTATGAGAAGTATGTGCTATGTGATGTATATATGAGTTATGTGATCCTATGAGATTATGA
* * *
566717 AAATAGATATGTGAACATGTGAATTATATGAAAAGTGATATGAATTACATGAAAATAAGCTATAT
391 AAAGAGATATGTGAACATGTGAATAATATGAAAAGTGATATGAATTACATGAAAAGAAGCTATAT
566782 GTCTACATGTATATGTGAAAGAAGCTATGAGCTTATATGAACATATGATATGAAAATGTATATGT
456 GTCTACATGTATATGTGAAAGAAGCTATGAGCTTATATGAACATATGATATGAAAATGTATATGT
* *
566847 GAAATTATATAAGTGAAAATGCCCATGTTATGTGTATTGAGAGCTAGAGGTATAGTTGGCATGCC
521 GAAATGATATAAGTGAAAATGCCCATGTTATGTGTATTGAGAGCTAGAGGTATAGTTGGCATACC
566912 AAGAGTCGAGGGTCTACGCGGTCCTTCGGG
586 AAGAGTCGAGGGTCTACGCGGTCCTTCGGG
*
566942 ATGTGAGTGCATATGATTATAGTATATGATTATATGGAAATTATACTTGCGATGAGTCTATTTCC
1 ATGTGAGTGCATATGATTATAGTATATGATTATATGGAAATTAGACTTGCGATGAGTCTATTTCC
567007 ATGTTTTGATTTTATGAATGCATGAAAATAAGTATAGTTGGTAGTCGTTAGTATGTGGATATGTA
66 ATGTTTTGATTTTATGAATGCATGAAAATAAGTATAGTTGGTAGTCGTTAGTATGTGGATATGTA
567072 TTGTTATGTTCTTTTCTATGTGATATGATTTATGTGATGATGTGACTCTGTGATATAAGTTATAT
131 TTGTTATGTTCTTTTCTATGTGATATGATTTATGTGATGATGTGACTCTGTGATATAAGTTATAT
567137 GATCATAAATTATGTAAATAATAATGACTTATGTAATGACAAGAGAAAGTGATATAAGATATGTG
196 GATCATAAATTATGTAAATAATAATGACTTATGTAATGACAAGAGAAAGTGATATAAGATATGTG
567202 GTATAGATATAAATGATTATATGAACATGTAATATAAATTATGTGATGAAGATCTATGTTTTTTA
261 GTATAGATATAAATGATTATATGAACATGTAATATAAATTATGTGATGAAGATCTATGTTTTTTA
567267 TATGTCTATGAGAAGTATGTGCTATGTGATGTATATATGAGTTATGTGATCCTATGAGATTATGA
326 TATGTCTATGAGAAGTATGTGCTATGTGATGTATATATGAGTTATGTGATCCTATGAGATTATGA
*
567332 AAAGAGATATGTGAACATGTGAATAATATGAAAAGTGATATGAATTACATGAAGAGAAGCTATAT
391 AAAGAGATATGTGAACATGTGAATAATATGAAAAGTGATATGAATTACATGAAAAGAAGCTATAT
*
567397 GTCTATATGTATATGTGAAAGAAGCTATGAGCTTATATGAACATATGATATGAAAATGTATATGT
456 GTCTACATGTATATGTGAAAGAAGCTATGAGCTTATATGAACATATGATATGAAAATGTATATGT
567462 GAAATGATATAAGTGAAAATGCCCATGTTATGTGTATTGAGAGCTAGAGGTATAGTTGGCATACC
521 GAAATGATATAAGTGAAAATGCCCATGTTATGTGTATTGAGAGCTAGAGGTATAGTTGGCATACC
567527 AAGAGTCGAGGGTCTACGCGGTCCTTCGGG
586 AAGAGTCGAGGGTCTACGCGGTCCTTCGGG
567557 A
1 A
567558 CATATGTGTT
Statistics
Matches: 604, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
615 604 1.00
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (615 bp):
ATGTGAGTGCATATGATTATAGTATATGATTATATGGAAATTAGACTTGCGATGAGTCTATTTCC
ATGTTTTGATTTTATGAATGCATGAAAATAAGTATAGTTGGTAGTCGTTAGTATGTGGATATGTA
TTGTTATGTTCTTTTCTATGTGATATGATTTATGTGATGATGTGACTCTGTGATATAAGTTATAT
GATCATAAATTATGTAAATAATAATGACTTATGTAATGACAAGAGAAAGTGATATAAGATATGTG
GTATAGATATAAATGATTATATGAACATGTAATATAAATTATGTGATGAAGATCTATGTTTTTTA
TATGTCTATGAGAAGTATGTGCTATGTGATGTATATATGAGTTATGTGATCCTATGAGATTATGA
AAAGAGATATGTGAACATGTGAATAATATGAAAAGTGATATGAATTACATGAAAAGAAGCTATAT
GTCTACATGTATATGTGAAAGAAGCTATGAGCTTATATGAACATATGATATGAAAATGTATATGT
GAAATGATATAAGTGAAAATGCCCATGTTATGTGTATTGAGAGCTAGAGGTATAGTTGGCATACC
AAGAGTCGAGGGTCTACGCGGTCCTTCGGG
Found at i:572887 original size:3 final size:3
Alignment explanation
