Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008550.1 Hibiscus syriacus cultivar Beakdansim tig00111445_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: 1154708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 3 of 6
Found at i:375177 original size:27 final size:27
Alignment explanation
Indices: 375139--375192 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
375129 CAAACTCGAT
375139 GATGATATGCATTTGTTTCTTGATCGG
1 GATGATATGCATTTGTTTCTTGATCGG
375166 GATGATATGCATTTGTTTCTTGATCGG
1 GATGATATGCATTTGTTTCTTGATCGG
375193 TCTTGGTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.26, T:0.44
Consensus pattern (27 bp):
GATGATATGCATTTGTTTCTTGATCGG
Found at i:376131 original size:19 final size:19
Alignment explanation
Indices: 376107--376162 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
376097 TATACTTTCA
376107 CAACGCGAAAATCAAATCG
1 CAACGCGAAAATCAAATCG
*
376126 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAATCAAA-TCG
*
376146 CAAAGC-AAAAGTCAAAT
1 CAACGCGAAAA-TCAAAT
376163 GCGCGTTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (19 bp):
CAACGCGAAAATCAAATCG
Found at i:376148 original size:20 final size:20
Alignment explanation
Indices: 376107--376162 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
376097 TATACTTTCA
*
376107 CAACGCGAAAATCAAA-TCG
1 CAACGCGAAAGTCAAATTCG
376126 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
* *
376146 CAAAGCAAAAGTCAAAT
1 CAACGCGAAAGTCAAAT
376163 GCGCGTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:376183 original size:14 final size:15
Alignment explanation
Indices: 376164--376192 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
376154 AAGTCAAATG
376164 CGCGTTGC-AATTTT
1 CGCGTTGCGAATTTT
376178 CGCGTTGCGAATTTT
1 CGCGTTGCGAATTTT
376193 ACTTTCGCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.41
Consensus pattern (15 bp):
CGCGTTGCGAATTTT
Found at i:376218 original size:20 final size:20
Alignment explanation
Indices: 376173--376220 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
376163 GCGCGTTGCA
*
376173 ATTTTCGCGTTGCGAATTTT
1 ATTTTCGCGTTGCGAATTTG
* *
376193 ACTTTCGCGTTTCGAATTTG
1 ATTTTCGCGTTGCGAATTTG
376213 ATTTTCGC
1 ATTTTCGC
376221 AATAATCGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.48
Consensus pattern (20 bp):
ATTTTCGCGTTGCGAATTTG
Found at i:376239 original size:29 final size:29
Alignment explanation
Indices: 376205--376290 Score: 145
Period size: 29 Copynumber: 3.0 Consensus size: 29
376195 TTTCGCGTTT
* *
376205 CGAATTTGATTTTCGCAATAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
376234 CGAATTTGACTTTCGCAACAATCGCAACG
1 CGAATTTGACTTTCGCAACAATCGCAACG
*
376263 CGAATTTGACTTTCGCAACAATTGCAAC
1 CGAATTTGACTTTCGCAACAATCGCAAC
376291 AAAATATCGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 54 1.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.28
Consensus pattern (29 bp):
CGAATTTGACTTTCGCAACAATCGCAACG
Found at i:376553 original size:18 final size:18
Alignment explanation
Indices: 376532--376567 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
376522 AGGCCGGTTG
376532 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
*
376550 TGATTGTGATTTTGATTT
1 TGATTGGGATTTTGATTT
376568 CCTTTTGCTT
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:0.17, C:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:378800 original size:24 final size:24
Alignment explanation
Indices: 378773--378819 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
378763 CAAAATCCGA
378773 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
378797 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
378820 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:378828 original size:24 final size:24
Alignment explanation
Indices: 378777--378828 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
378767 ATCCGAGTAT
** *
378777 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
378801 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
378825 TGAC
1 TGAC
378829 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:379777 original size:20 final size:19
Alignment explanation
Indices: 379733--379823 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
379723 CAAAACATTT
*
379733 GTGTTGCGAAAATAAAA-C
1 GTGTTGCGAAATTAAAATC
*
379751 CTGTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
379771 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* * *
379791 GAGTTGCGAATTTGAAATTC
1 GTGTTGCGAAATT-AAAATC
379811 AGTGTTGC-AAATT
1 -GTGTTGCGAAATT
379824 TGACTTATGT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
18 15 0.25
19 4 0.07
20 27 0.46
21 13 0.22
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:379859 original size:20 final size:20
Alignment explanation
Indices: 379793--379860 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
379783 CGAAAATCGA
*
379793 GTTGCGAATTTGAAATTCA-GT
1 GTTGCGAATTTG-ACTT-ATGT
*
379814 GTTGCAAATTTGACTTATGT
1 GTTGCGAATTTGACTTATGT
*
379834 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTATGT
379854 GTTGCGA
1 GTTGCGA
379861 TTTACATATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.02
20 30 0.71
21 11 0.26
ACGTcount: A:0.22, C:0.10, G:0.25, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTTATGT
Found at i:381234 original size:14 final size:14
Alignment explanation
Indices: 381205--381263 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
381195 TGTATTGATT
* *
381205 TTCTATAAATTAAA
1 TTCTAAAAAATAAA
*
381219 TTTTAAAAAATAAA
1 TTCTAAAAAATAAA
* **
381233 TTACTGAAATTTAAA
1 TT-CTAAAAAATAAA
381248 TTCTAAAAAATAAA
1 TTCTAAAAAATAAA
381262 TT
1 TT
381264 ATATTTCTGG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
14 24 0.71
15 10 0.29
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (14 bp):
TTCTAAAAAATAAA
Found at i:381580 original size:31 final size:29
Alignment explanation
Indices: 381473--381581 Score: 70
Period size: 33 Copynumber: 3.7 Consensus size: 29
381463 TATTATTTTT
*
381473 AAAATATTAAAATAATT-TA-TTTATTATTA
1 AAAATATT--AATAATTATATTTTATTAATA
381502 AATAATATT--T--TTATAATTTTATTAATA
1 AA-AATATTAATAATTAT-ATTTTATTAATA
*
381529 AAAATATTAATATTGATATATTTTATTGAAATA
1 AAAATATTAATAAT--TATATTTTATT--AATA
381562 AAAATATTACA-AATTATATT
1 AAAATATTA-ATAATTATATT
381582 AATTATTTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
24 2 0.03
25 1 0.02
26 8 0.12
27 11 0.17
28 1 0.02
29 2 0.03
30 7 0.11
31 14 0.22
32 3 0.05
33 15 0.23
34 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (29 bp):
AAAATATTAATAATTATATTTTATTAATA
Found at i:381588 original size:33 final size:33
Alignment explanation
Indices: 381525--381588 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
381515 TAATTTTATT
* *
381525 AATAAAAATATTAATATTGATATATTTTATTGA
1 AATAAAAATATTAAAATTGATATATATTATTGA
381558 AATAAAAATATTACAAATT-ATAT-TAATTATT
1 AATAAAAATATTA-AAATTGATATAT-ATTATT
381589 TATTAAAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 22 0.81
34 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.44
Consensus pattern (33 bp):
AATAAAAATATTAAAATTGATATATATTATTGA
Found at i:381661 original size:23 final size:23
Alignment explanation
Indices: 381612--381662 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
381602 GTGTTAGATT
**
381612 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
381635 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
381658 ATATT
1 ATATT
381663 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:381825 original size:23 final size:24
Alignment explanation
Indices: 381795--381855 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
381785 TTAAAATAAA
*
381795 AATATAATAT-CTTATATTATTAT
1 AATATAATATGATTATATTATTAT
*
381818 AATATAAT-TGATTATTTTATTAT
1 AATATAATATGATTATATTATTAT
* *
381841 AATATCATATTATTA
1 AATATAATATGATTA
381856 GAAATATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 26 0.81
24 5 0.16
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
AATATAATATGATTATATTATTAT
Found at i:385892 original size:248 final size:256
Alignment explanation
Indices: 385435--386052 Score: 830
Period size: 255 Copynumber: 2.4 Consensus size: 256
385425 CTTATTCATA
385435 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTCGGTTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATA-TTTTTTTATTATTTCGGGTC--G--GG-TTTCTAATTCATATATTCGGG
* *
385500 TC-GGTC-GGTAAAACTTTATTTTGGTCGGGTCGGCTCATTTTTTAAGTGTGATATTCAGGTCGG
60 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCATTTTTTAAGTGTGATATTCAGGTCGG
* *
385563 GTCGAGTTTGGATTTAGGGTGAAAAATACCCGACCTGACCCGACCCGACCCGAAAATATATATAA
125 GTC-AG--TCGATTTAGGGTGAAAAAT---C-A-CT-A-CCGACCCGACCCGAAAAAATATATAA
* *
385628 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATAT-ATTTTTTTTCAATTA
180 TTTTACATTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCAATTA
*
385692 AGTCATTGTTTT
245 AGTCACTGTTTT
385704 TATTGAATAAAAATA-TTTTTT-TTATTTC-GGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
* * *
385766 CGGGTGAAACTTCATTTTGGTCGGGTCGGGTCGGTTTTTTAAAGTGTGATATTCGGGTCGGGTTC
66 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTC-ATTTTTT-AAGTGTGATATTCAGGTCGGG-TC
*
385831 -G-CG-TTTAGGGTGAAAAAT-A-T-CCGACCCGGCCC-AAAAAATATATAATTTTACATTATAT
128 AGTCGATTTAGGGTGAAAAATCACTACCGACCCGACCCGAAAAAATATATAATTTTACATTATAT
*
385889 ATTTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTTTCCAATTAAGTCACTGTTTT
193 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCAATTAAGTCACTGTTTT
385953 TATTGAATAAAAATATTTTTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCG
1 TATTGAATAAAAATA---TTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCG
*
386018 GATCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
63 GGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
386053 TCGGATGGAG
Statistics
Matches: 323, Mismatches: 14, Indels: 38
0.86 0.04 0.10
Matches are distributed among these distances:
248 59 0.18
249 51 0.16
252 1 0.00
253 6 0.02
254 8 0.02
255 64 0.20
259 15 0.05
260 24 0.07
261 6 0.02
262 27 0.08
263 8 0.02
264 20 0.06
265 6 0.02
266 7 0.02
267 6 0.02
269 15 0.05
ACGTcount: A:0.26, C:0.14, G:0.19, T:0.41
