Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009145.1 Hibiscus syriacus cultivar Beakdansim tig00112657_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: 440284
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:262691 original size:80 final size:79
Alignment explanation
Indices: 262411--262706 Score: 305
Period size: 80 Copynumber: 3.7 Consensus size: 79
262401 GCTTGAAAGA
* * * * *
262411 CTTACAAATGACCCGAAGGATTTCATCATCAAGCTCGAAAGACTTATTGATGGATTTGCTTCTCT
1 CTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
262476 ACTCTTCCGTGAAGG
66 ACTCTT-CGTGAAGG
* *
262491 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAA--GGAC
1 CTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGAT-----GAATTTG-C
* *
262554 TTCA-T-CATCATACTCG-AAAGA
60 TTCACTAC-TC-T--TCGTGAAGG
** * * * *
262575 CTTACTGATGGCCCAAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
1 CTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
262640 ACTCTTCGGTGAAGG
66 ACTCTTC-GTGAAGG
*
262655 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
1 CTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATG
262707 GCACTTACTG
Statistics
Matches: 174, Mismatches: 26, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
78 2 0.01
79 4 0.02
80 101 0.58
81 4 0.02
82 2 0.01
83 4 0.02
84 52 0.30
85 4 0.02
86 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (79 bp):
CTTACAAATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
ACTCTTCGTGAAGG
Found at i:262714 original size:13 final size:13
Alignment explanation
Indices: 262696--262720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
262686 TGCTCGAAAG
262696 ACTTACTGATGGC
1 ACTTACTGATGGC
262709 ACTTACTGATGG
1 ACTTACTGATGG
262721 GTTTACTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:262798 original size:92 final size:93
Alignment explanation
Indices: 262616--262800 Score: 273
Period size: 92 Copynumber: 2.0 Consensus size: 93
262606 TGCTCGAAAG
* * * *
262616 ACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGAATTTACTTCACTACTCTTCCGTGAAGGCTTACAAATGACCCGAAGGACTTAAT
262681 CATCATGCTCGAAAGACTTACTGATGGC
66 CATCATGCTCGAAAGACTTACTGATGGC
** * * *
262709 ACTTACTGATGGGTTTACTTCACTACTCTTCCGTGAAGGCTTA-AGATGGCCTGAAGGACTTAAT
1 ACTTACTGATGAATTTACTTCACTACTCTTCCGTGAAGGCTTACAAATGACCCGAAGGACTTAAT
*
262773 CATCATGCTCGAAAGACTTATTGATGGC
66 CATCATGCTCGAAAGACTTACTGATGGC
262801 CCGAAGGACT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 43 0.52
93 39 0.48
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (93 bp):
ACTTACTGATGAATTTACTTCACTACTCTTCCGTGAAGGCTTACAAATGACCCGAAGGACTTAAT
CATCATGCTCGAAAGACTTACTGATGGC
Found at i:273532 original size:3 final size:3
Alignment explanation
Indices: 273524--273551 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
273514 TTTGTCCCAT
273524 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
273552 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:273609 original size:21 final size:21
Alignment explanation
Indices: 273583--273637 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
273573 TTAATTTTAT
* *
273583 AGGCCCAGATCTAGAACCCGG
1 AGGCCCAGATCCAAAACCCGG
273604 AGGCCCAGATCCAAAACCCGG
1 AGGCCCAGATCCAAAACCCGG
*
273625 AAGCCCAGATCCA
1 AGGCCCAGATCCA
273638 GACCCAACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.07
Consensus pattern (21 bp):
AGGCCCAGATCCAAAACCCGG
Found at i:276756 original size:28 final size:28
Alignment explanation
Indices: 276718--276804 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
276708 AAAAATTCAT
* *
276718 ATATTTAATTTATAATTCTTTTTTTCAAA
1 ATATTT-ATTTATAATTATTATTTTCAAA
* * *
276747 ATTTTTATTTATACTTATTATTTTCATA
1 ATATTTATTTATAATTATTATTTTCAAA
276775 ATATTTATATGTAT-ATTATCTTATTTTCAA
1 ATATTTAT-T-TATAATTA--TTATTTTCAA
276805 GTATTAAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 25 0.54
29 9 0.20
30 3 0.07
31 9 0.20
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (28 bp):
ATATTTATTTATAATTATTATTTTCAAA
Found at i:287324 original size:39 final size:40
Alignment explanation
Indices: 287238--287335 Score: 173
Period size: 39 Copynumber: 2.5 Consensus size: 40
287228 ATTTCCAAGT
287238 AGAA-TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
287277 AGAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
287316 AGAAGTTCATAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
287336 GCTTGTTCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 31 0.54
40 26 0.46
ACGTcount: A:0.48, C:0.08, G:0.24, T:0.19
Consensus pattern (40 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
Found at i:287538 original size:123 final size:122
Alignment explanation
Indices: 287279--287715 Score: 707
Period size: 122 Copynumber: 3.6 Consensus size: 122
287269 AAGGAAGAAG
*
287279 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
287344 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCTGCATCAACTTTTCCAGAGA
66 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGA
* * *
287401 AAGTTCATAATGAGAATAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
287466 AACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCCAGAGA
66 AACC-TTTGTATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGA
* * *
287524 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAATAGCTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
287589 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAGA-A
66 AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGA
** * *
287645 GTGTTCATAATGAGAAGAACTCATCTAAAGAAGG-AGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
287709 CAACCTT
65 CAACCTT
287716 GCCTTAATTC
Statistics
Matches: 291, Mismatches: 22, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
121 61 0.21
122 117 0.40
123 113 0.39
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (122 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTGTATGACTCTATCACAGAAGGAGATAGATCAGCATCAACATTTCCAGAGA
Found at i:287794 original size:137 final size:136
Alignment explanation
Indices: 287630--287989 Score: 479
Period size: 137 Copynumber: 2.6 Consensus size: 136
287620 TAGATCAGCA
* * * *
287630 TCAATATTTCCAGAA-GTGTTCATAATGAGAAGAACTCATCTAAAGAAGGAGAAGAAGTTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAA-AAGGAGAAGAAATTCATAA
* * * *
287694 TGAGAAGAACTTGTTCAACCTTGCCTTAATTCGTTACATATGAAGCCAAATTAACAACCCCTCTT
65 TGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
287759 TTGAGGG
130 TTGAGGG
* * *
287766 TCAACATTTCCAGAAGGAGTTCATAATGAGAATAACTCATCTGAATATGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAA-AAGGAGAAGAAATTCATAA
* * *** ** *
287831 TGAGAAGAACTTGTTCAACCTTGCTTTAATTCATCATATATGAAGTTGAATCAATGATACCTCTT
65 TGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTT
287896 TTGAGGG
130 TTGAGGG
* * * *
287903 TCAGCATTTCCAGAAGGAGATCATAATGAGAAGAAATCATCTGAATAGGAAGAAGAAATTCATAA
1 TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAGG-AGAAGAAATTCATAA
287968 TGAGAAGAACTTGTTCAACCTT
65 TGAGAAGAACTTGTTCAACCTT
287990 TTGCTAGATT
Statistics
Matches: 195, Mismatches: 27, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
136 15 0.08
137 180 0.92
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (136 bp):
TCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAGAAGAAATTCATAAT
GAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGCCAAATCAACAACACCTCTTT
TGAGGG
Found at i:288235 original size:3 final size:3
Alignment explanation
Indices: 288229--288256 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
288219 TTTTTCCCAT
288229 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
288257 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:288314 original size:21 final size:21
Alignment explanation
Indices: 288288--288382 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
288278 TTAATTTTAT
* *
288288 AGGCCCAAATCTAGAACTCGG
1 AGGCCCAGATCTAGAACCCGG
* *
288309 AGGCCCGGATCTAGAACCCAG
1 AGGCCCAGATCTAGAACCCGG
*
288330 AGGCCCAGATCTAGAACCCGA
1 AGGCCCAGATCTAGAACCCGG
* * *
288351 AGGCCCAGATCCAAAACTCGG
1 AGGCCCAGATCTAGAACCCGG
*
288372 AAGCCCAGATC
1 AGGCCCAGATC
288383 CAGATCCAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.33, C:0.33, G:0.24, T:0.11
Consensus pattern (21 bp):
AGGCCCAGATCTAGAACCCGG
Found at i:290727 original size:778 final size:778
Alignment explanation
Indices: 289233--290793 Score: 3104
Period size: 778 Copynumber: 2.0 Consensus size: 778
289223 AATTGTACCT
289233 GTAACCACTATGATTTTAAAATATTTCAATTTAATCCCGAAAAATAAGTTTTAATTTATTTTAAT
1 GTAACCACTATGATTTTAAAATATTTCAATTTAATCCCGAAAAATAAGTTTTAATTTATTTTAAT
289298 TTGATATTCGAATTTTAGGTTATTATAATTTAGTCCTTGACTTAATTATATATATTTTAAGTAAA
66 TTGATATTCGAATTTTAGGTTATTATAATTTAGTCCTTGACTTAATTATATATATTTTAAGTAAA
289363 ATAACAAATTTAGCCATGTAATTTTATTAATTTATGCTTTAATCCTGATTAATTTATTATGGTTA
131 ATAACAAATTTAGCCATGTAATTTTATTAATTTATGCTTTAATCCTGATTAATTTATTATGGTTA
289428 AATTATATTAATAATACTTATATTTAATAATTTAAAATTAGGATTATTAATTTAAATATTTTATA
196 AATTATATTAATAATACTTATATTTAATAATTTAAAATTAGGATTATTAATTTAAATATTTTATA
289493 ATCTTATAATTTTAATCACTAAAATTATATTTTATGAATTTTAATTTAGATTTTAAATTTTATTT
261 ATCTTATAATTTTAATCACTAAAATTATATTTTATGAATTTTAATTTAGATTTTAAATTTTATTT
*
289558 TATTACGTTTTAGTCATTTAATTTATCGTAATTTAAATTTTCAGTCAAATTAATATAATTCAAAT
326 TATTACGTTTTAGTCATTTAATTTATCGTAATTCAAATTTTCAGTCAAATTAATATAATTCAAAT
289623 TTTGAATCCCTTTGTTGTCATTAGCTGATCCACATTAAAATTAGGATAAGGACGTTTGGTGGCCT
391 TTTGAATCCCTTTGTTGTCATTAGCTGATCCACATTAAAATTAGGATAAGGACGTTTGGTGGCCT
289688 ATTAAAGACAATAGTTTTCCTCCACCTAACATAAATAATATAATAATAAAAAAACTTTAGCAAAT
456 ATTAAAGACAATAGTTTTCCTCCACCTAACATAAATAATATAATAATAAAAAAACTTTAGCAAAT
289753 AGTTTTTTTCTTTCCTTCATCAATGGCACCGTTTCTTCCTTTAAATATTGAAATTTAAGCTCTTG
521 AGTTTTTTTCTTTCCTTCATCAATGGCACCGTTTCTTCCTTTAAATATTGAAATTTAAGCTCTTG
289818 GTTACTATTATAAGTTTGACAATATTTTAGTAATATTTTTCTTATAATATTTTATTTCTTATAAT
586 GTTACTATTATAAGTTTGACAATATTTTAGTAATATTTTTCTTATAATATTTTATTTCTTATAAT
289883 TAAATATTGGAAAGGATTTTCTCCAATTAAAGAACAAAAAAACACTGTCATGGTGTAGAATTTAA
651 TAAATATTGGAAAGGATTTTCTCCAATTAAAGAACAAAAAAACACTGTCATGGTGTAGAATTTAA
289948 TATAATAAATATACTATAATATTATACATTTGTCGTTATTATCTGAGGGTAAGAAACAAGAAA
716 TATAATAAATATACTATAATATTATACATTTGTCGTTATTATCTGAGGGTAAGAAACAAGAAA
290011 GTAACCACTATGATTTTAAAATATTTCAATTTAATCCCGAAAAATAAGTTTTAATTTATTTTAAT
1 GTAACCACTATGATTTTAAAATATTTCAATTTAATCCCGAAAAATAAGTTTTAATTTATTTTAAT
290076 TTGATATTCGAATTTTAGGTTATTATAATTTAGTCCTTGACTTAATTATATATATTTTAAGTAAA
66 TTGATATTCGAATTTTAGGTTATTATAATTTAGTCCTTGACTTAATTATATATATTTTAAGTAAA
290141 ATAACAAATTTAGCCATGTAATTTTATTAATTTATGCTTTAATCCTGATTAATTTATTATGGTTA
131 ATAACAAATTTAGCCATGTAATTTTATTAATTTATGCTTTAATCCTGATTAATTTATTATGGTTA
290206 AATTATATTAATAATACTTATATTTAATAATTTAAAATTAGGATTATTAATTTAAATATTTTATA
196 AATTATATTAATAATACTTATATTTAATAATTTAAAATTAGGATTATTAATTTAAATATTTTATA
290271 ATCTTATAATTTTAATCACTAAAATTATATTTTATGAATTTTAATTTAGATTTTAAATTTTATTT
261 ATCTTATAATTTTAATCACTAAAATTATATTTTATGAATTTTAATTTAGATTTTAAATTTTATTT
290336 TATTACGTTTTAGTCATTTAATTTATCGTAATTCAAATTTTCAGTCAAATTAATATAATTCAAAT
326 TATTACGTTTTAGTCATTTAATTTATCGTAATTCAAATTTTCAGTCAAATTAATATAATTCAAAT
290401 TTTGAATCCCTTTGTTGTCATTAGCTGATCCACATTAAAATTAGGATAAGGACGTTTGGTGGCCT
391 TTTGAATCCCTTTGTTGTCATTAGCTGATCCACATTAAAATTAGGATAAGGACGTTTGGTGGCCT
*
290466 ATTAAAGACAATAGTTTTCCTCCACCTAACATAAATAATATAATAATAATAAAACTTTAGCAAAT
456 ATTAAAGACAATAGTTTTCCTCCACCTAACATAAATAATATAATAATAAAAAAACTTTAGCAAAT
290531 AGTTTTTTTCTTTCCTTCATCAATGGCACCGTTTCTTCCTTTAAATATTGAAATTTAAGCTCTTG
521 AGTTTTTTTCTTTCCTTCATCAATGGCACCGTTTCTTCCTTTAAATATTGAAATTTAAGCTCTTG
290596 GTTACTATTATAAGTTTGACAATATTTTAGTAATATTTTTCTTATAATATTTTATTTCTTATAAT
586 GTTACTATTATAAGTTTGACAATATTTTAGTAATATTTTTCTTATAATATTTTATTTCTTATAAT
290661 TAAATATTGGAAAGGATTTTCTCCAATTAAAGAACAAAAAAACACTGTCATGGTGTAGAATTTAA
651 TAAATATTGGAAAGGATTTTCTCCAATTAAAGAACAAAAAAACACTGTCATGGTGTAGAATTTAA
290726 TATAATAAATATACTATAATATTATACATTTGTCGTTATTATCTGAGGGTAAGAAACAAGAAA
716 TATAATAAATATACTATAATATTATACATTTGTCGTTATTATCTGAGGGTAAGAAACAAGAAA
290789 GTAAC
1 GTAAC
290794 TTAATTGATA
Statistics
Matches: 781, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
778 781 1.00
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (778 bp):
GTAACCACTATGATTTTAAAATATTTCAATTTAATCCCGAAAAATAAGTTTTAATTTATTTTAAT
TTGATATTCGAATTTTAGGTTATTATAATTTAGTCCTTGACTTAATTATATATATTTTAAGTAAA
ATAACAAATTTAGCCATGTAATTTTATTAATTTATGCTTTAATCCTGATTAATTTATTATGGTTA
AATTATATTAATAATACTTATATTTAATAATTTAAAATTAGGATTATTAATTTAAATATTTTATA
ATCTTATAATTTTAATCACTAAAATTATATTTTATGAATTTTAATTTAGATTTTAAATTTTATTT
TATTACGTTTTAGTCATTTAATTTATCGTAATTCAAATTTTCAGTCAAATTAATATAATTCAAAT
TTTGAATCCCTTTGTTGTCATTAGCTGATCCACATTAAAATTAGGATAAGGACGTTTGGTGGCCT
ATTAAAGACAATAGTTTTCCTCCACCTAACATAAATAATATAATAATAAAAAAACTTTAGCAAAT
AGTTTTTTTCTTTCCTTCATCAATGGCACCGTTTCTTCCTTTAAATATTGAAATTTAAGCTCTTG
GTTACTATTATAAGTTTGACAATATTTTAGTAATATTTTTCTTATAATATTTTATTTCTTATAAT
TAAATATTGGAAAGGATTTTCTCCAATTAAAGAACAAAAAAACACTGTCATGGTGTAGAATTTAA
TATAATAAATATACTATAATATTATACATTTGTCGTTATTATCTGAGGGTAAGAAACAAGAAA
Found at i:293371 original size:32 final size:34
Alignment explanation
Indices: 293302--293376 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 34
293292 ATGTATGTGA
*
293302 TATAT-ATATATGTTTTGTGATATGAATTATATG
1 TATATGATATATGTTGTGTGATATGAATTATATG
*
293335 -ATATGATATATG-TGTGTGTTAATG-ATTAT-TG
1 TATATGATATATGTTGTGTGAT-ATGAATTATATG
*
293366 TATATGTTATA
1 TATATGATATA
293377 AGATATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.06
32 24 0.67
33 10 0.28
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (34 bp):
TATATGATATATGTTGTGTGATATGAATTATATG
Found at i:294317 original size:25 final size:25
Alignment explanation
Indices: 294264--294325 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
294254 TCGAACACCA
**
294264 AAAG-AAAATAGAAAAGAAAAATTG
1 AAAGAAAAATAGAAAAGAAAAAACG
*
294288 GAAGAAAAAT-GAAAAGAAGAAAACG
1 AAAGAAAAATAGAAAAGAA-AAAACG
*
294313 AAAGAAAGATAGA
1 AAAGAAAAATAGA
294326 GAGAGTGAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 11 0.37
25 17 0.57
26 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.08
Consensus pattern (25 bp):
AAAGAAAAATAGAAAAGAAAAAACG
Found at i:297729 original size:17 final size:17
Alignment explanation
Indices: 297707--297744 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
297697 TTATTGTTAC
297707 TATTTTATTAATACTAT
1 TATTTTATTAATACTAT
* *
297724 TATTTTATTTATATTAT
1 TATTTTATTAATACTAT
297741 TATT
1 TATT
297745 AATAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTATTAATACTAT
Found at i:300741 original size:54 final size:54
Alignment explanation
Indices: 300659--300779 Score: 215
Period size: 54 Copynumber: 2.2 Consensus size: 54
300649 TATGTATTGC
* **
300659 AATTTCCGTATTGGCACTGTATGTGCAACTTAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTGTATGTGCAACCCAAGAAATTCATAATGAGTTTATG
300713 AATTTCCGTATTGACACTGTATGTGCAACCCAAGAAATTCATAATGAGTTTATG
1 AATTTCCGTATTGACACTGTATGTGCAACCCAAGAAATTCATAATGAGTTTATG
300767 AATTTCCGTATTG
1 AATTTCCGTATTG
300780 GCATTTGTCG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.36
Consensus pattern (54 bp):
AATTTCCGTATTGACACTGTATGTGCAACCCAAGAAATTCATAATGAGTTTATG
Found at i:301638 original size:24 final size:24
Alignment explanation
Indices: 301611--301656 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
301601 AATGGAACAT
301611 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
301635 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
301657 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:301894 original size:2 final size:2
Alignment explanation
Indices: 301887--301950 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
301877 CATTAAATAA
301887 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
301929 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
301951 GAACAAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:302120 original size:49 final size:50
Alignment explanation
Indices: 302054--302187 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 50
302044 ATGGCTATTC
* *
302054 TTCCTAAGACACATTAAACAAATATATATGTATATGAAC-AAAGAATCAGT
1 TTCC-AAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
**
302104 TTCCAAGACATGTTAAACAAATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
* *
302154 TTCCAAGACACATTAAATAAATAAATATATATAT
1 TTCCAAGACACATTAAACAAATATATATATATAT
302188 ATACACGTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
49 31 0.41
50 44 0.59
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (50 bp):
TTCCAAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
Found at i:302247 original size:194 final size:187
Alignment explanation
Indices: 301937--302294 Score: 644
Period size: 194 Copynumber: 1.9 Consensus size: 187
301927 ATATATATAT
301937 ATATATATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGT
1 ATATATATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGT
302002 TTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACA
66 TTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACA
302067 TTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAA
131 TTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAA
302124 ATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATATATATATA
1 ATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAAT--A-AAA-ATATATATA
*
302189 TACACGTTTAACAGATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTA
61 T--ACGTTTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTA
302254 AGACACATTAAACAAATATATATGTATATGAACAAAGAATC
124 AGACACATTAAACAAATATATATGTATATGAACAAAGAATC
302295 TAAACAAGCA
Statistics
Matches: 163, Mismatches: 1, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
187 18 0.11
188 29 0.18
190 1 0.01
191 3 0.02
192 10 0.06
194 102 0.63
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (187 bp):
ATATATATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGT
TTAACAAATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACA
TTAAACAAATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTTAAACAA
Found at i:302759 original size:15 final size:15
Alignment explanation
Indices: 302739--302771 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
302729 TAGTGTGACT
302739 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
302754 AAAATAAAATACTTA
1 AAAATAAAATACTTA
302769 AAA
1 AAA
302772 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:304115 original size:3 final size:3
Alignment explanation
Indices: 304100--304141 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
304090 TAAATACACT
* *
304100 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA -AA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
304142 TTTTTTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 30 0.91
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:304453 original size:105 final size:107
Alignment explanation
Indices: 304277--304572 Score: 330
Period size: 105 Copynumber: 2.8 Consensus size: 107
304267 TCGTTAGATT
* * * * *
304277 GAACAAGTTCTTCTCATTATGAAC-TTCTTTTTTCTCGTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTCTCTCTTAT--AGGACGAGTTCTTCTCATTATGAACTC
* * * *
304341 TTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAAA-
64 TTCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAAAG
* *
304385 GAACATGTTTTTCTCATTATGAACTTTCTC-CTT-TAGGACGAGTTCTTCTCATTATGAACTCTT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCTCTTATAGGACGAGTTCTTCTCATTATGAACTCTT
* * ** * *
304448 CTGGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAAG
66 CTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
* * *
304490 GAACAAGTTCTTCTCATTATGAACTTTCTCTTTTATATGATGAGTTCTTCTCATTATGAACTCTT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCTCTTATAGGACGAGTTCTTCTCATTATGAACTCTT
*
304555 CATTGGAAATGTCGATCC
66 C--TGGAAATGTTGATCC
304573 CTCAAGCGAG
Statistics
Matches: 158, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
104 8 0.05
105 78 0.49
106 2 0.01
107 30 0.19
108 24 0.15
109 16 0.10
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (107 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCTCTTATAGGACGAGTTCTTCTCATTATGAACTCTT
CTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
Found at i:304881 original size:225 final size:225
Alignment explanation
Indices: 304490--304929 Score: 654
Period size: 225 Copynumber: 2.0 Consensus size: 225
304480 AATTTGAAAG
*
304490 GAACAAGTTCTTCTCATTATGAACTTTCTCTTTTATATGATGAGTTCTTCTCATTATGAACTCTT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCTTTCATATGATGAGTTCTTCTCATTATGAACTCTT
* * * * * * * *
304555 CATTGGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAG
66 CACTGAAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAA
* *
304620 GTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGA
131 GTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGA
304685 ACTCTCCATTGAAAATGTTGATGCGAATTT
196 ACTCTCCATTGAAAATGTTGATGCGAATTT
*
304715 GAACAAGTTCTTCTCATTATGAAC-TTCTTCTTCCTCGT-TGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGTTCTTCTCATTATGAACTTTC-TCTT--TCATAT-GATGAGTTCTTCTCATTATGAAC
* *
304778 TC-TC-CTGAAAATATCAATCCCTCAAGCGAGGTGTCACTGATTCAAAATGTCATAAATCGAGTG
62 TCTTCACTGAAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTG
* * *
304841 ATAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATT
127 ATAAGTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATT
*
304906 ATGAACTCTCCATTGGAAATGTTG
192 ATGAACTCTCCATTGAAAATGTTG
304930 GTTCACCTCC
Statistics
Matches: 193, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
224 3 0.02
225 160 0.83
226 3 0.02
227 27 0.14
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (225 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCTTTCATATGATGAGTTCTTCTCATTATGAACTCTT
CACTGAAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAA
GTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGA
ACTCTCCATTGAAAATGTTGATGCGAATTT
Found at i:305808 original size:8 final size:8
Alignment explanation
Indices: 305797--305886 Score: 50
Period size: 8 Copynumber: 11.5 Consensus size: 8
305787 CCTTTTTCTC
305797 TTTTCATT
1 TTTTCATT
305805 TTTTCA--
1 TTTTCATT
*
305811 -TTTCTTT
1 TTTTCATT
305818 TTTTCA-T
1 TTTTCATT
305825 TTTTCATTTTT
1 TTTTCA---TT
305836 TTTTCATT
1 TTTTCATT
*
305844 TTTT-TTCT
1 TTTTCAT-T
305852 TTTTCATT
1 TTTTCATT
305860 TTTT-ATCT
1 TTTTCAT-T
305868 TTTT-ATT
1 TTTTCATT
* *
305875 TGTTCCTT
1 TTTTCATT
305883 TTTT
1 TTTT
305887 TCTTCAAGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 22
0.69 0.08 0.24
Matches are distributed among these distances:
5 4 0.06
7 14 0.22
8 38 0.59
9 1 0.02
11 7 0.11
ACGTcount: A:0.09, C:0.12, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:305814 original size:13 final size:13
Alignment explanation
Indices: 305798--305847 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
305788 CTTTTTCTCT
305798 TTTCATTTTTTCA
1 TTTCATTTTTTCA
*
305811 TTTCTTTTTTTCA
1 TTTCATTTTTTCA
305824 TTTTTCATTTTTT--
1 --TTTCATTTTTTCA
305837 TTTCATTTTTT
1 TTTCATTTTTT
305848 TTCTTTTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 11 0.33
13 12 0.36
15 10 0.30
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCATTTTTTCA
Found at i:305820 original size:20 final size:19
Alignment explanation
Indices: 305791--305862 Score: 89
Period size: 16 Copynumber: 3.9 Consensus size: 19
305781 AACCCTCCTT
*
305791 TTTCTCTTTTCATTTTTTCA
1 TTTCTTTTTTCA-TTTTTCA
305811 TTTCTTTTTTTCATTTTTCA
1 TTTC-TTTTTTCATTTTTCA
305831 TTT-TTTTTTCATTTTT--
1 TTTCTTTTTTCATTTTTCA
305847 TTTC-TTTTTCATTTTT
1 TTTCTTTTTTCATTTTT
305863 TATCTTTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
16 15 0.31
18 13 0.27
20 14 0.29
21 7 0.14
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:305829 original size:28 final size:26
Alignment explanation
Indices: 305789--305863 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 26
305779 CAAACCCTCC
305789 TTTTTCTCTTTTCATTTTTTCATTTC-TT
1 TTTTTCT-TTTTCATTTTTT--TTTCATT
305817 TTTTTCATTTTTCATTTTTTTTTCATTT
1 TTTTTC-TTTTTCATTTTTTTTTCA-TT
305845 TTTTTCTTTTTCATTTTTT
1 TTTTTCTTTTTCATTTTTT
305864 ATCTTTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
26 4 0.09
27 13 0.30
28 26 0.59
29 1 0.02
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (26 bp):
TTTTTCTTTTTCATTTTTTTTTCATT
Found at i:305836 original size:16 final size:16
Alignment explanation
Indices: 305797--305888 Score: 70
Period size: 16 Copynumber: 5.9 Consensus size: 16
305787 CCTTTTTCTC
305797 TTTTCA-TTTTTTCA-
1 TTTTCATTTTTTTCAT
305811 -TTTC-TTTTTTTCAT
1 TTTTCATTTTTTTCAT
305825 TTTTCATTTTTTTTTCAT
1 TTTTCA--TTTTTTTCAT
*
305843 TTTT-TTTCTTTTTCAT
1 TTTTCATT-TTTTTCAT
* *
305859 TTTTTATCTTTTT-AT
1 TTTTCATTTTTTTCAT
*
305874 TTGTTCCTTTTTTTC
1 TT-TTCATTTTTTTC
305889 TTCAAGCATA
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
13 12 0.19
15 10 0.16
16 25 0.40
17 1 0.02
18 14 0.23
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTCATTTTTTTCAT
Found at i:305838 original size:11 final size:11
Alignment explanation
Indices: 305803--305849 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
305793 TCTCTTTTCA
305803 TTTTTTCATTT
1 TTTTTTCATTT
* *
305814 CTTTTT--TTC
1 TTTTTTCATTT
*
305823 ATTTTTCATTT
1 TTTTTTCATTT
305834 TTTTTTCATTT
1 TTTTTTCATTT
305845 TTTTT
1 TTTTT
305850 CTTTTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
9 7 0.24
11 22 0.76
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:305870 original size:22 final size:22
Alignment explanation
Indices: 305789--305890 Score: 64
Period size: 22 Copynumber: 4.5 Consensus size: 22
305779 CAAACCCTCC
* * *
305789 TTTTTCTCTTTTCATTTTTTCA
1 TTTTTTTCTTTTTATTTGTTCA
* *
305811 TTTCTTT-TTTTCATTT-TTCA
1 TTTTTTTCTTTTTATTTGTTCA
* *
305831 TTTTTTTTTCATTTTTTTTCTTTTTCA
1 --TTTTTTTC--TTTTTAT-TTGTTCA
*
305858 TTTTTTATCTTTTTATTTGTTCC
1 TTTTTT-TCTTTTTATTTGTTCA
305881 TTTTTTTCTT
1 TTTTTTTCTT
305891 CAAGCATAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
20 4 0.06
21 9 0.14
22 15 0.23
23 11 0.17
24 6 0.09
25 11 0.17
26 4 0.06
27 4 0.06
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (22 bp):
TTTTTTTCTTTTTATTTGTTCA
Found at i:317638 original size:24 final size:24
Alignment explanation
Indices: 317611--317656 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
317601 AATGGAACAT
317611 TATACTTATTAAATAAATGATAAC
1 TATACTTATTAAATAAATGATAAC
317635 TATACTTATTAAATAAATGATA
1 TATACTTATTAAATAAATGATA
317657 TAAAGAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (24 bp):
TATACTTATTAAATAAATGATAAC
Found at i:317766 original size:2 final size:2
Alignment explanation
Indices: 317759--317792 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
317749 ATAATTTAAA
317759 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
317793 CCAGCTAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:317965 original size:55 final size:54
Alignment explanation
Indices: 317855--317973 Score: 213
Period size: 53 Copynumber: 2.2 Consensus size: 54
317845 TGTTAAACAA
317855 ATATATATATATATATGAACAAAAAAAATCAGTTTCCAAGACACATTAAATAAAT
1 ATATATATATATATATGAAC-AAAAAAATCAGTTTCCAAGACACATTAAATAAAT
*
317910 ATATATATATATATATGAAC-AAAAAATCAGTTTCCAAGACACATTAAATAAAA
1 ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAT
317963 ATATATATATA
1 ATATATATATA
317974 CGTTTAACAA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
53 43 0.68
55 20 0.32
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.30
Consensus pattern (54 bp):
ATATATATATATATATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAAT
Found at i:318095 original size:49 final size:50
Alignment explanation
Indices: 318029--318162 Score: 198
Period size: 50 Copynumber: 2.7 Consensus size: 50
318019 ATGGCTATTC
* *
318029 TTCCTAAGACACATTAAACAAATATATATGTATATGAAC-AAAGAATCAGT
1 TTCC-AAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
**
318079 TTCCAAGACATGTTAAACAAATATATATATATATGAACAAAAAAATCAGT
1 TTCCAAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
* *
318129 TTCCAAGACACATTAAATAAATAAATATATATAT
1 TTCCAAGACACATTAAACAAATATATATATATAT
318163 ATACACGTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
49 31 0.41
50 44 0.59
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.29
Consensus pattern (50 bp):
TTCCAAGACACATTAAACAAATATATATATATATGAACAAAAAAATCAGT
Found at i:318265 original size:194 final size:191
Alignment explanation
Indices: 317789--318269 Score: 720
Period size: 194 Copynumber: 2.5 Consensus size: 191
317779 ATATATATAT
* * * **
317789 ATATCCAGCTAAGCTATACGTTAAACAAATAAA-ATATGCCTATTCTTCCTAAGACATGTTAAAC
1 ATATCCAACTAAGCTATATGTTAAACAAATAAATA-ATGGCTATTCTTCCTAAGACACATTAAAC
* *
317853 AAATATATATATATATATGAACAAAAAAAATCAGTTTCCAAGACACATTAAATAAATATATATAT
65 -AA-ATATATATGTATATGAAC--AAAGAATCAGTTTCCAAGACACATTAAATAAATATATATAT
317918 ATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACA
126 ATATATATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACA
317983 A
191 A