Indices: 572879--572918 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
572869 GATGGAAAGA
572879 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
572919 GTGAAAAGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:578847 original size:57 final size:56
Alignment explanation
Indices: 578768--578956 Score: 261
Period size: 56 Copynumber: 3.4 Consensus size: 56
578758 AAATTAGGGC
* * *
578768 CCCGAAATCGAATATATTTATCAATTGTTGTCATTAATAAGCATAAAAAATAGGGGT
1 CCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAGCAT-AAAAATAGGGGT
* ** * * *
578825 CCCGAAATCGAGTATATCTATCAGTTGTTACCATTAAGAAACATAAAAATAGGAGC
1 CCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAGCATAAAAATAGGGGT
* *
578881 CCCGATATCGAATATATCTATCAGTTGTTGTCATTAAGAAGCATAAAAATAAGGGT
1 CCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAGCATAAAAATAGGGGT
*
578937 CCCGAAATTGAATATATCTA
1 CCCGAAATCGAATATATCTA
578957 GAAAATAGGG
Statistics
Matches: 113, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
56 76 0.67
57 37 0.33
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (56 bp):
CCCGAAATCGAATATATCTATCAGTTGTTGTCATTAAGAAGCATAAAAATAGGGGT
Found at i:582969 original size:16 final size:16
Alignment explanation
Indices: 582926--582970 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
582916 TAATAAATAA
*
582926 ACGAACATAAAAGAAC
1 ACGAACATAAACGAAC
*
582942 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
582958 ACGAACATAAACG
1 ACGAACATAAACG
582971 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.60, C:0.22, G:0.11, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:583905 original size:10 final size:10
Alignment explanation
Indices: 583890--583937 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
583880 ATAAACGAAT
583890 GAACATAAAC
1 GAACATAAAC
583900 GAACATAACCGAAC
1 GAACAT-A---AAC
583914 GAACATAAAC
1 GAACATAAAC
*
583924 GAACATAACC
1 GAACATAAAC
583934 GAAC
1 GAAC
583938 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:583912 original size:24 final size:24
Alignment explanation
Indices: 583877--583938 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
583867 GATTGAGTTA
* *
583877 AACATAAACGAATGAACATAAACG
1 AACATAACCGAACGAACATAAACG
583901 AACATAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
583925 AACATAACCGAACG
1 AACATAACCGAACG
583939 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:583927 original size:14 final size:14
Alignment explanation
Indices: 583877--583927 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
583867 GATTGAGTTA
*
583877 AACATAAACGAATG
1 AACATAAACGAACG
583891 AACAT--A--AACG
1 AACATAAACGAACG
*
583901 AACATAACCGAACG
1 AACATAAACGAACG
583915 AACATAAACGAAC
1 AACATAAACGAAC
583928 ATAACCGAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
10 8 0.27
12 1 0.03
14 21 0.70
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:583938 original size:14 final size:14