Consensus pattern (256 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
CGGGTGAAACTTTATTTTGGTCGGGTCGGGTCATTTTTTAAGTGTGATATTCAGGTCGGGTCAGT
CGATTTAGGGTGAAAAATCACTACCGACCCGACCCGAAAAAATATATAATTTTACATTATATATT
TAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCCAATTAAGTCACTGTTTT
Found at i:386443 original size:18 final size:17
Alignment explanation
Indices: 386402--386453 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
386392 ATATAGAATT
*
386402 GGATTCCAATTCCTGAC
1 GGATTCCAATTCCTCAC
*
386419 AGATTCCAATTCCTTCAC
1 GGATTCCAATTCC-TCAC
386437 GGATTCCAATTCTCTCA
1 GGATTCCAATTC-CTCA
386454 TAAACATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 12 0.40
18 17 0.57
19 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.12, T:0.33
Consensus pattern (17 bp):
GGATTCCAATTCCTCAC
Found at i:387307 original size:2 final size:2
Alignment explanation
Indices: 387300--387327 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
387290 TATTTGTGTA
387300 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
387328 TTTAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:388090 original size:2 final size:2
Alignment explanation
Indices: 388083--388116 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
388073 CATAAGAGGA
388083 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
388117 TACTTTATTT
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:389600 original size:49 final size:49
Alignment explanation
Indices: 389547--389695 Score: 114
Period size: 49 Copynumber: 3.1 Consensus size: 49
389537 TAGTAGTTAT
389547 CTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGGGTATTAGAAAATGA
1 CTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGGGTATTAGAAAATGA
*** * * * * * * * *
389596 CTTTTCAGT--TTTGC-TCTGTTCAGTATT-T-TA-TGTATTTAG-TAGTTA
1 CTTTT-AGTCCGAGGCTTGTGTTC-TTCTTATAAAGGGTA-TTAGAAAATGA
389641 TCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGGGTATTAGAAAATGA
1 -CTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGGGTATTAGAAAATGA
389691 CTTTT
1 CTTTT
389696 CAGTTTTGCT
Statistics
Matches: 67, Mismatches: 22, Indels: 22
0.60 0.20 0.20
Matches are distributed among these distances:
45 9 0.13
46 10 0.15
47 12 0.18
48 12 0.18
49 15 0.22
50 9 0.13
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.46
Consensus pattern (49 bp):
CTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGGGTATTAGAAAATGA
Found at i:389679 original size:95 final size:95
Alignment explanation
Indices: 389516--389707 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
389506 ATAAACTTTC
389516 CTGTTCAGTATTTTATGTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAG
1 CTGTTCAGTATTTTATGTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAG
389581 GGTATTAGAAAATGACTTTTCAGTTTTGCT
66 GGTATTAGAAAATGACTTTTCAGTTTTGCT
389611 CTGTTCAGTATTTTATGTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAG
1 CTGTTCAGTATTTTATGTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAG
389676 GGTATTAGAAAATGACTTTTCAGTTTTGCT
66 GGTATTAGAAAATGACTTTTCAGTTTTGCT
389706 CT
1 CT
389708 CTTGGGTTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (95 bp):
CTGTTCAGTATTTTATGTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAG
GGTATTAGAAAATGACTTTTCAGTTTTGCT
Found at i:389681 original size:50 final size:50
Alignment explanation
Indices: 389532--389681 Score: 118
Period size: 50 Copynumber: 3.1 Consensus size: 50
389522 AGTATTTTAT
389532 GTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGG
1 GTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGG
* * * *** * * * * *
389582 GTA-TTAGAAAATGA-CTTTTCAGT--TTTGC-TCTGTTCAGTATT-T-TA-T
1 GTATTTAG-TAGTTATCTTTT-AGTCCGAGGCTTGTGTTC-TTCTTATAAAGG
389627 GTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGG
1 GTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGG
389677 GTATT
1 GTATT
389682 AGAAAATGAC
Statistics
Matches: 67, Mismatches: 22, Indels: 22
0.60 0.20 0.20
Matches are distributed among these distances:
45 9 0.13
46 10 0.15
47 12 0.18
48 12 0.18
49 10 0.15
50 14 0.21
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.47
Consensus pattern (50 bp):
GTATTTAGTAGTTATCTTTTAGTCCGAGGCTTGTGTTCTTCTTATAAAGG
Found at i:395245 original size:39 final size:39
Alignment explanation
Indices: 395191--395269 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
395181 GACGATGTCC
395191 ACTTCGATTTGCTCCCAAACATCATCCAGGATCAGTAGG
1 ACTTCGATTTGCTCCCAAACATCATCCAGGATCAGTAGG
395230 ACTTCGATTTGCTCCCAAACATCATCCAGGATCAGTAGG
1 ACTTCGATTTGCTCCCAAACATCATCCAGGATCAGTAGG
395269 A
1 A
395270 ACCTTCCCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (39 bp):
ACTTCGATTTGCTCCCAAACATCATCCAGGATCAGTAGG
Found at i:398938 original size:15 final size:16
Alignment explanation
Indices: 398910--398942 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
398900 AAAATCTTTC
398910 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
398926 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
398941 TT
1 TT
398943 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:399718 original size:16 final size:16
Alignment explanation
Indices: 399694--399727 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
399684 TATCGTCGAC
*
399694 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
399710 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
399726 CG
1 CG
399728 CGAATAGTAA
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:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:402140 original size:2 final size:2
Alignment explanation
Indices: 402133--402158 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
402123 CTTCATTTTA
402133 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
402159 TAAAAAGAGA
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:404342 original size:146 final size:145
Alignment explanation
Indices: 404136--404428 Score: 577
Period size: 146 Copynumber: 2.0 Consensus size: 145
404126 ATATACTCAT
404136 CTTTTATACTTTTCTTGGATAATATACGAGAAAAAGTTCTTAATTTAAGTTGTTATGTAAAATTA
1 CTTTTATACTTTTCTTGGATAATATACGAGAAAAAGTTCTTAATTTAAGTTGTTATGTAAAATTA
404201 TAAAAATGAGATAGGTGCATAACTACTTTATTTATAGAATATTGGACACGATATGATTGTTCTTG
66 TAAAAATGAGATAGGTGCATAACTACTTTATTTATAGAATATTGGACACGATATGATTGTTCTTG
404266 CTTGTGTCATTGCCTC
131 CTT-TGTCATTGCCTC
404282 CTTTTATACTTTTCTTGGATAATATACGAGAAAAAGTTCTTAATTTAAGTTGTTATGTAAAATTA
1 CTTTTATACTTTTCTTGGATAATATACGAGAAAAAGTTCTTAATTTAAGTTGTTATGTAAAATTA
404347 TAAAAATGAGATAGGTGCATAACTACTTTATTTATAGAATATTGGACACGATATGATTGTTCTTG
66 TAAAAATGAGATAGGTGCATAACTACTTTATTTATAGAATATTGGACACGATATGATTGTTCTTG
404412 CTTTGTCATTGCCTC
131 CTTTGTCATTGCCTC
404427 CT
1 CT
404429 CTGCTTCTCT
Statistics
Matches: 147, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
145 14 0.10
146 133 0.90
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (145 bp):
CTTTTATACTTTTCTTGGATAATATACGAGAAAAAGTTCTTAATTTAAGTTGTTATGTAAAATTA
TAAAAATGAGATAGGTGCATAACTACTTTATTTATAGAATATTGGACACGATATGATTGTTCTTG
CTTTGTCATTGCCTC
Found at i:407911 original size:21 final size:21
Alignment explanation
Indices: 407887--407928 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
407877 GAAATCCTGA
407887 AGAA-AATAGAGATTGAGGTTG
1 AGAAGAAT-GAGATTGAGGTTG
*
407908 AGAAGAATGTGATTGAGGTTG
1 AGAAGAATGAGATTGAGGTTG
407929 GGGCTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (21 bp):
AGAAGAATGAGATTGAGGTTG
Found at i:409768 original size:7 final size:7
Alignment explanation
Indices: 409756--409805 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
409746 GTCAAAGAAA
409756 GTCAACG
1 GTCAACG
409763 GTCAACG
1 GTCAACG
409770 GTC-ACG
1 GTCAACG
*
409776 GTCAATG
1 GTCAACG
409783 GTC-ACG
1 GTCAACG
409789 GTCAACG
1 GTCAACG
409796 GTCAACG
1 GTCAACG
409803 GTC
1 GTC
409806 GGGTCGGGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 11 0.28
7 28 0.72
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:409778 original size:13 final size:13
Alignment explanation
Indices: 409760--409805 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
409750 AAGAAAGTCA
409760 ACGGTCAACGGTC
1 ACGGTCAACGGTC
*
409773 ACGGTCAATGGTC
1 ACGGTCAACGGTC
409786 ACGGTCAACGGTC
1 ACGGTCAACGGTC
409799 AACGGTC
1 -ACGGTC
409806 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 24 0.80
14 6 0.20
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.17
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:409785 original size:20 final size:20
Alignment explanation
Indices: 409756--409805 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
409746 GTCAAAGAAA
409756 GTCAACGGTCAACGGTCACG
1 GTCAACGGTCAACGGTCACG
*
409776 GTCAATGGTC-ACGGTCAACG
1 GTCAACGGTCAACGGTC-ACG
409796 GTCAACGGTC
1 GTCAACGGTC
409806 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18
Consensus pattern (20 bp):
GTCAACGGTCAACGGTCACG
Found at i:409817 original size:17 final size:17
Alignment explanation
Indices: 409795--409835 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
409785 CACGGTCAAC
*
409795 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
409812 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
409829 GGTCAAC
1 GGTCAAC
409836 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:409853 original size:19 final size:18
Alignment explanation
Indices: 409829--409887 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 18
409819 AGTCGGGTCG
* *
409829 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGG-TCAAACC
409848 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
*
409866 GGTTCGAACCGGTCAAACC
1 GG-TCAAACCGGTCAAACC
409885 GGT
1 GGT
409888 TTTCTAGCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.25
19 27 0.75
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:409859 original size:9 final size:9
Alignment explanation
Indices: 409829--409887 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
409819 AGTCGGGTCG
*
409829 GGTCAACCC
1 GGTCAAACC
*
409838 GGTTCAGACC
1 GG-TCAAACC
409848 GGTCAAACC
1 GGTCAAACC
409857 GGTCAAACC
1 GGTCAAACC
*
409866 GGTTCGAACC
1 GG-TCAAACC
409876 GGTCAAACC
1 GGTCAAACC
409885 GGT
1 GGT