317984 ATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAAACA
1 ATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAAACA
** *
318049 AATATATATGTATATGAACAAAGAATCAGTTTCCAAGACATGTT-AA-ACA-A-ATATATATATA
66 AATATATATGTATATGAACAAAGAATCAGTTTCCAAGACACATTAAATAAATATATATATATATA
318110 TATGAACAAAAAAATCAGTTTCCAAGACACATTAAATAAATAAATATATATATATACACGTTTAA
131 TATGAAC-AAAAAATCAGTTTCCAAGACACATTAAAT--A-AAA-ATATATATAT--ACGTTTAA
*
318175 CAG
189 CAA
318178 ATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAAACA
1 ATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAAACA
318243 AATATATATGTATATGAACAAAGAATC
66 AATATATATGTATATGAACAAAGAATC
318270 TAAACAAGCA
Statistics
Matches: 267, Mismatches: 11, Indels: 17
0.91 0.04 0.06
Matches are distributed among these distances:
187 18 0.07
188 30 0.11
189 2 0.01
190 3 0.01
191 25 0.09
192 10 0.04
193 17 0.06
194 104 0.39
195 57 0.21
196 1 0.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (191 bp):
ATATCCAACTAAGCTATATGTTAAACAAATAAATAATGGCTATTCTTCCTAAGACACATTAAACA
AATATATATGTATATGAACAAAGAATCAGTTTCCAAGACACATTAAATAAATATATATATATATA
TATGAACAAAAAATCAGTTTCCAAGACACATTAAATAAAAATATATATATACGTTTAACAA
Found at i:318737 original size:15 final size:15
Alignment explanation
Indices: 318717--318749 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
318707 TAGTGTGACT
318717 AAAATATAAATA-TTA
1 AAAATA-AAATACTTA
318732 AAAATAAAATACTTA
1 AAAATAAAATACTTA
318747 AAA
1 AAA
318750 CAAAATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAAATACTTA
Found at i:320095 original size:3 final size:3
Alignment explanation
Indices: 320080--320122 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
320070 TAAATACACT
* *
320080 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
320123 TTTTTTAACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 34 0.97
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:320258 original size:54 final size:54
Alignment explanation
Indices: 320175--320374 Score: 283
Period size: 54 Copynumber: 3.7 Consensus size: 54
320165 CAGCATTGTA
320175 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
1 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
* * * *
320229 TGTGCAACCTAAGAAATTCATTATAAGTTTATGAATTTTCGTATTGGCACTGTG
1 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
* **
320283 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTAAG
1 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
** * * *
320337 TGTGCAAACCCACGTAATTCATAATGAGTTTGTGAATT
1 TGTGC-AACTTAAGAAATTCATAATGAGTTTATGAATT
320375 ATTGTATTGA
Statistics
Matches: 129, Mismatches: 16, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 102 0.79
55 27 0.21
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (54 bp):
TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
Found at i:320374 original size:55 final size:54
Alignment explanation
Indices: 320175--320398 Score: 270
Period size: 54 Copynumber: 4.1 Consensus size: 54
320165 CAGCATTGTA
* * *
320175 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTG
1 TGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATG
* * * * *
320229 TGTGCAACCTAAGAAATTCATTATAAGTTTATGAATTTTCGTATTGGCACTGTG
1 TGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATG
* *
320283 TGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTAAG
1 TGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATG
* * * * * *
320337 TGTGCAAACCCACGTAATTCATAATGAGTTTGTGAATTAT-TGTATTGACACTACG
1 TGTGC-AACCTAAGAAATTCATAATGAGTTTATGAATT-TCCGTATTGACACTATG
*
320392 AGTGCAA
1 TGTGCAA
320399 ACCATAGAAT
Statistics
Matches: 149, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
54 104 0.70
55 44 0.30
56 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (54 bp):
TGTGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGACACTATG
Found at i:320523 original size:24 final size:25
Alignment explanation
Indices: 320494--320543 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
320484 TATGCCTCAC
320494 TAAGTGATTACTTAACGT-TGTTAA
1 TAAGTGATTACTTAACGTGTGTTAA
320518 TAAGTGATTACTTAACGTGTGTTAA
1 TAAGTGATTACTTAACGTGTGTTAA
320543 T
1 T
320544 TTCACGCGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (25 bp):
TAAGTGATTACTTAACGTGTGTTAA
Found at i:324601 original size:40 final size:40
Alignment explanation
Indices: 324546--324627 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 40
324536 TGCAGGTTTA
324546 TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
324586 TAATACACTT-CGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACA-TTACGGTGTATATGGTGGGCACGACCTTATGTG
324626 TA
1 TA
324628 GCACTACGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACATTACGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:325080 original size:11 final size:11
Alignment explanation
Indices: 325064--325089 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
325054 AATTAGTGGC
325064 ATGTAATTATT
1 ATGTAATTATT
325075 ATGTAATTATT
1 ATGTAATTATT
325086 ATGT
1 ATGT
325090 TTTATTTGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (11 bp):
ATGTAATTATT
Found at i:328014 original size:18 final size:18
Alignment explanation
Indices: 327987--328040 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
327977 ATTTTCCAAA
327987 AATTGGTATCTTTTTAAC
1 AATTGGTATCTTTTTAAC
*
328005 AATTGATATCATTTTGTTAAC
1 AATTGGTATC--TTT-TTAAC
*
328026 AATTGGTATATTTTT
1 AATTGGTATCTTTTT
328041 CATTAAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 11 0.37
19 3 0.10
20 3 0.10
21 13 0.43
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (18 bp):
AATTGGTATCTTTTTAAC
Found at i:328040 original size:21 final size:21
Alignment explanation
Indices: 328000--328039 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
327990 TGGTATCTTT
328000 TTAACAATTGATATCATTTTG
1 TTAACAATTGATATCATTTTG
*
328021 TTAACAATTGGTAT-ATTTT
1 TTAACAATTGATATCATTTT
328040 TCATTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (21 bp):
TTAACAATTGATATCATTTTG
Found at i:330395 original size:35 final size:35
Alignment explanation
Indices: 330351--330479 Score: 109
Period size: 35 Copynumber: 3.5 Consensus size: 35
330341 ATGGAAAGAA
*
330351 GCATTGCACTTTCGATTCAAGTAGAACGAAAGGAG
1 GCATAGCACTTTCGATTCAAGTAGAACGAAAGGAG
*
330386 GCATAGCACTTT-GATTCTCCTCTAAAGTAGAACGGAAA-GAA
1 GCATAGCACTTTCGA---T--TC--AAGTAGAAC-GAAAGGAG
* * *
330427 GCATAGTACTTTCGATTCAAGTTGAACAAAAGGAG
1 GCATAGCACTTTCGATTCAAGTAGAACGAAAGGAG
* *
330462 GCATAGTACTTTTGATTC
1 GCATAGCACTTTCGATTC
330480 TTGTTGACAT
Statistics
Matches: 77, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
34 5 0.06
35 38 0.49
37 3 0.04
39 3 0.04
41 22 0.29
42 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (35 bp):
GCATAGCACTTTCGATTCAAGTAGAACGAAAGGAG
Found at i:330473 original size:76 final size:76
Alignment explanation
Indices: 330196--330480 Score: 367
Period size: 76 Copynumber: 3.7 Consensus size: 76
330186 ATAACAAAAG
* * * * *
330196 GAAGCATCGCACTTGCGATTCAAGTTGAACGAAA-GAGGCATAGCACTTTCGATTCTCGTATAAA
1 GAAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGGCATAGCACTTT-GATTCTCCTCTAAA
*
330260 GTAGGACGG-AA
65 GTAGAACGGAAA
* * * *
330271 GAAAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGACACAACACTTCGATTCTCCTCTAAA