Alignment explanation
Indices: 583897--583938 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
583887 AATGAACATA
583897 AACGAACATAACCG
1 AACGAACATAACCG
583911 AACGAACAT-A---
1 AACGAACATAACCG
583921 AACGAACATAACCG
1 AACGAACATAACCG
583935 AACG
1 AACG
583939 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:588175 original size:25 final size:24
Alignment explanation
Indices: 588147--588198 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
588137 AATAGTGTTA
* *
588147 TTAAAAAAATTAATATTTTAATATT
1 TTAAAAAAAGTAATA-TTTAAAATT
* *
588172 TTAAATAAAGTATTATTTAAAATT
1 TTAAAAAAAGTAATATTTAAAATT
588196 TTA
1 TTA
588199 TTTTTCTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (24 bp):
TTAAAAAAAGTAATATTTAAAATT
Found at i:589920 original size:23 final size:23
Alignment explanation
Indices: 589868--589921 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
589858 ACAACAAGGA
*
589868 CTCCTCACCCTATATAAAGGAGG
1 CTCCTCCCCCTATATAAAGGAGG
589891 CTCCTCCCCCTATATAAAGGAGG
1 CTCCTCCCCCTATATAAAGGAGG
589914 CTCCTCCC
1 CTCCTCCC
589922 ACCATTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.22
Consensus pattern (23 bp):
CTCCTCCCCCTATATAAAGGAGG
Found at i:590689 original size:186 final size:187
Alignment explanation
Indices: 590362--590735 Score: 709
Period size: 186 Copynumber: 2.0 Consensus size: 187
590352 CTTCATTCTT
590362 TGATCGAATCTAAATCTTTATAGGTTTAATTATTCAATGACGAGCAACATTCATAACTCTGATGT
1 TGATCGAATCTAAATCTTTATAGGTTTAATTATTCAATGACGAGCAACATTCATAACTCTGATGT
590427 CATTCCTTATCAATTGGTATCAGATTTAGATCGATTCTTAGAGAGAATCAAGCAATCTTGCACTT
66 CATTCCTTATCAATTGGTATCAGATTTAGATCGATTCTTAGAGAGAATCAAGCAATCTTGCACTT
590492 TTTGATCTTAGTGCTTTCGATTC-TTTGTTTTTACCATT-TTGTTCCTTTACATTGTC
131 TTTGATCTTAGTGCTTTCGATTCTTTTG-TTTTACCATTCTTGTTCCTTTACATTGTC
590548 TGATCGAATCTAAATCTTTATAGGTTTAATTATTCAATGACGAGCAACATTCATAACTCTGATGT
1 TGATCGAATCTAAATCTTTATAGGTTTAATTATTCAATGACGAGCAACATTCATAACTCTGATGT
590613 CATTCCTTATCAATTGGTATCAGATTTAGATCGATTCTTAGAGAG-ATCAAGCAATCTTGCACTT
66 CATTCCTTATCAATTGGTATCAGATTTAGATCGATTCTTAGAGAGAATCAAGCAATCTTGCACTT
590677 TTTGATTCTTAGTGCTTTCGATTCTTTTGTTTTACCATTCTTGTTCCTTTACATTGTC
131 TTTGA-TCTTAGTGCTTTCGATTCTTTTGTTTTACCATTCTTGTTCCTTTACATTGTC
590735 T
1 T
590736 AACACATTCT
Statistics
Matches: 185, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
185 24 0.13
186 138 0.75
187 23 0.12
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (187 bp):
TGATCGAATCTAAATCTTTATAGGTTTAATTATTCAATGACGAGCAACATTCATAACTCTGATGT
CATTCCTTATCAATTGGTATCAGATTTAGATCGATTCTTAGAGAGAATCAAGCAATCTTGCACTT
TTTGATCTTAGTGCTTTCGATTCTTTTGTTTTACCATTCTTGTTCCTTTACATTGTC
Found at i:592915 original size:21 final size:21
Alignment explanation
Indices: 592891--592935 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
592881 ATCCATATGT
* *
592891 TCCGAATAACATAGGTAACTG
1 TCCGAAGAAAATAGGTAACTG
*