409888 TTTCTAGCAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 28 0.65
10 15 0.35
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:409869 original size:28 final size:28
Alignment explanation
Indices: 409829--409887 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
409819 AGTCGGGTCG
*
409829 GGTCAACCCGGTTC-AGACCGGTCAAACC
1 GGTCAAACCGGTTCGA-ACCGGTCAAACC
409857 GGTCAAACCGGTTCGAACCGGTCAAACC
1 GGTCAAACCGGTTCGAACCGGTCAAACC
409885 GGT
1 GGT
409888 TTTCTAGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.15
Consensus pattern (28 bp):
GGTCAAACCGGTTCGAACCGGTCAAACC
Found at i:411597 original size:9 final size:9
Alignment explanation
Indices: 411583--411641 Score: 73
Period size: 9 Copynumber: 6.3 Consensus size: 9
411573 CTGCTAGAAA
411583 ACCGGTTTG
1 ACCGGTTTG
*
411592 ACCGGTTCG
1 ACCGGTTTG
411601 AACCGGTTTG
1 -ACCGGTTTG
411611 ACCGGTTTG
1 ACCGGTTTG
*
411620 ACCGGTCTG
1 ACCGGTTTG
*
411629 AACCGGGTTG
1 -ACCGGTTTG
411639 ACC
1 ACC
411642 CGACCCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 28 0.65
10 15 0.35
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:411623 original size:28 final size:28
Alignment explanation
Indices: 411583--411641 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
411573 CTGCTAGAAA
*
411583 ACCGGTTTGACCGGT-TCGAACCGGTTTG
1 ACCGGTTTGACCGGTCT-GAACCGGGTTG
411611 ACCGGTTTGACCGGTCTGAACCGGGTTG
1 ACCGGTTTGACCGGTCTGAACCGGGTTG
411639 ACC
1 ACC
411642 CGACCCGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.25
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTGAACCGGGTTG
Found at i:411633 original size:19 final size:18
Alignment explanation
Indices: 411583--411641 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 18
411573 CTGCTAGAAA
*
411583 ACCGGTTTGACCGGTTCG
1 ACCGGTTTGACCGGTTTG
411601 AACCGGTTTGACCGGTTTG
1 -ACCGGTTTGACCGGTTTG
* *
411620 ACCGGTCTGAACCGGGTTG
1 ACCGGTTTG-ACCGGTTTG
411639 ACC
1 ACC
411642 CGACCCGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 8 0.22
19 28 0.78
ACGTcount: A:0.15, C:0.27, G:0.32, T:0.25
Consensus pattern (18 bp):
ACCGGTTTGACCGGTTTG
Found at i:411657 original size:17 final size:17
Alignment explanation
Indices: 411635--411675 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
411625 TCTGAACCGG
*
411635 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
411652 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
411669 GTTGACC
1 GTTGACC
411676 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:411677 original size:7 final size:7
Alignment explanation
Indices: 411665--411701 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
411655 GACCCGACCC
411665 GACCGTT
1 GACCGTT
411672 GACCGTT
1 GACCGTT
411679 GACCG-T
1 GACCGTT
411685 GACCGTT
1 GACCGTT
411692 GACCGTT
1 GACCGTT
411699 GAC
1 GAC
411702 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:411689 original size:13 final size:13
Alignment explanation
Indices: 411665--411697 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
411655 GACCCGACCC
411665 GACCGTTGACCGTT
1 GACCG-TGACCGTT
411679 GACCGTGACCGTT
1 GACCGTGACCGTT
411692 GACCGT
1 GACCGT
411698 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:418679 original size:20 final size:20
Alignment explanation
Indices: 418654--418691 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
418644 GCTGCTAGAA
418654 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACCAGTTTTG
*
418674 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCAGTTT
418692 GACCGGTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.34
Consensus pattern (20 bp):
AACCGGTTTGACCAGTTTTG
Found at i:418687 original size:9 final size:9
Alignment explanation
Indices: 418655--418714 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
418645 CTGCTAGAAA
418655 ACCGGTTTG
1 ACCGGTTTG
*
418664 ACCAGTTTTG
1 ACC-GGTTTG
418674 AACCGGTTTG
1 -ACCGGTTTG
418684 ACCGGTTTG
1 ACCGGTTTG
*
418693 ACCGGTCTG
1 ACCGGTTTG
*
418702 AACCGGGTTG
1 -ACCGGTTTG
418712 ACC
1 ACC
418715 CGACCCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 23 0.53
10 17 0.40
11 3 0.07
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:418706 original size:19 final size:18
Alignment explanation
Indices: 418655--418714 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
418645 CTGCTAGAAA
* *
418655 ACCGGTTTGACCAGTTTTG
1 ACCGGTCTGACC-GGTTTG
*
418674 AACCGGTTTGACCGGTTTG
1 -ACCGGTCTGACCGGTTTG
*
418693 ACCGGTCTGAACCGGGTTG
1 ACCGGTCTG-ACCGGTTTG
418712 ACC
1 ACC
418715 CGACCCGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.22
19 16 0.44
20 12 0.33
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTCTGACCGGTTTG
Found at i:418710 original size:29 final size:28
Alignment explanation
Indices: 418655--418714 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
418645 CTGCTAGAAA
* *
418655 ACCGGTTTGACCAGTTTTGAACCGGTTTG
1 ACCGGTTTGACCAGGTCTGAACCGG-TTG
418684 ACCGGTTTGACC-GGTCTGAACCGGGTTG
1 ACCGGTTTGACCAGGTCTGAACC-GGTTG
418712 ACC
1 ACC
418715 CGACCCGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.17, C:0.25, G:0.30, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCAGGTCTGAACCGGTTG
Found at i:418730 original size:17 final size:17
Alignment explanation
Indices: 418708--418748 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
418698 TCTGAACCGG
*
418708 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
418725 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
418742 GTTGACC
1 GTTGACC
418749 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:418750 original size:7 final size:7
Alignment explanation
Indices: 418738--418787 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
418728 GACCCGACCC
418738 GACCGTT
1 GACCGTT
418745 GACCGTT
1 GACCGTT
418752 GACCG-T
1 GACCGTT
418758 GACCGTT
1 GACCGTT
418765 GACCG-T
1 GACCGTT
418771 GACCGTT
1 GACCGTT
418778 GACCGTT
1 GACCGTT
418785 GAC
1 GAC
418788 TTTCTTTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:418762 original size:13 final size:13
Alignment explanation
Indices: 418738--418783 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
418728 GACCCGACCC
418738 GACCGTTGACCGTT
1 GACCG-TGACCGTT
418752 GACCGTGACCGTT
1 GACCGTGACCGTT
418765 GACCGTGACCGTT
1 GACCGTGACCGTT
418778 GACCGT
1 GACCGT
418784 TGACTTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 27 0.84
14 5 0.16
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:418763 original size:20 final size:20
Alignment explanation
Indices: 418738--418787 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
418728 GACCCGACCC
418738 GACCGTTGACCGTTGACCG-T
1 GACCGTTGACCG-TGACCGTT
418758 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
418778 GACCGTTGAC
1 GACCGTTGAC
418788 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:420737 original size:29 final size:31
Alignment explanation
Indices: 420705--420764 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
420695 AAATTTTGAA
420705 TAAATTCAATT-AAGT-CAAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAA-ACCATTTTG
420734 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
420765 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 11 0.39
30 5 0.18
31 12 0.43
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:423591 original size:34 final size:32
Alignment explanation
Indices: 423531--423600 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
423521 CCTTACAAAC
*
423531 TCCCTAGTTTTTCCGGGATAAACTAGAACATT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* * *
423563 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
423597 TCCC
1 TCCC
423601 GTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:423911 original size:21 final size:21
Alignment explanation
Indices: 423885--423926 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
423875 CCAAAATGGG
*
423885 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
423906 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
423927 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:424060 original size:19 final size:19
Alignment explanation
Indices: 424032--424098 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
424022 TAGCCTCGGA
*
424032 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAT
* *
424051 TTAGTGTTCAAATAGTAAT
1 TTACTGTTCAAACAGTAAT
* *
424070 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAT
*
424089 TTACTATTCA
1 TTACTGTTCA
424099 TACAAACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAT
Found at i:424195 original size:29 final size:31
Alignment explanation
Indices: 424163--424222 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
424153 AAATTTTGAA
* *
424163 TAAATTCAATT-AAGTCTAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
424192 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
424223 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 11 0.41
30 9 0.33
31 7 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:447833 original size:15 final size:15
Alignment explanation
Indices: 447798--447843 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
447788 TGTATGAGTC
447798 TTTTCTTTTC-TCTT-
1 TTTT-TTTTCTTCTTA
447812 TTGTTTTTT-TTCTTA
1 TT-TTTTTTCTTCTTA
447827 TTTTTTTTCTTCTTA
1 TTTTTTTTCTTCTTA
447842 TT
1 TT
447844 GCTTTGGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTTCTTA
Found at i:450194 original size:20 final size:20
Alignment explanation
Indices: 450170--450218 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
450160 CACAGGTTCC
450170 AAAATCGCAACGCGAATAT-
1 AAAATCGCAACGCGAATATG
*
450189 ATAAATCGCAACGTGAATATG
1 A-AAATCGCAACGCGAATATG
450210 AAAATCGCA
1 AAAATCGCA
450219 TATCTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATG
Found at i:450895 original size:33 final size:33
Alignment explanation
Indices: 450857--450922 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
450847 ATGCTGTATA
*
450857 GTTTCACGACCGGATTAATCTAAAGGTGCGTTT
1 GTTTCACGACCGGAATAATCTAAAGGTGCGTTT
*
450890 GTTTCACGACTGGAATAATCTAAAGGTGCGTTT
1 GTTTCACGACCGGAATAATCTAAAGGTGCGTTT
450923 AATTCACGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (33 bp):
GTTTCACGACCGGAATAATCTAAAGGTGCGTTT