1 G-AAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGGCATAGCACTTTGATTCTCCTCTAAA
* *
330336 GTATAATGGAAA
65 GTAGAACGGAAA
* *
330348 GAAGCATTGCACTTTCGATTCAAGTAGAACGAAAGGAGGCATAGCACTTTGATTCTCCTCTAAAG
1 GAAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGGCATAGCACTTTGATTCTCCTCTAAAG
330413 TAGAACGGAAA
66 TAGAACGGAAA
* * * *
330424 GAAGCATAGTACTTTCGATTCAAGTTGAACAAAAGGAGGCATAGTACTTTTGATTCT
1 GAAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGGCATAGCAC-TTTGATTCT
330481 TGTTGACATA
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
75 1 0.01
76 157 0.87
77 23 0.13
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (76 bp):
GAAGCATCGCACTTTCGATTCAAGTAGAACAAAAGGAGGCATAGCACTTTGATTCTCCTCTAAAG
TAGAACGGAAA
Found at i:334108 original size:18 final size:18
Alignment explanation
Indices: 334077--334111 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
334067 GTTAAACCCG
*
334077 ATAATAATAGATAATAAA
1 ATAATAATAAATAATAAA
*
334095 ATAATGATAAATAATAA
1 ATAATAATAAATAATAA
334112 TCATATATCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
ATAATAATAAATAATAAA
Found at i:334336 original size:34 final size:34
Alignment explanation
Indices: 334252--334337 Score: 113
Period size: 34 Copynumber: 2.5 Consensus size: 34
334242 ATAAAATAAA
*
334252 TAAATATTCAAAAGATAATAATATCTTTTAATAT
1 TAAATATTCAAAATATAATAATATCTTTTAATAT
* *
334286 T-CATATTTAAACATATAATAATATCTTTTAAT-T
1 TAAATATTCAAA-ATATAATAATATCTTTTAATAT
334319 TAAAATATTCAAAATATAA
1 T-AAATATTCAAAATATAA
334338 AGTAACCTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 10 0.23
34 26 0.59
35 8 0.18
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (34 bp):
TAAATATTCAAAATATAATAATATCTTTTAATAT
Found at i:337019 original size:22 final size:22
Alignment explanation
Indices: 336965--337016 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
336955 TAATGTTTTA
* *
336965 TAAATATTGTATTTTAATTAAAT
1 TAAAT-TTATATTTTAACTAAAT
*
336988 TAAATTTATATTTTAACTAATT
1 TAAATTTATATTTTAACTAAAT
337010 TATAATT
1 TA-AATT
337017 ATACGTTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TAAATTTATATTTTAACTAAAT
Found at i:337227 original size:22 final size:23
Alignment explanation
Indices: 337202--337245 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
337192 AATTAAGTTT
337202 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTACAAAGT-ATTTCAAAA
*
337224 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAAGTATTTCAAA
337246 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATCTTACAAAGTATTTCAAAA
Found at i:339271 original size:21 final size:21
Alignment explanation
Indices: 339246--339285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
339236 AAGACTCTAT
339246 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
339267 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
339286 AAATAGTCTT
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:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:343140 original size:23 final size:22
Alignment explanation
Indices: 343098--343158 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
343088 TTAGTGCAGA
* *
343098 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
343120 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
343143 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
343159 CCACAGGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:343166 original size:22 final size:22
Alignment explanation
Indices: 343098--343168 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 22
343088 TTAGTGCAGA
* * **
343098 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTCCAAG
**
343120 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TCCAAG
343143 GGGAACCGATTCCCCC-CCACAG
1 GGGAACCGATTCCCCCTCCA-AG
343165 GGGA
1 GGGA
343169 GTCGATACCC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 20 0.47
23 22 0.51
ACGTcount: A:0.24, C:0.32, G:0.28, T:0.15
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTCCAAG
Found at i:350593 original size:21 final size:21
Alignment explanation
Indices: 350567--350606 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
350557 TCCTATAAAG
350567 GCAACTGCTTTAACACGGGAC
1 GCAACTGCTTTAACACGGGAC
*
350588 GCAACTGCTTTAACCCGGG
1 GCAACTGCTTTAACACGGG
350607 TTCTCTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.30, G:0.25, T:0.20
Consensus pattern (21 bp):
GCAACTGCTTTAACACGGGAC
Found at i:351057 original size:268 final size:263
Alignment explanation
Indices: 350588--351555 Score: 1433
Period size: 267 Copynumber: 3.7 Consensus size: 263
350578 AACACGGGAC
* * * *
350588 GCAACTGCTTTAACCCGGGTTCTCTAGACATAATAACATTTTATTTTACTACTAAATTCGGATTC
1 GCAACTGCTTTAACCCAGGTTCTGTAGAGATAATAACATTTCATTTTACTACTAAATTCGGATTC
*
350653 AC-AAATGAATATGCTTAAATTTACCCCACATGATAGAAGAC--AGCTCCCACAATAGCCCTTAG
66 ACAAAATGAATATGCTTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCCCTTAG
*
350715 CTGCAGAACTATTACACTAGAGCCTCCCAAATAGGATCAAAAAGATTATGTTTTTTAAATAATCT
131 CTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAAAGATTATGTTTTTTAAATAATCT
* * *
350780 AAAGGGATTACAAATAGTATTTATTCATAACTTTTCTTAACAATTGAAAACACACACTTCTTATG
196 AACGGGATTACAAATAGTATTTGTTCATAACTTTTCTTAACAATTGAAAACGCACACTTCTTATG
350845 AAG
261 AAG
* *
350848 GCAACTGCTTTAACCCAAGTTCTGTATAGATAATAACATTTTCATTTTACTACTAAATAAATCCG
1 GCAACTGCTTTAACCCAGGTTCTGTAGAGATAATAACA-TTTCATTTTACTACTAAAT---T-CG
350913 GATTCACAAAATGAATATGCTTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCC
61 GATTCACAAAATGAATATGCTTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCC
* *
350978 CTTAGCTGCAGAACTATTACACCAGAGCATCCCAAATAGGATCAAAATGATTATGTTTTTTAAAT
126 CTTAGCTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAAAGATTATGTTTTTTAAAT
* * * *
351043 AATTTAACGGGATTAAAAATA-TAATTCGTTCATAACTTTTCTTAACAATCGAAAACGCACACTT
191 AATCTAACGGGATTACAAATAGT-ATTTGTTCATAACTTTTCTTAACAATTGAAAACGCACACTT
*
351107 CCTATGAAG
255 CTTATGAAG
* *
351116 GCAACTGCTTTAACCCAGGTTCTGTATAGATAATAACATTTCATTTAACTACTAAATAAATTCGG
1 GCAACTGCTTTAACCCAGGTTCTGTAGAGATAATAACATTTCATTT---TACT-ACTAAATTCGG
* * *
351181 ACTCAAAAAATGAATATGCTTAAATTTACCCTACATGATAGAATACAAAGCTCCCACAATAGCCC
62 ATTCACAAAATGAATATGCTTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCCC
* * *
351246 TTAGCTGCAGAACTATTACACTAGTGCATCCCAAATAGGATCAAAACGATTAAGTTTTTTAAATA
127 TTAGCTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAAAGATTATGTTTTTTAAATA
* *
351311 ATCTAACGGGAATACAAATAGTATTTGTTCATAACTTTTCTTAACAA-TCAAATACGCACACTTC
192 ATCTAACGGGATTACAAATAGTATTTGTTCATAACTTTTCTTAACAATTGAAA-ACGCACACTTC
*
351375 TTATAAAG
256 TTATGAAG
* * ** * *
351383 GCAGCTGCTTTAACCCGGGTTCAATAGAGATAATAACATTCCATTTTACTACTAAATTCAGATTC
1 GCAACTGCTTTAACCCAGGTTCTGTAGAGATAATAACATTTCATTTTACTACTAAATTCGGATTC
* * * * *
351448 ACCAAATGAATATGCTTTAAGTTTACCCTACATGCTAGAAGACAAAGCTCCCACAATAGTCCTTC
66 ACAAAATGAATATGC-TTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCCCTTA
351513 GCTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAA
130 GCTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAA
351556 GTTAAGAAAC
Statistics
Matches: 640, Mismatches: 52, Indels: 28
0.89 0.07 0.04
Matches are distributed among these distances:
260 33 0.05
261 18 0.03
263 25 0.04
264 91 0.14