592912 TCCGAAGAAAATAGGTAATTG
1 TCCGAAGAAAATAGGTAACTG
592933 TCC
1 TCC
592936 ATATGTCCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (21 bp):
TCCGAAGAAAATAGGTAACTG
Found at i:592969 original size:31 final size:30
Alignment explanation
Indices: 592913--593020 Score: 123
Period size: 30 Copynumber: 3.5 Consensus size: 30
592903 AGGTAACTGT
*
592913 CCGAAGAAAATAGGTAAT-TGTCCATATGTC
1 CCGAAG-ACATAGGTAATCTGTCCATATGTC
592943 CCGAAGACATAGGTAATCCTGTCCATATGTC
1 CCGAAGACATAGGTAAT-CTGTCCATATGTC
*
592974 CCGAAGGACATAGGTAAACAT-T-CATATGTC
1 CCGAA-GACATAGGTAATC-TGTCCATATGTC
*
593004 TCGAAAGACATAGGTAA
1 CCG-AAGACATAGGTAA
593021 CCCTCAACTC
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
29 10 0.14
30 27 0.39
31 21 0.30
32 12 0.17
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (30 bp):
CCGAAGACATAGGTAATCTGTCCATATGTC
Found at i:593183 original size:21 final size:21
Alignment explanation
Indices: 593159--593222 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
593149 TATAGACACA
593159 TTCACATAGTTCATATCACTT
1 TTCACATAGTTCATATCACTT
* *
593180 TTCATAT-GATTCATATTC-GTGT
1 TTCACATAG-TTCATA-TCACT-T
* *
593202 TTCACATAGCTCATAACACTT
1 TTCACATAGTTCATATCACTT
593223 CTCATGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 15 0.47
23 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (21 bp):
TTCACATAGTTCATATCACTT
Found at i:598726 original size:31 final size:31
Alignment explanation
Indices: 598674--598745 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
598664 ATTTCGAGAC
* *
598674 ATGGACAGTATACCTATGTTCTAAGGAA-CA
1 ATGGACAGTTTACCTAGGTTCTAAGGAACCA
* **
598704 TATGGACAGTTTACCTGGGTTCTTCGGAACCA
1 -ATGGACAGTTTACCTAGGTTCTAAGGAACCA
598736 ATGGACAGTT
1 ATGGACAGTT
598746 GTCGAGGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (31 bp):
ATGGACAGTTTACCTAGGTTCTAAGGAACCA
Found at i:600514 original size:21 final size:21
Alignment explanation
Indices: 600416--600504 Score: 108
Period size: 21 Copynumber: 4.2 Consensus size: 21
600406 AAGATTGTCC
600416 AGGGGATACAGATTCCCCCCCA
1 AGGGGA-ACAGATTCCCCCCCA
*
600438 GGGGGAACAGATTCCCCCCCA
1 AGGGGAACAGATTCCCCCCCA
* *
600459 AGGGAAATAGATT-CCCCCCA
1 AGGGGAACAGATTCCCCCCCA
* *
600479 AAGGGAACAAATTCCCCCCCA
1 AGGGGAACAGATTCCCCCCCA
*
600500 GGGGG
1 AGGGG
600505 TATCGATTCC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
20 16 0.29
21 35 0.62
22 5 0.09
ACGTcount: A:0.29, C:0.34, G:0.26, T:0.11
Consensus pattern (21 bp):
AGGGGAACAGATTCCCCCCCA
Found at i:603255 original size:19 final size:20
Alignment explanation
Indices: 603226--603368 Score: 182
Period size: 20 Copynumber: 7.2 Consensus size: 20
603216 AATTAGATTG
603226 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
603246 CCCA-GGGGTACAGATTCTCC
1 CCCAGGGGGTACAGATTC-CC
*
603266 CCCAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
603286 TCCA-GGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* **