Found at i:450929 original size:33 final size:33
Alignment explanation
Indices: 450859--450930 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
450849 GCTGTATAGT
* **
450859 TTCACGACCGGATTAATCTAAAGGTGCGTTTGT
1 TTCACGACCGGAATAATCTAAAGGTGCGTTTAA
*
450892 TTCACGACTGGAATAATCTAAAGGTGCGTTTAA
1 TTCACGACCGGAATAATCTAAAGGTGCGTTTAA
450925 TTCACG
1 TTCACG
450931 GAATGTAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (33 bp):
TTCACGACCGGAATAATCTAAAGGTGCGTTTAA
Found at i:454237 original size:24 final size:25
Alignment explanation
Indices: 454202--454252 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
454192 AATGAAGTTG
454202 AAAAATAGATTTTACAAGTTATTCT
1 AAAAATAGATTTTACAAGTTATTCT
454227 AAAAATA-ATTTTACAAGTTATTCT
1 AAAAATAGATTTTACAAGTTATTCT
454251 AA
1 AA
454253 TGAAGTGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (25 bp):
AAAAATAGATTTTACAAGTTATTCT
Found at i:463338 original size:30 final size:30
Alignment explanation
Indices: 463304--463363 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
463294 GTCTTATAAA
*
463304 TCTTAAAAGAATCCTTTTATTTTTCTCTTT
1 TCTTAAAAGAATCCTTTTATTTTCCTCTTT
463334 TCTTAAAAGAATCCTTTTATTTTCCTCTTT
1 TCTTAAAAGAATCCTTTTATTTTCCTCTTT
463364 CTCCTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.03, T:0.55
Consensus pattern (30 bp):
TCTTAAAAGAATCCTTTTATTTTCCTCTTT
Found at i:463400 original size:18 final size:17
Alignment explanation
Indices: 463368--463405 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
463358 CTCTTTCTCC
463368 TTTCATCTTCATCTTCAT
1 TTTCATCTTCATCTTC-T
463386 TTTCATCTTTC-TCTTCT
1 TTTCATC-TTCATCTTCT
463403 TTT
1 TTT
463406 TTTCCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 12 0.63
19 3 0.16
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTCATCTTCATCTTCT
Found at i:464510 original size:2 final size:2
Alignment explanation
Indices: 464503--464530 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
464493 CTGATATGAC
464503 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
464531 GAATGAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:467481 original size:53 final size:53
Alignment explanation
Indices: 467441--467699 Score: 385
Period size: 53 Copynumber: 4.9 Consensus size: 53
467431 TTTTAAAAAT
* * **
467441 GGGTTCGCTCCCTATTACTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * * * * *
467494 GGGTTCACTTCATCTTGCTTTAGGAAGTA-AACTCGAACAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
467546 GGGTTCGCTCCCTTTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTCCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
467599 GGGTTCTCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
467652 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
467700 GTGTGATTCT
Statistics
Matches: 183, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 45 0.25
53 138 0.75
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.31
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:467567 original size:105 final size:106
Alignment explanation
Indices: 467441--467699 Score: 403
Period size: 105 Copynumber: 2.5 Consensus size: 106
467431 TTTTAAAAAT
* ** *
467441 GGGTTCGCTCCCTATTACTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACGGGTTCACTTCA
1 GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCA
* *
467506 TCTTGCTTTAGGAAGT-AAACTCGAACAATCTTCTGCTTAC
66 TCTTGCTTCAGGAAGTAAAACTCGAACAATCTTCTGCCTAC
* * * *
467546 GGGTTCGCTCCCTTTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTCCCTACGGGTTCTCTCCC
1 GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCA
*
467611 TCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCTAC
66 TCTTGCTTCAGGAAGTAAAACTCGAACAATCTTCTGCCTAC
*
467652 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
1 GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
467700 GTGTGATTCT
Statistics
Matches: 140, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
105 71 0.51
106 69 0.49
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.31
Consensus pattern (106 bp):
GGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTCACTCCA
TCTTGCTTCAGGAAGTAAAACTCGAACAATCTTCTGCCTAC
Found at i:468147 original size:42 final size:41
Alignment explanation
Indices: 468101--468279 Score: 113
Period size: 42 Copynumber: 4.4 Consensus size: 41
468091 TTATCATCTC
468101 GCTCGAAAGACTTACAAATGACCCGAAGGATTTCATCACCAT
1 GCTCGAAAGACTTACAAATGACCCGAA-GATTTCATCACCAT
* * *
468143 GCTCGAAAGACTTAC---TGA--TG-A-ATTTGCTTCACTACT
1 GCTCGAAAGACTTACAAATGACCCGAAGATTT-CATCACCA-T
* * * * *
468179 -CTTCGGTGAAGGCTTACAAATTACCCGAAGATTTTAATCATCAT
1 GC-TC-G-AAAGACTTACAAATGACCCGAAGA-TTTCATCACCAT
** * *
468223 GCTCGAAAGACTTACTGATGGCCCGAAGGATTTCATCATCAT
1 GCTCGAAAGACTTACAAATGACCCGAA-GATTTCATCACCAT
*
468265 GCTCAAAAGACTTAC
1 GCTCGAAAGACTTAC
468280 TGATGGCACT
Statistics
Matches: 103, Mismatches: 19, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
34 4 0.04
35 7 0.07
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
41 2 0.02
42 56 0.54
43 4 0.04
44 4 0.04
45 6 0.06
46 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
GCTCGAAAGACTTACAAATGACCCGAAGATTTCATCACCAT
Found at i:468280 original size:42 final size:42
Alignment explanation
Indices: 468202--468286 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
468192 TTACAAATTA
*
468202 CCCGAAGATTTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGATTTTAATCATCATGCTCAAAAGACTTACTGATGG
*
468244 CCCGAAGGA-TTTCATCATCATGCTCAAAAGACTTACTGATGG
1 CCCGAA-GATTTTAATCATCATGCTCAAAAGACTTACTGATGG
468286 C
1 C
468287 ACTTACTGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 38 0.95
43 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
CCCGAAGATTTTAATCATCATGCTCAAAAGACTTACTGATGG
Found at i:468292 original size:13 final size:13
Alignment explanation
Indices: 468274--468298 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
468264 TGCTCAAAAG
468274 ACTTACTGATGGC
1 ACTTACTGATGGC
468287 ACTTACTGATGG
1 ACTTACTGATGG
468299 ATTTGCTTCA
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:468385 original size:13 final size:13
Alignment explanation
Indices: 468367--468391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
468357 TGCTCGAAAG
468367 ACTTACTGATGGC
1 ACTTACTGATGGC
468380 ACTTACTGATGG
1 ACTTACTGATGG
468392 GTTTGCTTCA
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:468397 original size:93 final size:93
Alignment explanation
Indices: 468244--468472 Score: 395
Period size: 93 Copynumber: 2.5 Consensus size: 93
468234 TTACTGATGG
* *
468244 CCCGAAGGATTTCATCATCATGCTCAAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCA
*
468309 CTACTCTTCGGTGAAGGCTTACAAATTA
66 CAACTCTTCGGTGAAGGCTTACAAATTA
*
468337 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCA
468402 CAACTCTTCGGTGAAGGCTTACAAATTA
66 CAACTCTTCGGTGAAGGCTTACAAATTA
* * *
468430 CCCGAATGATTTAATCATCATACTCGAAAGACTTATTGATGGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
468473 CCGAAGGACT
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 129 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (93 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTCA
CAACTCTTCGGTGAAGGCTTACAAATTA
Found at i:477324 original size:17 final size:17
Alignment explanation
Indices: 477302--477334 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
477292 CTTTTACATA
477302 AAACCTAAACTAATATT
1 AAACCTAAACTAATATT
477319 AAACCTAAACTAATAT
1 AAACCTAAACTAATAT
477335 CACCTCTGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACCTAAACTAATATT
Found at i:484847 original size:25 final size:25
Alignment explanation
Indices: 484793--484847 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
484783 AGTCACATTT
484793 CATATAACACTTATATTACATATTC
1 CATATAACACTTATATTACATATTC
*
484818 C-TATAATTACTTATATTA-ATA-TC
1 CATATAA-CACTTATATTACATATTC
484841 ACATATA
1 -CATATA
484848 TCAAAGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 2 0.08
24 9 0.35
25 15 0.58
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (25 bp):
CATATAACACTTATATTACATATTC
Found at i:485322 original size:20 final size:22
Alignment explanation
Indices: 485287--485344 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
485277 TTTCCCTTGA
* *
485287 AGTGCATCGGTACATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
485307 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
485330 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
485345 CTATCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.47
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:487351 original size:25 final size:25
Alignment explanation
Indices: 487321--487371 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
487311 TTAACTCCTC
*
487321 AGTTACAAAGGTTATATGCCTCAGA
1 AGTTACAAAGGTTATATGCCACAGA
487346 AGTTACAAAGGTTATATGCCACAGA
1 AGTTACAAAGGTTATATGCCACAGA
487371 A
1 A
487372 ATTTCTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (25 bp):
AGTTACAAAGGTTATATGCCACAGA
Found at i:488286 original size:3 final size:3
Alignment explanation
Indices: 488278--488310 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
488268 ACATAAAATA
488278 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
488311 ATATATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:490071 original size:13 final size:14
Alignment explanation
Indices: 490045--490099 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 14
490035 ACACGACCTA
490045 ACCCT-ACCCATTG
1 ACCCTGACCCATTG
*
490058 A-CCTGACCCGTTG
1 ACCCTGACCCATTG
490071 ACCCT-ACCCATTG
1 ACCCTGACCCATTG
* *
490084 ATCC-GACCCGTTG
1 ACCCTGACCCATTG
490097 ACC
1 ACC
490100 GTTGACCGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 28 0.82
14 3 0.09
ACGTcount: A:0.20, C:0.44, G:0.15, T:0.22
Consensus pattern (14 bp):
ACCCTGACCCATTG
Found at i:490074 original size:26 final size:26
Alignment explanation
Indices: 490045--490099 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
490035 ACACGACCTA
490045 ACCCTACCCATTGA-CCTGACCCGTTG
1 ACCCTACCCATTGATCC-GACCCGTTG
490071 ACCCTACCCATTGATCCGACCCGTTG
1 ACCCTACCCATTGATCCGACCCGTTG
490097 ACC
1 ACC