265 9 0.01
266 41 0.06
267 233 0.36
268 180 0.28
270 4 0.01
271 6 0.01
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (263 bp):
GCAACTGCTTTAACCCAGGTTCTGTAGAGATAATAACATTTCATTTTACTACTAAATTCGGATTC
ACAAAATGAATATGCTTAAATTTACCCTACATGATAGAAGACAAAGCTCCCACAATAGCCCTTAG
CTGCAGAACTATTACACTAGAGCATCCCAAATAGGATCAAAAAGATTATGTTTTTTAAATAATCT
AACGGGATTACAAATAGTATTTGTTCATAACTTTTCTTAACAATTGAAAACGCACACTTCTTATG
AAG
Found at i:354532 original size:19 final size:19
Alignment explanation
Indices: 354505--354554 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
354495 ATGTAATTTG
*
354505 TGTACCGATGCATGGATAA
1 TGTATCGATGCATGGATAA
*
354524 TGTATCGATGCATGGATAG
1 TGTATCGATGCATGGATAA
*
354543 TGTATTGATGCA
1 TGTATCGATGCA
354555 CATGTTAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.32
Consensus pattern (19 bp):
TGTATCGATGCATGGATAA
Found at i:354593 original size:20 final size:20
Alignment explanation
Indices: 354522--354600 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
354512 ATGCATGGAT
* *
354522 AATGTATCGATGCA-TGGAT
1 AATGTATCGATGCACTGTAG
* *
354541 AGTGTATTGATGCACATGTTAAGG
1 AATGTATCGATGCAC-TG-T-A-G
*
354565 AATGCATCGATGCACTGTAG
1 AATGTATCGATGCACTGTAG
354585 AATGTATCGATGCACT
1 AATGTATCGATGCACT
354601 TCAATGGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
19 12 0.26
20 16 0.34
21 3 0.06
22 1 0.02
23 3 0.06
24 12 0.26
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (20 bp):
AATGTATCGATGCACTGTAG
Found at i:357751 original size:2 final size:2
Alignment explanation
Indices: 357744--357779 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
357734 AGTAAGAAAG
357744 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
357780 TGAGTATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:358837 original size:20 final size:23
Alignment explanation
Indices: 358784--358841 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 23
358774 GCATGGATAG
358784 TGTATCGATGCACATGTTAAGGAA
1 TGTATCGATGCAC-TGTTAAGGAA
* *
358808 TGCATTGATGCACTG-T-A-GAA
1 TGTATCGATGCACTGTTAAGGAA
358828 TGTATCGATGCACT
1 TGTATCGATGCACT
358842 TCAATAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 1 0.03
23 2 0.07
24 11 0.37
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (23 bp):
TGTATCGATGCACTGTTAAGGAA
Found at i:359617 original size:18 final size:18
Alignment explanation
Indices: 359594--359628 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
359584 AGGGATTATC
*
359594 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGGGACAT
359612 AGTGGTCCTACGGGACA
1 AGTGGTCCTACGGGACA
359629 AATTCTACGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:360901 original size:41 final size:42
Alignment explanation
Indices: 360846--360926 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 42
360836 TAATGAGTAC
360846 GTAATTTTTTTAACACATTCAATTAAATTTAATTATTTTTAT
1 GTAATTTTTTTAACACATTCAATTAAATTTAATTATTTTTAT
360888 GTAA-TTTTTTAACACATTCAATTAAATTTAATTATTTTT
1 GTAATTTTTTTAACACATTCAATTAAATTTAATTATTTTT
360927 TCAAAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (42 bp):
GTAATTTTTTTAACACATTCAATTAAATTTAATTATTTTTAT
Found at i:364393 original size:22 final size:21
Alignment explanation
Indices: 364346--364396 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
364336 CAATGAATGT
*
364346 AATTTTAAAATAATAAAATTA
1 AATTTTAAAATAATAAAATCA
* * *
364367 TATTTTTAAATATTAAAAATCA
1 AATTTTAAAATAAT-AAAATCA
364389 AATTTTAA
1 AATTTTAA
364397 TATTTAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTAAAATAATAAAATCA
Found at i:365042 original size:98 final size:97
Alignment explanation
Indices: 364854--365046 Score: 305
Period size: 98 Copynumber: 2.0 Consensus size: 97
364844 CCGAATTCAG
*
364854 GGTCCGTTTGGAATACATATGGAAATGCTTTTATCCCAAAATTTCATTTTAAACGTAAAATTATT
1 GGTCCGTTTGGAATACATATGGAAATGCTTTTATCCCAAAATTTCATTTTAAACGCAAAATTATT
* *
364919 CCCAAACAATTTATTTTCAGTAAAAGTTCATA
66 CCCAAACAACTTATTTTCAGCAAAAGTTCATA
* * * * *
364951 GGTCCGTTTGAGAATGCTTATGGAAATGTTTTTATCTCAAAATTTCATTTTAAACGCAAAGTTAT
1 GGTCCGTTTG-GAATACATATGGAAATGCTTTTATCCCAAAATTTCATTTTAAACGCAAAATTAT
365016 TCCCAAACAACTTATTTTCAGCAAAAGTTCA
65 TCCCAAACAACTTATTTTCAGCAAAAGTTCA
365047 CATTTGAGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
97 10 0.11
98 77 0.89
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (97 bp):
GGTCCGTTTGGAATACATATGGAAATGCTTTTATCCCAAAATTTCATTTTAAACGCAAAATTATT
CCCAAACAACTTATTTTCAGCAAAAGTTCATA
Found at i:372428 original size:35 final size:34
Alignment explanation
Indices: 372343--372429 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
372333 AATATAATTT
*
372343 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
372377 TAAATGATAA-ACAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA--G-TATTAAATGG
372415 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
372430 ACCAAAATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 4 0.09
38 11 0.24
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:372495 original size:34 final size:35
Alignment explanation
Indices: 372422--372496 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
372412 TGGTAATAAA
* * *
372422 CAAAATTAACCAAAATACATTAACAAAAAGTCCAG
1 CAAATTTAACCAAAATAAATTAACAAAAAGTCCAC
372457 CAAATTTAA-CAAAATAAATTAA-AATAAA-TCCAAC
1 CAAATTTAACCAAAATAAATTAACAA-AAAGTCC-AC
372491 CAAATT
1 CAAATT
372497 AATGAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
33 5 0.14
34 22 0.63
35 8 0.23
ACGTcount: A:0.59, C:0.17, G:0.03, T:0.21
Consensus pattern (35 bp):
CAAATTTAACCAAAATAAATTAACAAAAAGTCCAC
Found at i:373690 original size:24 final size:24
Alignment explanation
Indices: 373663--373708 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
373653 ATATAAGTTT
373663 TATCAAAATAATAATCTAATTACA
1 TATCAAAATAATAATCTAATTACA
373687 TATCAAAATAATAATCTAATTA
1 TATCAAAATAATAATCTAATTA
373709 TATAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (24 bp):
TATCAAAATAATAATCTAATTACA
Found at i:374836 original size:17 final size:17
Alignment explanation
Indices: 374801--374854 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
374791 TATATTTGCA
* *
374801 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
374817 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
*
374834 -AAATACTTAAGTAAATT
1 AAAATA-TTAAATAAATT
374851 AAAA
1 AAAA
374855 ACAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 18 0.56
17 11 0.34
18 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:379405 original size:35 final size:34
Alignment explanation
Indices: 379320--379406 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
379310 AAAATAATTT
*
379320 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
379354 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
379392 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
379407 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:379645 original size:15 final size:15
Alignment explanation
Indices: 379625--379654 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
379615 GACTCCTCGC
379625 TGTCATCATCGTCGT
1 TGTCATCATCGTCGT
*
379640 TGTCATCGTCGTCGT
1 TGTCATCATCGTCGT
379655 CCTGAGTAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.27, G:0.23, T:0.40
Consensus pattern (15 bp):