603305 CCCAAGGGAAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
603325 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
603345 CCTCAGGGGGAACAAATTCCC
1 CC-CAGGGGGTACAGATTCCC
603366 CCC
1 CCC
603369 CCCCCAGGGG
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
19 30 0.28
20 47 0.44
21 29 0.27
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:603272 original size:40 final size:39
Alignment explanation
Indices: 603226--603368 Score: 205
Period size: 40 Copynumber: 3.6 Consensus size: 39
603216 AATTAGATTG
*
603226 CCCAGGGGGTACAGATTCCCCCCAGGGGTACAGATTCTCC
1 CCCAGGGGGAACAGATTCCCCCCAGGGGTACAGATTC-CC
*
603266 CCCAGGGGGAACAGATTCCCTCCAGGGGTACAGATTCCC
1 CCCAGGGGGAACAGATTCCCCCCAGGGGTACAGATTCCC
* * *
603305 CCCAAGGGAAACAGATTCCCCCCAGGGGGTACCGATTCCC
1 CCCAGGGGGAACAGATTCCCCCCA-GGGGTACAGATTCCC
*
603345 CCTCAGGGGGAACAAATTCCCCCC
1 CC-CAGGGGGAACAGATTCCCCCC
603369 CCCCCAGGGG
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 23 0.25
40 51 0.55
41 18 0.20
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (39 bp):
CCCAGGGGGAACAGATTCCCCCCAGGGGTACAGATTCCC
Found at i:607993 original size:2 final size:2
Alignment explanation
Indices: 607982--608030 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
607972 ATAGCACTTG
607982 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
608023 TA TA TA TA
1 TA TA TA TA
608031 AGTAGCACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:608664 original size:17 final size:17
Alignment explanation
Indices: 608635--608670 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
608625 TGGGAGTTTC
608635 TTCTCTTCTTTTTCTTT
1 TTCTCTTCTTTTTCTTT
608652 TTCT-TTCTATTTTCTTT
1 TTCTCTTCT-TTTTCTTT
608669 TT
1 TT
608671 TTTTTCTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (17 bp):
TTCTCTTCTTTTTCTTT
Found at i:609294 original size:28 final size:28
Alignment explanation
Indices: 609262--609318 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
609252 CCATTTGAAA
609262 TAGTTTATGGTTTCAATCCACTAACTAC
1 TAGTTTATGGTTTCAATCCACTAACTAC
* *
609290 TAGTTTATGGTTTCAATCCATTACCTAC
1 TAGTTTATGGTTTCAATCCACTAACTAC
609318 T
1 T
609319 TTAGATCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (28 bp):
TAGTTTATGGTTTCAATCCACTAACTAC
Found at i:610663 original size:14 final size:14
Alignment explanation
Indices: 610644--610696 Score: 78
Period size: 14 Copynumber: 4.1 Consensus size: 14
610634 CATCCGTGAA
610644 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
610658 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
610672 CG-T---TTATGTT
1 CGTTCGGTTATGTT
610682 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
610696 C
1 C
610697 ATTTATGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.26
11 1 0.03
13 1 0.03
14 24 0.69
ACGTcount: A:0.08, C:0.15, G:0.26, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Done.