490100 GTTGACCGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.20, C:0.44, G:0.15, T:0.22
Consensus pattern (26 bp):
ACCCTACCCATTGATCCGACCCGTTG
Found at i:498345 original size:30 final size:31
Alignment explanation
Indices: 498276--498352 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
498266 TAAGAGAATG
498276 ATCATAATAAAAAATATTAAAAAAATATGGAC
1 ATCATAATAAAAAATATTAAAAAAATAT-GAC
* *
498308 ATC-TAATAAAAAGTATTGAAAAAATTAT-AC
1 ATCATAATAAAAAATATT-AAAAAAATATGAC
*
498338 -TCATAATAACAAATA
1 ATCATAATAAAAAATA
498353 AATATTAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.05
30 12 0.31
31 13 0.33
32 12 0.31
ACGTcount: A:0.60, C:0.08, G:0.05, T:0.27
Consensus pattern (31 bp):
ATCATAATAAAAAATATTAAAAAAATATGAC
Found at i:499449 original size:183 final size:181
Alignment explanation
Indices: 499230--500208 Score: 1273
Period size: 183 Copynumber: 5.4 Consensus size: 181
499220 CGATCCAAAT
* * *
499230 TAAAAATGTATCTATCCATATCAATGTAACAGGTAAAAATATGACAAAACCGGTTTCATTATGAC
1 TAAAAATGTATCGATCCATAT-AATATAACAGGTAAAAATATGACAAAACCGGTTTCA-AATGAC
* * *
499295 AAAACCGGTAAAGCGCTACCGAATATGTTGATAGTATCGATTAGATTGAA-ATAAGTATCAACAC
64 AAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGA-TAGATTGAATATAAGTATCGACAC
499359 TTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
128 TTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * ** *
499413 TAAAAATGTATCGATCTATATCAATATAATAGGTAAAAATATGACAAAAATGGTTTCATTATGAC
1 TAAAAATGTATCGATCCATAT-AATATAACAGGTAAAAATATGACAAAACCGGTTTCA-AATGAC
*
499478 AAAACCGGTAAAGCGCTACCGGATATGTTGAAAG-GATCGATTAGATTGAA-ATAAGTATCGACA
64 AAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTG-TCGA-TAGATTGAATATAAGTATCGACA
* * *
499541 CTTTAGGAATTTAAAAGAAAAGCAGTAATAGCGTCTATAAAGTGTCGATACTTTA
127 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * * *
499596 TAAAAATGTATCGCTCCATAATGATATAACATGTAAAAATATGACAAAACCGATATCGAAATGAC
1 TAAAAATGTATCGATCCAT-ATAATATAACAGGTAAAAATATGACAAAACCGGTTTC-AAATGAC
* *
499661 AAAACCGATAAAGCGCTACC-AGATCTGTTGAAAGTGTCGATACG-TT-AATATAAGTATCGACA
64 AAAACCGGTAAAGCGCTACCGA-ATATGTTGAAAGTGTCGATA-GATTGAATATAAGTATCGACA
*
499723 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTC
127 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * * *
499778 TAAACATGTATCGATCCATA-ACGATATAACAGGTAAAAATATTACAAAATCGGTCTCGCAATGA
1 TAAAAATGTATCGATCCATATA--ATATAACAGGTAAAAATATGACAAAACCGGTTTC-AAATGA
* * * *
499842 CAAAACCGGTAAAGCGCTATCGAATCTGTTGAAAGTGTCGATA-CTTTAATATAAGTATCGACAC
63 CAAAACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATAGATTGAATATAAGTATCGACAC
* * *
499906 TTTGGGAATTTAAAAGAGAAGAAGAAATA-CACCTATAAAGTGTCGATACTTTA
128 TTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * *
499959 TAAAAATGTATCGATCCATAATGATATAATAGGTAAAAATATGATAAAACCGGTTTCCAAATGAC
1 TAAAAATGTATCGATCCAT-ATAATATAACAGGTAAAAATATGACAAAACCGGTTT-CAAATGAC
* * *
500024 AAAACCGGTAAAGCGCTACC-AGATATATTGAAAGTGTCGATA-CTTTAATATAAGTATCGACAC
64 AAAACCGGTAAAGCGCTACCGA-ATATGTTGAAAGTGTCGATAGATTGAATATAAGTATCGACAC
*
500087 TTTGGGAATTTAAAAAAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
128 TTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* ** * * *
500141 TAAAAATATATCGATCCATA-ACGA-AACAGTTAAAAATATGACAAAACCGGTCTCCAAATGATA
1 TAAAAATGTATCGATCCATATAATATAACAGGTAAAAATATGACAAAACCGGT-TTCAAATGACA
500204 AAACC
65 AAACC
500209 AGAATTGGAT
Statistics
Matches: 709, Mismatches: 69, Indels: 40
0.87 0.08 0.05
Matches are distributed among these distances:
179 37 0.05
180 3 0.00
181 164 0.23
182 246 0.35
183 255 0.36
184 4 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (181 bp):
TAAAAATGTATCGATCCATATAATATAACAGGTAAAAATATGACAAAACCGGTTTCAAATGACAA
AACCGGTAAAGCGCTACCGAATATGTTGAAAGTGTCGATAGATTGAATATAAGTATCGACACTTT
GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
Found at i:499798 original size:182 final size:180
Alignment explanation
Indices: 499230--500208 Score: 1296
Period size: 182 Copynumber: 5.4 Consensus size: 180
499220 CGATCCAAAT
* * * *
499230 TAAAAATGTATCTATCCAT-ATCAATGTAACAGGTAAAAATATGACAAAACCGGTTTCATTATGA
1 TAAAAATGTATCGATCCATAAT-GATATAACAGGTAAAAATATGACAAAACCGGTTTCA-AATGA
* * *
499294 CAAAACCGGTAAAGCGCTACCGAATATGTTGATAGTATCGATTA-GATTGAA-ATAAGTATCAAC
64 CAAAACCGGTAAAGCGCTACCG-ATATGTTGAAAGTGTCGA-TACG-TT-AATATAAGTATCGAC
499357 ACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
125 ACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * ** *
499413 TAAAAATGTATCGATCTAT-ATCAATATAATAGGTAAAAATATGACAAAAATGGTTTCATTATGA
1 TAAAAATGTATCGATCCATAAT-GATATAACAGGTAAAAATATGACAAAACCGGTTTCA-AATGA
499477 CAAAACCGGTAAAGCGCTACCGGATATGTTGAAAG-GATCGATTA-GATTGAA-ATAAGTATCGA
64 CAAAACCGGTAAAGCGCTACC-GATATGTTGAAAGTG-TCGA-TACG-TT-AATATAAGTATCGA
* * *
499539 CACTTTAGGAATTTAAAAGAAAAGCAGTAATAGCGTCTATAAAGTGTCGATACTTTA
124 CACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * *
499596 TAAAAATGTATCGCTCCATAATGATATAACATGTAAAAATATGACAAAACCGATATCGAAATGAC
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTC-AAATGAC
* *
499661 AAAACCGATAAAGCGCTACCAGATCTGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
65 AAAACCGGTAAAGCGCTACC-GATATGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
*
499726 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTC
129 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * * * *
499778 TAAACATGTATCGATCCATAACGATATAACAGGTAAAAATATTACAAAATCGGTCTCGCAATGAC
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTC-AAATGAC
* * *
499843 AAAACCGGTAAAGCGCTATCGAATCTGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAAACCGGTAAAGCGCTACCG-ATATGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
* * *
499908 TGGGAATTTAAAAGAGAAGAAGAAATA-CACCTATAAAGTGTCGATACTTTA
129 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* *
499959 TAAAAATGTATCGATCCATAATGATATAATAGGTAAAAATATGATAAAACCGGTTTCCAAATGAC
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTT-CAAATGAC
* *
500024 AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
65 AAAACCGGTAAAGCGCTACC-GATATGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
*
500089 TGGGAATTTAAAAAAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
129 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
* * * * *
500141 TAAAAATATATCGATCCATAACG--A-AACAGTTAAAAATATGACAAAACCGGTCTCCAAATGAT
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGT-TTCAAATGAC
500203 AAAACC
65 AAAACC
500209 AGAATTGGAT
Statistics
Matches: 717, Mismatches: 67, Indels: 28
0.88 0.08 0.03
Matches are distributed among these distances:
179 37 0.05
180 2 0.00
181 164 0.23
182 255 0.36
183 254 0.35
184 5 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (180 bp):
TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTCAAATGACA
AAACCGGTAAAGCGCTACCGATATGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTTG
GGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
Found at i:500074 original size:363 final size:364
Alignment explanation
Indices: 499230--500208 Score: 1363
Period size: 363 Copynumber: 2.7 Consensus size: 364
499220 CGATCCAAAT
* * * *
499230 TAAAAATGTATCTATCCAT-ATCAATGTAACAGGTAAAAATATGACAAAACCGGTTT-CATTATG
1 TAAAAATGTATCGATCCATAAT-GATATAACAGGTAAAAATATGACAAAACCGGTTTCCA-AATG
* * * * *
499293 ACAAAACCGGTAAAGCGCTACC-GAATATGTTGATAGTATCGATTAGATTGAA-ATAAGTATCAA
64 ACAAAACCGGTAAAGCGCTACCAG-ATATGTTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGA
499356 CACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
126 CACTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATG
* * * * *
499421 TATCGATCTATATCAATATAATAGGTAAAAATATGACAAAAAT-GGT-TTCATTATGACAAAACC
191 TATCGATCCATAACGATATAACAGGTAAAAATATGAC-AAAATCGGTCTCCA--ATGACAAAACC
*
499484 GGTAAAGCGCTACCGGATATGTTGAAAGGATCGATTAGATTGAAATAAGTATCGACACTTTAGGA
253 GGTAAAGCGCTACCGAATATGTTGAAAGGATCGATTAGATTGAAATAAGTATCGACACTTTAGGA
* * **
499549 ATTTAAAAGAAAAGCAGTAATAGCGTCTATAAAGTGTCGATACTTTA
318 ATTTAAAAGAAAAGAAGAAATAGCACCTATAAAGTGTCGATACTTTA
* * * * *
499596 TAAAAATGTATCGCTCCATAATGATATAACATGTAAAAATATGACAAAACCGATATCGAAATGAC
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTCCAAATGAC
* * *
499661 AAAACCGATAAAGCGCTACCAGATCTGTTGAAAGTGTCGATACGTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
499726 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTCTAAACATGTATCG
131 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCG
*
499791 ATCCATAACGATATAACAGGTAAAAATATTACAAAATCGGTCTCGCAATGACAAAACCGGTAAAG
196 ATCCATAACGATATAACAGGTAAAAATATGACAAAATCGGTCTC-CAATGACAAAACCGGTAAAG
* * * * *
499856 CGCTATCGAATCTGTTGAAAGTG-TCGA-TA-CTTTAATATAAGTATCGACACTTTGGGAATTTA
260 CGCTACCGAATATGTTGAAAG-GATCGATTAGATTGAA-ATAAGTATCGACACTTTAGGAATTTA
*
499918 AAAGAGAAGAAGAAATA-CACCTATAAAGTGTCGATACTTTA
323 AAAGAAAAGAAGAAATAGCACCTATAAAGTGTCGATACTTTA
* *
499959 TAAAAATGTATCGATCCATAATGATATAATAGGTAAAAATATGATAAAACCGGTTTCCAAATGAC
1 TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTCCAAATGAC
*
500024 AAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
66 AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* *
500089 TGGGAATTTAAAAAAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATATATCG
131 TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCG
* * *
500154 ATCCATAACG--A-AACAGTTAAAAATATGACAAAACCGGTCTCCAAATGATAAAACC
196 ATCCATAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCC-AATGACAAAACC
500209 AGAATTGGAT
Statistics
Matches: 548, Mismatches: 55, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
359 1 0.00
360 38 0.07
361 1 0.00
363 216 0.39
364 49 0.09
365 150 0.27
366 87 0.16
367 6 0.01
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.27
Consensus pattern (364 bp):
TAAAAATGTATCGATCCATAATGATATAACAGGTAAAAATATGACAAAACCGGTTTCCAAATGAC
AAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCG
ATCCATAACGATATAACAGGTAAAAATATGACAAAATCGGTCTCCAATGACAAAACCGGTAAAGC
GCTACCGAATATGTTGAAAGGATCGATTAGATTGAAATAAGTATCGACACTTTAGGAATTTAAAA
GAAAAGAAGAAATAGCACCTATAAAGTGTCGATACTTTA
Found at i:503372 original size:15 final size:15
Alignment explanation
Indices: 503352--503381 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
503342 TTGTAGGGGT
503352 GGATGACGGTCAGGG
1 GGATGACGGTCAGGG
*