TGTCATCATCGTCGT
Found at i:394228 original size:20 final size:18
Alignment explanation
Indices: 394183--394237 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
394173 GCACTGAATA
394183 TTTGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
*
394201 TATGTCCCGAAGGACCAC
1 TTTGTCCCGAAGGACCAC
394219 TGTTTGTCCCGAAGGACCA
1 --TTTGTCCCGAAGGACCA
394238 TTGATAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 17 0.52
20 16 0.48
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (18 bp):
TTTGTCCCGAAGGACCAC
Found at i:397085 original size:12 final size:12
Alignment explanation
Indices: 397062--397096 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
397052 CATGTAACAA
397062 ATACACTACATAT
1 ATACA-TACATAT
397075 ATACATACATAT
1 ATACATACATAT
397087 ATACATACAT
1 ATACATACAT
397097 GTCATTATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (12 bp):
ATACATACATAT
Found at i:397498 original size:18 final size:18
Alignment explanation
Indices: 397475--397509 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
397465 CCCGAAAGAC
397475 CACTATGTTCTGAAGGAA
1 CACTATGTTCTGAAGGAA
397493 CACTATGTTCTGAAGGA
1 CACTATGTTCTGAAGGA
397510 CCATTGGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (18 bp):
CACTATGTTCTGAAGGAA
Found at i:397581 original size:20 final size:20
Alignment explanation
Indices: 397539--397581 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
397529 ACCCCTATGC
* **
397539 CCCGAAGGACCACTGTTTGT
1 CCCGAAGGACCACTGATAAT
397559 CCCGAAGGACCACTGATAAT
1 CCCGAAGGACCACTGATAAT
397579 CCC
1 CCC
397582 TCGACTCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.19
Consensus pattern (20 bp):
CCCGAAGGACCACTGATAAT
Found at i:400254 original size:2 final size:2
Alignment explanation
Indices: 400247--400276 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
400237 CATGAATTAG
400247 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
400277 TCATATGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401809 original size:14 final size:14
Alignment explanation
Indices: 401790--401822 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
401780 GCATAAGGAT
401790 AGCTGGCACTGGAC
1 AGCTGGCACTGGAC
401804 AGCTGGCACTGGAC
1 AGCTGGCACTGGAC
401818 AGCTG
1 AGCTG
401823 TCCCTGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.15
Consensus pattern (14 bp):
AGCTGGCACTGGAC
Found at i:404685 original size:21 final size:21
Alignment explanation
Indices: 404659--404718 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
404649 CAATTAAGAA
* *
404659 TCAAGGAGCTTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
404680 TCAAGGCGCCTTACTTCATAG
1 TCAAGGCGCCTTACTTCATAG
404701 TCAAGGCGCCTTACTTCA
1 TCAAGGCGCCTTACTTCA
404719 AAGCCATAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (21 bp):
TCAAGGCGCCTTACTTCATAG
Found at i:409140 original size:19 final size:21
Alignment explanation
Indices: 409103--409145 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
409093 TAACTTTTTC
409103 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
409123 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
409143 TTT
1 TTT
409146 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:409151 original size:19 final size:20
Alignment explanation
Indices: 409102--409151 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
409092 TTAACTTTTT
*
409102 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
409122 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
409141 CTTTTACCTTT
1 CTTTTACCTTT
409152 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:416317 original size:19 final size:21
Alignment explanation
Indices: 416280--416322 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
416270 TAACTTTTTC
416280 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
416300 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
416320 TTT
1 TTT
416323 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:416328 original size:19 final size:20
Alignment explanation
Indices: 416279--416328 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
416269 TTAACTTTTT
*
416279 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
416299 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
416318 CTTTTACCTTT
1 CTTTTACCTTT
416329 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:421349 original size:2 final size:2
Alignment explanation
Indices: 421342--421379 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
421332 CATGAATTAG
421342 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
421380 TCATATGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424523 original size:2 final size:2
Alignment explanation
Indices: 424516--424545 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
424506 AAATGCATGG
424516 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
424546 GATTGGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:426034 original size:21 final size:18
Alignment explanation
Indices: 425992--426065 Score: 112
Period size: 18 Copynumber: 3.9 Consensus size: 18
425982 ACTAAATATT
425992 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
426010 TGTCTCGAAGGACCACTGATA
1 TGTCCCGAAGGACCAC---TA
426031 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
426049 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
426066 GATAATCCCT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 34 0.67
21 17 0.33
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:426046 original size:39 final size:39
Alignment explanation
Indices: 425992--426069 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
425982 ACTAAATATT
*
425992 TGTCCCGAAGGACCACTATGTCTCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
426031 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
1 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
426070 ATCCCTCGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.19
Consensus pattern (39 bp):
TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGATA
Found at i:429332 original size:2 final size:2
Alignment explanation
Indices: 429327--429380 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
429317 TGTGTGTGTG
429327 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
429369 TA TA TA TCA TA T
1 TA TA TA T-A TA T
429381 GATTTGGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:429795 original size:23 final size:23
Alignment explanation
Indices: 429731--429795 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
429721 ATTATATTGT
429731 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * *
429754 ACTACGGTGCAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
*
429777 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTCTACG
429796 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:434365 original size:6 final size:6
Alignment explanation
Indices: 434351--434396 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
434341 AGGATAATGA
*
434351 AGTGGT AGTGAT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTG
1 AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTGGT AGTG
434397 CAGCATGTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.33
Consensus pattern (6 bp):
AGTGGT
Done.