503367 GGATGACGGTGAGGG
1 GGATGACGGTCAGGG
503382 AAAACAAAGT
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:0.20, C:0.10, G:0.57, T:0.13
Consensus pattern (15 bp):
GGATGACGGTCAGGG
Found at i:503632 original size:66 final size:66
Alignment explanation
Indices: 503507--503632 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 66
503497 AAAGTGGAAG
* ** * *
503507 AAAAAATAGATGGAGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGAACTTAAGATGGTGACGGGT
1 AAAAAATAGATGGAGTGGTCAAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGACGGGT
503572 A
66 A
* * * * * * *
503573 AAAAAATTGATGGAGTGGTCAAGGACGTTGTGGAATTGATGAGTGAACTTACGGGGGTGA
1 AAAAAATAGATGGAGTGGTCAAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGA
503633 AATAGGTGGT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
66 48 1.00
ACGTcount: A:0.33, C:0.05, G:0.38, T:0.24
Consensus pattern (66 bp):
AAAAAATAGATGGAGTGGTCAAAGAAGTTGAGGAATTGAGGAGTGAACTTAAGAGGGTGACGGGT
A
Found at i:505333 original size:19 final size:19
Alignment explanation
Indices: 505309--505357 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
505299 AATGTAGGGT
505309 TAATTTTGTATAAGATTAA
1 TAATTTTGTATAAGATTAA
* *
505328 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTAA
505347 TAATTTTGTAT
1 TAATTTTGTAT
505358 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTAA
Found at i:506224 original size:201 final size:201
Alignment explanation
Indices: 505729--507095 Score: 2032
Period size: 201 Copynumber: 6.8 Consensus size: 201
505719 GTAAACAGAT
*
505729 GTGTCGATACATTTATAAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAAT
* * * *
505794 AGGTAATTTTTCAATGTAATCGGTATAAATATACCTGTTTTATGAGATAATATGTCTACATAATG
65 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* * *
505859 CATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAATTA-GTGAAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
*
505923 ACATAAA
195 GCATAAA
* * * * *
505930 GTGTAGATACATTTATAAAAAGTATCGATCTCAAAAATATTGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAATA
* * *
505995 GGTACTTTTTCAATGTAACCGGTATAAATATACCAGCTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * *
506060 ATCGACACTTTTGAATTTTGTGTCGATCCTTTTTGTCAAGAATGAATGCCCAAACTAGGTGCACA
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
506125 CATAAA
196 CATAAA
* *
506131 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAATA
** *
506196 GGTAATTTTTCAATGTAACCAATATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * *
506261 ATCAACACTTTTGAAATTTGTGTTGATACTTTTTATCCAGAATGAATGCCCAAACTAGGTG--CG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
506324 CATAAA
196 CATAAA
* *
506330 GTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAACCCATAATTTTAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAATA
* * * *
506395 GGTAAATTTTCAATGTAATCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTGCATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
506460 ATCGACACTTTTGAAATTTGTGTTGATACTTTTTGTCCATAATGAATGCCCAAACTAGGTGCACG
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
506525 CATAAA
196 CATAAA
* *
506531 GTGTCGATACATTTATAAAAAGTATCGATACAAAAAACATCGAAA-CCATTAATTTTAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCA-TAATTTTAATGTAAT
* * * *
506595 AGTTAATTTTTCAATGTAACCAGTATAAAAATACCAGTTTTATGAGAGAATAGGTCTACATAATG
65 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
506660 TATCGACACTTTTGAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
506724 GCATAAA
195 GCATAAA
* * *
506731 GTGTCGATA-ACCTTATAAAAAGTATCGATCCTAAAAACATCGAAACCAATAATTTTAATGTAAT
1 GTGTCGATACA-TTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAAT
* * *
506795 ATGTAA-TTTTCAATGTAACCGGTATAAAAATACCGGTTTTATGAGAGAATAGGTGTACATAATG
65 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* * * * *
506859 TATCGATATTTTTTAAATTTATGTCGATACTTTTTGTCCAGAATGAATGCTCAAACTAGGTGCAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
506924 GCATAAA
195 GCATAAA
* * *
506931 GTATCGATACATTTATAAAAATTATCGATCCTAAAAACATCGAAACCCATAATTTTAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAATA
* * * * * * * *
506996 GGTAATTTTTCAATGTAATCAGTATAAATATATCGGTTTAATTACAAAATATGTC-AGCATAATG
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
507060 TATCGACACTTTAT-AAATTTGTGTCGATACATTTTT
130 TATCGACACTTT-TGAAATTTGTGTCGATAC-TTTTT
507096 TAAATTACGC
Statistics
Matches: 1061, Mismatches: 93, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
199 266 0.25
200 363 0.34
201 426 0.40
202 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (201 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTTTAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGCACG
CATAAA
Found at i:506404 original size:19 final size:20
Alignment explanation
Indices: 506380--506418 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
506370 CGAAACCCAT
506380 AATTTT-AATATAATAGGTA
1 AATTTTCAATATAATAGGTA
* *
506399 AATTTTCAATGTAATCGGTA
1 AATTTTCAATATAATAGGTA
506419 TAAATATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
AATTTTCAATATAATAGGTA
Found at i:506506 original size:400 final size:401
Alignment explanation
Indices: 505729--507095 Score: 2059
Period size: 400 Copynumber: 3.4 Consensus size: 401
505719 GTAAACAGAT
505729 GTGTCGATACATTTATAAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAA-TATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
505794 AGGTAATTTTTCAATGTAATCGGTATAAATATACCTGTTTTATGAGATAATATGTCTACATAATG
65 AGGTAATTTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
* *
505859 CATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAATTA-GTGAAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTG-AC
* * * * *
505923 ACATAAAGTGTAGATACATTTATAAAAAGTATCGAT-CTCAAAAATATTGAAACCCATAATTATA
194 GCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCT-AAAAACATCGAAACCCATAATTTTA
** * *
505987 ATGTAATAGGTACTTTTTCAATGTAACCGGTATAAATATACCAGCTTTATGAGAGAATAGGTCTA
258 ATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA
* * *
506052 CATAATGTATCGACACTTTTGAATTTTGTGTCGATCCTTTTTGTCAAGAATGAATGCCCAAACTA
323 CATAATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTA
*
506117 GGTGCACACATAAA
388 GGTGCACGCATAAA
506131 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
506196 GGTAATTTTTCAATGTAACCAATATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * *
506261 ATCAACACTTTTGAAATTTGTGTTGATACTTTTTATCCAGAATGAATGCCCAAACTAGGTG-CGC
131 ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGACGC
*
506325 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAACCCATAATTTTAATA
196 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAACCCATAATTTTAATG
* * *
506390 TAATAGGTAAATTTTCAATGTAATCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTGCAT
261 TAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAT
* *
506455 AATGTATCGACACTTTTGAAATTTGTGTTGATACTTTTTGTCCATAATGAATGCCCAAACTAGGT
326 AATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGT
506520 GCACGCATAAA
391 GCACGCATAAA
* * * *
506531 GTGTCGATACATTTATAAAAAGTATCGATACAAAAAACATCGAAA-CCATTAATTTTAATGTAAT
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCA-TAATTATAATGTAAT
* * *
506595 AGTTAATTTTTCAATGTAACCAGTATAAAAATACCAGTTTTATGAGAGAATAGGTCTACATAATG
65 AGGTAATTTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATG
506660 TATCGACACTTTTGAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCCAAACTAGGTGCAC
130 TATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTG-AC
* *
506724 GCATAAAGTGTCGATA-ACCTTATAAAAAGTATCGATCCTAAAAACATCGAAACCAATAATTTTA
194 GCATAAAGTGTCGATACA-TTTATAAAAAGTATCGATCCTAAAAACATCGAAACCCATAATTTTA
* * *
506788 ATGTAATATGT-AATTTTCAATGTAACCGGTATAAAAATACCGGTTTTATGAGAGAATAGGTGTA
258 ATGTAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA
* * * * *
506852 CATAATGTATCGATATTTTTTAAATTTATGTCGATACTTTTTGTCCAGAATGAATGCTCAAACTA
323 CATAATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTA
506917 GGTGCACGCATAAA
388 GGTGCACGCATAAA
* * * *
506931 GTATCGATACATTTATAAAAATTATCGATCCTAAAAACATCGAAACCCATAATTTTAATGTAATA
1 GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * * *
506996 GGTAATTTTTCAATGTAATCAGTATAAATATATCGGTTTAATTACAAAATATGTC-AGCATAATG
66 GGTAATTTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA-CATAATG
507060 TATCGACACTTTAT-AAATTTGTGTCGATACATTTTT
130 TATCGACACTTT-TGAAATTTGTGTCGATAC-TTTTT
507096 TAAATTACGC
Statistics
Matches: 881, Mismatches: 73, Indels: 22
0.90 0.07 0.02
Matches are distributed among these distances:
399 34 0.04
400 589 0.67
401 229 0.26
402 29 0.03
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (401 bp):
GTGTCGATACATTTATAAAAAATATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCAGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGTGACGC
ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAACCCATAATTTTAATG
TAATAGGTAAATTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAT
AATGTATCGACACTTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAGGT
GCACGCATAAA
Found at i:508565 original size:3 final size:3
Alignment explanation
Indices: 508546--508589 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
508536 CAATCGTTCA
* *
508546 ATG AAG ATG AAG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
508590 CCAAACAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:511411 original size:15 final size:15
Alignment explanation
Indices: 511391--511421 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
511381 ATGTATCGAT
511391 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
511406 ACATAAAGTTTCCAA
1 ACATAAAGTTTCCAA
511421 A
1 A
511422 AAAAAAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (15 bp):
ACATAAAGTTTCCAA
Found at i:511428 original size:15 final size:15
Alignment explanation
Indices: 511395--511429 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
511385 ATCGATACAT
* *
511395 AAAGTTTCCAAACAT
1 AAAGTTTCCAAAAAA
511410 AAAGTTTCCAAAAAA
1 AAAGTTTCCAAAAAA
511425 AAAGT
1 AAAGT
511430 GTCGACACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.14, G:0.09, T:0.23
Consensus pattern (15 bp):
AAAGTTTCCAAAAAA
Found at i:512055 original size:22 final size:21
Alignment explanation
Indices: 512030--512073 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
512020 AAAATAAGTA
512030 TACATAATGTATCGACACTTTT
1 TACAT-ATGTATCGACACTTTT
* * *
512052 TACATTTGTGTCGATACTTTT
1 TACATATGTATCGACACTTTT
512073 T
1 T
512074 GTCTAGAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (21 bp):
TACATATGTATCGACACTTTT
Found at i:512129 original size:198 final size:197
Alignment explanation
Indices: 511864--512465 Score: 821
Period size: 199 Copynumber: 3.0 Consensus size: 197
511854 ACATAATGTA
* * *
511864 TCGACACTTTTTGTCCAGAATGAATGCTCAAAGAGGTACACACATAAAGTGTCGATACATTTAAA
1 TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTACACGCATAAAGTGTCGATACATTTAAA
*
511929 ATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAA
66 ATTGTATCGATCCCAAAAACATCGAAACC-ATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * * * *
511994 CCTGTACAAAATACCGGTTTTATGAGAAAATAAGTATACATAATGTATCGACACTTTTTACATTT
130 CCGGTACAATATACCGGTTTTATGAGAAAATAGGTATACATAATATATCGACACTTTTAAAATTT
512059 GTG
195 GTG
* * *
512062 TCGATACTTTTTGTCTAGAATGAATGCTCAACGAGGTTCACGCATAAAGTGTCCATACATTTAAA
1 TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTACACGCATAAAGTGTCGATACATTTAAA
* * **
512127 ATTGTATCGATCCCAAAAATATCGAAACTCATAATTATAATGTAATAGGTAATTTTGGAATGTAA
66 ATTGTATCGATCCCAAAAACATCGAAAC-CATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * * * *
512192 CCGGTATAAGTATACCAGTTTAATTAGAAAACAGGTCA-ACATAATATATCGACACGTTTAAAAT
130 CCGGTACAA-TATACCGGTTTTATGAGAAAATAGGT-ATACATAATATATCGACACTTTTAAAAT
*
512256 ATGTG
193 TTGTG
* * * *
512261 TCGATACTTTTTGTCCAGAATGCATG-ACAACGAGGTGCATGCATAAAGTGTCGATACATTTTAA
1 TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTACACGCATAAAGTGTCGATACA-TTTAA
* *
512325 ATTTGTATGGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTA
65 AATTGTATCGATCCCAAAAACATCGAAA-CCATAATTATAATGTAATAGGTAAATTTACAATGTA
* * * *
512390 ACCGGTAGACATATACCGATTTTATGAGAGAATAGGTCTACATAATATATCGACACTTTTAAAAT
129 ACCGGTACA-ATATACCGGTTTTATGAGAAAATAGGTATACATAATATATCGACACTTTTAAAAT
512455 TTGTG
193 TTGTG
512460 TCGATA
1 TCGATA
512466 ATTGCTTTAA
Statistics
Matches: 352, Mismatches: 45, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
198 153 0.43
199 196 0.56
200 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (197 bp):
TCGATACTTTTTGTCCAGAATGAATGCTCAACGAGGTACACGCATAAAGTGTCGATACATTTAAA
ATTGTATCGATCCCAAAAACATCGAAACCATAATTATAATGTAATAGGTAAATTTACAATGTAAC
CGGTACAATATACCGGTTTTATGAGAAAATAGGTATACATAATATATCGACACTTTTAAAATTTG
TG
Found at i:516644 original size:200 final size:198
Alignment explanation
Indices: 516252--516953 Score: 924
Period size: 200 Copynumber: 3.5 Consensus size: 198
516242 ACCTAAATAT
* * * *
516252 GTGTCGATACATTT-TCTAAAAGTATCGACCCCAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
* ** * * * * * *
516316 AGGTAAATTAACAATGTAACCGGTATAAATATATCGG-TTAATTAGAAAACAGTTCAACATAATG
65 AGGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATG
**
516380 TATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCAC
130 TATCGACACTT-TTTAATTTGTGTCGATACTT-TTGTCCAGAATGAATG-CCAAACGAGGTGCAC
*
516445 ACATAGA
192 ACATAAA
*
516452 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAAAATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
** *
516517 CATAATTTTTCAATTTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
* *
516582 ATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGAATGCCAAATGGGGTGCACAC
131 ATCGACACTTTTTAA-TTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACAC
516647 ATAAA
194 ATAAA
* *
516652 GTGTCGATACATCTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTACAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* *
516717 GGTAATTTTTCAATGCAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * *
516782 ATCGAAACTTTTTAAGTTGTGTCGATACTTTTTGTCCAGAATAAATGCCCAACGAGGTGTACGCA
131 ATCGACACTTTTTAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACACA
516847 TAAA
195 TAAA
* ** * * *
516851 GTGTCGATATATTTA-AAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
516915 GGTAAATTTGCAATGTTATCAGTATAAATATACCGGTTT
66 GGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTT
516954 AGTTAGAAAA
Statistics
Matches: 445, Mismatches: 53, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
198 76 0.17
199 59 0.13
200 246 0.55
201 62 0.14
202 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACACAT
AAA
Found at i:517062 original size:87 final size:87
Alignment explanation
Indices: 516971--517133 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
516961 AAATAGGTCA
516971 ATATAAGTC-CTACATATTACATTATATAACCGCTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAG-CGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTACTTGATAATATT
517035 TCCGGTTAAATGCCTATTTTATT
65 TCCGGTTAAATGCCTATTTTATT
* * *
517058 ATATAAGCGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTACTTGATAATATTT
517123 CCGGTTAAATG
66 CCGGTTAAATG
517134 ATATAACATA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
86 1 0.01
87 71 0.99
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACATATTACATTATATAACCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:517105 original size:23 final size:23
Alignment explanation
Indices: 517055--517099 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
517045 TGCCTATTTT
*
517055 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
517078 ATTATATAAGCGGTACCTAATA
1 ATTATATAAGCGCTACCTAATA
517100 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:517426 original size:26 final size:29
Alignment explanation
Indices: 517393--517455 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
517383 TTATTTTTAT
517393 TTTGATCAAT-AAA-TTAAAAAA-ATTAA
1 TTTGATCAATAAAATTTAAAAAATATTAA
* *
517419 TTTGATCACTAAAATTTAAAAAATTTTAA
1 TTTGATCAATAAAATTTAAAAAATATTAA
517448 TTTGATCA
1 TTTGATCA
517456 TTCAACTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 9 0.28
27 3 0.09
28 8 0.25
29 12 0.38
ACGTcount: A:0.49, C:0.06, G:0.05, T:0.40
Consensus pattern (29 bp):
TTTGATCAATAAAATTTAAAAAATATTAA
Found at i:517450 original size:29 final size:27
Alignment explanation
Indices: 517387--517455 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 27
517377 TTATTCTTAT
*
517387 TTTTATTTTGATCAATAAATTAAAAAA
1 TTTTAATTTGATCAATAAATTAAAAAA
* *
517414 -ATTAATTTGATCACTAAAATTTAAAAAA
1 TTTTAATTTGATCAAT-AAA-TTAAAAAA
517442 TTTTAATTTGATCA
1 TTTTAATTTGATCA
517456 TTCAACTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 12 0.34
27 3 0.09
28 8 0.23
29 12 0.34
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (27 bp):
TTTTAATTTGATCAATAAATTAAAAAA
Found at i:518933 original size:11 final size:11
Alignment explanation
Indices: 518919--518947 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
518909 GTGGATTGTA
518919 ATACTATATAT
1 ATACTATATAT
518930 ATACTATATAT
1 ATACTATATAT
518941 ATA-TATA
1 ATACTATA
518948 AATCATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (11 bp):
ATACTATATAT
Found at i:521922 original size:53 final size:53
Alignment explanation
Indices: 521864--521970 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 53
521854 TTGGTGAGGT
* * * *
521864 TTTCTGTTGTATTAGGTTCAATATGCTTTAAAGATTGTTAACAAACCAGATGG
1 TTTCTGTTGTATTAGATTAAATATGCTCTAAAGATTGTTAACAAAACAGATGG
* * * *
521917 TTTCTGTTGTGTTAGATTAAATATTCTCTAAAGATTGTTGACAAAACAGGTGG
1 TTTCTGTTGTATTAGATTAAATATGCTCTAAAGATTGTTAACAAAACAGATGG
521970 T
1 T
521971 GTTAGGTGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (53 bp):
TTTCTGTTGTATTAGATTAAATATGCTCTAAAGATTGTTAACAAAACAGATGG
Found at i:523491 original size:29 final size:30
Alignment explanation
Indices: 523459--523524 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
523449 ATATTTACAT
523459 TAGCTCACTAGC-T-T-TGCATCCATATTTTC
1 TAGCTCACTAGCATGTATGCAT-C-TATTTTC
* *
523488 TAGCTCATTTGCATGTATGCATCTATTTTC
1 TAGCTCACTAGCATGTATGCATCTATTTTC
523518 TAGCTCA
1 TAGCTCA
523525 TGTATGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 10 0.31
30 15 0.47
31 2 0.06
32 5 0.16
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (30 bp):
TAGCTCACTAGCATGTATGCATCTATTTTC
Found at i:526259 original size:21 final size:19
Alignment explanation
Indices: 526229--526268 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
526219 TGCTCTCGAG
526229 GCTTTCTTCAATTCGTATAAA
1 GCTTTCTTCAA-TCG-ATAAA
*
526250 GCTTTGTTCAATCGATAAA
1 GCTTTCTTCAATCGATAAA
526269 TTTTATCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (19 bp):
GCTTTCTTCAATCGATAAA
Found at i:529412 original size:15 final size:15
Alignment explanation
Indices: 529382--529422 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
529372 TCCGTTCAAA
*
529382 CTTTCTCT-CTCGTT
1 CTTTCTCTCCCCGTT
529396 CTTTCTCTCCCCGTT
1 CTTTCTCTCCCCGTT
529411 CTTTCTCTCCCC
1 CTTTCTCTCCCC
529423 ACACCGAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.00, C:0.46, G:0.05, T:0.49
Consensus pattern (15 bp):
CTTTCTCTCCCCGTT
Found at i:530724 original size:136 final size:138
Alignment explanation
Indices: 530247--530886 Score: 696
Period size: 136 Copynumber: 4.7 Consensus size: 138
530237 AAACAAGCTA
* *
530247 AGGTTGAACAAGTTCTTCTCATTATGAACTCCTTCTCCCT-TATCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* * * * **
530311 GAACTCTCCA-CTGAAAATGTTGATTCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGAT
66 GAACTCTCCATTTG-AAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAA---CATATGTGAT
*
530375 GAATC-A-AGAT
127 GAATCGAGTGAT
* * * *
530385 AAGGTTGCACAAGTTCTTCTCATTATGAACTTCTTCTCCTTC-ATCGGATGAGTTTTTCTCATTA
1 -AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTA
* * ** *** *
530449 TGAACTCTCCA-CTGAAAATGTTGATCCCTCGAGTAAGGTGTTGTTGATTCAACTCCATATGTGC
65 TGAACTCTCCATTTG-AAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAA---CATATGTGA
530513 TGAATCGAGCT-A-
126 TGAATCGAG-TGAT
* * * * *
530525 AGGTTGAATACGTTCTTCTCATTATGAACTTCTTCTCCCTCTTTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
*
530590 GAACTCTCCATTTGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGA-A-ATGTCG-TGAA
66 GAACTCTCCATTTGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAACATATGT-GATGAA
530652 TCGAGTGAT
130 TCGAGTGAT
* * *
530661 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* * * * * *
530726 GAACTCTCTATTTAAAATGTTGATCCTTCAAGCGAGGAGCCACTGATTCGA-A-ATGTCG-TGAA
66 GAACTCTCCATTTGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAACATATGT-GATGAA
530788 TCGAGTGAT
130 TCGAGTGAT
* * * *
530797 AGGTCGAACAAGATCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGCTCTTCTCATTAT
1 AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
* *
530862 AAACTATCCATTTGAAATGTTGATC
66 GAACTCTCCATTTGAAATGTTGATC
530887 GGTTCATCTT
Statistics
Matches: 448, Mismatches: 44, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
134 1 0.00
135 14 0.03
136 208 0.46
139 161 0.36
140 61 0.14
141 3 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (138 bp):
AGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
GAACTCTCCATTTGAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCAACATATGTGATGAAT
CGAGTGAT
Found at i:531274 original size:3 final size:3
Alignment explanation
Indices: 531266--531329 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
531256 TTCGAGTTAA
531266 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
531314 TAT TAT TATT TAT TAT
1 TAT TAT TA-T TAT TAT
531330 CCAAAAAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:538538 original size:22 final size:22
Alignment explanation
Indices: 538486--538545 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
538476 ATCAGTGCAT
**
538486 GTGCAGCCCGCTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
538508 GTGCAGCCTACTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
*
538530 GTGCAGCCTTCTTCCA
1 GTGCAGCCTACTTCCA
538546 CCATCCGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.15, C:0.38, G:0.20, T:0.27
Consensus pattern (22 bp):
GTGCAGCCTACTTCCAGCATTC
Found at i:538755 original size:28 final size:28
Alignment explanation
Indices: 538718--538853 Score: 102
Period size: 28 Copynumber: 4.9 Consensus size: 28
538708 TTATGAGAAG
* *
538718 TTGTCCTTTATTTTATTTTATAAAAAAA
1 TTGTCCTTTATTATAATTTATAAAAAAA
538746 TTGTCCTTTATTATAATTTATAAAAAAA
1 TTGTCCTTTATTATAATTTATAAAAAAA
* * * *
538774 -AG---TATACTT-TATTTTATAAAAAAG
1 TTGTCCTTTA-TTATAATTTATAAAAAAA
* **
538798 TTTTACACTTTATTATAATTTATAAACAATT
1 TTGT-C-CTTTATTATAATTTATAAA-AAAA
**
538829 TTGTATTTTATTATAATTTATAAAA
1 TTGTCCTTTATTATAATTTATAAAA
538854 CCTTTTGTCA
Statistics
Matches: 84, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
24 16 0.19
25 2 0.02
27 1 0.01
28 27 0.32
29 20 0.24
30 13 0.15
31 5 0.06
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (28 bp):
TTGTCCTTTATTATAATTTATAAAAAAA
Found at i:538774 original size:29 final size:29
Alignment explanation
Indices: 538718--538853 Score: 97
Period size: 29 Copynumber: 4.9 Consensus size: 29
538708 TTATGAGAAG
* *
538718 TTGTCCTTTATTTTATTTTAT-AAAAAAA
1 TTGTCCTTTATTATAATTTATAAAAAAAA
538746 TTGTCCTTTATTATAATTTATAAAAAAAA
1 TTGTCCTTTATTATAATTTATAAAAAAAA
* * * *
538775 GTATAC--T-TTAT--TTTAT-AAAAAAG
1 TTGTCCTTTATTATAATTTATAAAAAAAA
* * **
538798 TTTTACACTTTATTATAATTTATAAACAATT
1 TTGT-C-CTTTATTATAATTTATAAAAAAAA
**
538829 TTGTATTTTATTATAATTTATAAAA
1 TTGTCCTTTATTATAATTTATAAAA
538854 CCTTTTGTCA
Statistics
Matches: 83, Mismatches: 16, Indels: 17
0.72 0.14 0.15
Matches are distributed among these distances:
23 8 0.10
24 5 0.06
25 1 0.01
26 4 0.05
27 2 0.02
28 23 0.28
29 28 0.34
30 5 0.06
31 7 0.08
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (29 bp):
TTGTCCTTTATTATAATTTATAAAAAAAA
Found at i:539134 original size:24 final size:24
Alignment explanation
Indices: 539107--539155 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
539097 ACATTAACGT
539107 CACTACATGTTTAACAATACGTGA
1 CACTACATGTTTAACAATACGTGA
539131 CACTACATGTTTAACAATACGTGA
1 CACTACATGTTTAACAATACGTGA
539155 C
1 C
539156 GATAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (24 bp):
CACTACATGTTTAACAATACGTGA
Found at i:547719 original size:36 final size:37
Alignment explanation
Indices: 547617--547728 Score: 127
Period size: 37 Copynumber: 3.1 Consensus size: 37
547607 AAGAAAATTG
* * * *
547617 ATCTTAAGCCTTCACGAAAGAGTAGGGAAGCAAGTCA
1 ATCTTAAGCCTTCAAGGAAGAGTAGTGAAGCAAATCA
* *
547654 ATCTTAAGCCTTCATGGAATAGTAGTGAAGCAAATCA
1 ATCTTAAGCCTTCAAGGAAGAGTAGTGAAGCAAATCA
* * * *
547691 AT-TTTAGCCTTCAAGGGAGAGTATTGAAGCAAACCA
1 ATCTTAAGCCTTCAAGGAAGAGTAGTGAAGCAAATCA
547727 AT
1 AT
547729 GTTTGAGTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
36 30 0.47
37 34 0.53
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCAAGGAAGAGTAGTGAAGCAAATCA
Found at i:547807 original size:55 final size:55
Alignment explanation
Indices: 547739--548141 Score: 202
Period size: 55 Copynumber: 7.3 Consensus size: 55
547729 GTTTGAGTCA
* *
547739 TATACTCCCTGAAATAATAGGGAACAGACA-CGTTTGT-TGAAGATTGTTCGAGTTC
1 TATACTCCCTGAAAGAATAGGGAACAGA-ATCGTTT-TCAGAAGATTGTTCGAGTTC
* *
547794 TATACTCCTTGAAAGAATAGGG-AGAGAATTCGTTTTCAGAAGATTGTTCGAGTTC
1 TATACTCCCTGAAAGAATAGGGAACAGAA-TCGTTTTCAGAAGATTGTTCGAGTTC
* * * * *
547849 TATACTCCCTGAAAGAATAGGGAGC-GGACCTGTTTTCAAAAGATTTCTCTCGAG-TC
1 TATACTCCCTGAAAGAATAGGGAACAGAATC-GTTTTCAGAAGA-TTGT-TCGAGTTC
* * * * * *
547905 T-TATCTCCCTGAAAGAAGAGTGGAGCAGACTCATCTTCAAAAGATT-TCTCGAG-TC
1 TATA-CTCCCTGAAAGAATAG-GGAACAGAATCGTTTTCAGAAGATTGT-TCGAGTTC
* * * * *
547960 T-TATCTCCCTGAAAGAAGT-GTGGAGCAGACTCATCTTCAAAAGATT-TCTCGAG-TC
1 TATA-CTCCCTGAAAGAA-TAG-GGAACAGAATCGTTTTCAGAAGATTGT-TCGAGTTC
* * * *
548015 T-TATCTCCCTGAAAGAAGAGTGAAGCA-AACTCGTCTTCTA-AAGATT-TCTAGAG-TC
1 TATA-CTCCCTGAAAGAATAGGGAA-CAGAA-TCGTTTTC-AGAAGATTGT-TCGAGTTC
* * *
548070 TTATA-TCCCAGAAAGAATAGTGGAGCAGATTCGTTTTCCA-AAGATT-TCTCGAGTAT-
1 -TATACTCCCTGAAAGAATAG-GGAACAGAATCGTTTT-CAGAAGATTGT-TCGAGT-TC
548126 TAT-CTCCCTGAAAGAA
1 TATACTCCCTGAAAGAA
548142 GAGTAGAGCA
Statistics
Matches: 293, Mismatches: 32, Indels: 46
0.79 0.09 0.12
Matches are distributed among these distances:
53 1 0.00
54 9 0.03
55 229 0.78
56 29 0.10
57 23 0.08
58 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (55 bp):
TATACTCCCTGAAAGAATAGGGAACAGAATCGTTTTCAGAAGATTGTTCGAGTTC
Found at i:548151 original size:55 final size:55
Alignment explanation
Indices: 547798--548167 Score: 419
Period size: 55 Copynumber: 6.7 Consensus size: 55
547788 GAGTTCTATA
* * * * *
547798 CTCCTTGAAAGAATAG-GGAG-AGAATTCGTTTTCAGAAGATTGT-TCGAGT-TCTAT
1 CTCCCTGAAAGAAGAGTGGAGCAG-ACTCGTCTTCAAAAGATT-TCTCGAGTCT-TAT
* * *
547852 ACTCCCTGAAAGAATAG-GGAGCGGAC-CTGTTTTCAAAAGATTTCTCTCGAGTCTTAT
1 -CTCCCTGAAAGAAGAGTGGAGCAGACTC-GTCTTCAAAAGA-TT-TCTCGAGTCTTAT
*
547909 CTCCCTGAAAGAAGAGTGGAGCAGACTCATCTTCAAAAGATTTCTCGAGTCTTAT
1 CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTCGAGTCTTAT
* *
547964 CTCCCTGAAAGAAGTGTGGAGCAGACTCATCTTCAAAAGATTTCTCGAGTCTTAT
1 CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTCGAGTCTTAT
* * * *
548019 CTCCCTGAAAGAAGAGTGAAGCAAACTCGTCTTCTAAAGATTTCTAGAGTCTTAT
1 CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTCGAGTCTTAT
* * * * * * *
548074 ATCCCAGAAAGAATAGTGGAGCAGATTCGTTTTCCAAAGATTTCTCGAGTATTAT
1 CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTCGAGTCTTAT
*
548129 CTCCCTGAAAGAAGAGTAGAGCAGACTCGTCTTCCAAAA
1 CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTT-CAAAA
548168 TTGATCTGAA
Statistics
Matches: 274, Mismatches: 33, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
54 1 0.00
55 219 0.80
56 25 0.09
57 27 0.10
58 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (55 bp):
CTCCCTGAAAGAAGAGTGGAGCAGACTCGTCTTCAAAAGATTTCTCGAGTCTTAT
Found at i:548291 original size:131 final size:131
Alignment explanation
Indices: 548068--548307 Score: 302
Period size: 131 Copynumber: 1.8 Consensus size: 131
548058 ATTTCTAGAG
* * ** * * * *
548068 TCTTATATCCCAGAAAGAATAGTGGAGCAGATTCGTTTTCCAAAGATTTCTCGAGTATTATCTCC
1 TCTTATATCCCAGAAAGAAGAGTGGAGCAGAATCGTTTTCCAAAGACATATCAAGTATGATCTCA
* **
548133 CTGAAAGAAGAGTAGAGCAGACTCGTCTTCCAAAATTGATCTGAATACCCGAAAAAGATGAACAT
66 CTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAAAAGATCTGAATACCCGAAAAAGATGAACAT
548198 A
131 A
* * * * *
548199 TCTTATCTCCCTGAAAGAAGAGTGGAGCAGAATCTTTTTTCAAAGACATATCAAGTCTGATCTTC
1 TCTTATATCCCAGAAAGAAGAGTGGAGCAGAATCGTTTTCCAAAGACATATCAAGTATGATC-TC
* *
548264 ACTGAAAGAA-AGTGGAGTAGACCCGTCTTCCAAAAAAGATCTGA
65 ACTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAAAAGATCTGA
548308 CCTACCCTAA
Statistics
Matches: 90, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
131 79 0.88
132 11 0.12
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (131 bp):
TCTTATATCCCAGAAAGAAGAGTGGAGCAGAATCGTTTTCCAAAGACATATCAAGTATGATCTCA
CTGAAAGAAGAGTAGAGCAGACCCGTCTTCCAAAAAAGATCTGAATACCCGAAAAAGATGAACAT
A
Found at i:548460 original size:3 final size:3
Alignment explanation
Indices: 548452--548498 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
548442 TTTGTTCAAG
548452 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
548498 T
1 T
548499 AAAAAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:550109 original size:21 final size:21
Alignment explanation
Indices: 550083--550127 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
550073 TTTTTTATGA
550083 ATTGGAATAATTAAAATCTGC
1 ATTGGAATAATTAAAATCTGC
550104 ATTGGAATAATTAAAATCTGC
1 ATTGGAATAATTAAAATCTGC
550125 ATT
1 ATT
550128 ATCTTCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTGGAATAATTAAAATCTGC
Found at i:556366 original size:36 final size:36
Alignment explanation
Indices: 556319--556446 Score: 134
Period size: 36 Copynumber: 3.5 Consensus size: 36
556309 CAGATGATTA
* *
556319 TCTCACTTGAGATTGTTTTTCTTAAAACATACTTTG
1 TCTCACTTGAGACTGTTTTTCTTAAAACAGACTTTG
* *
556355 TCTCACTTGAGACTGTTTTACTTGAAAGA-AGA-TTTA
1 TCTCACTTGAGACTGTTTTTCTT-AAA-ACAGACTTTG
* ** **
556391 TTTCACTCAAAGTTTGTTTTTCTTAAAACAGACTTTG
1 TCTCACT-TGAGACTGTTTTTCTTAAAACAGACTTTG
556428 TCTCACTTGAGACTGTTTT
1 TCTCACTTGAGACTGTTTT
556447 ACTCGGAAGA
Statistics
Matches: 71, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
35 1 0.01
36 44 0.62
37 25 0.35
38 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (36 bp):
TCTCACTTGAGACTGTTTTTCTTAAAACAGACTTTG
Found at i:556408 original size:73 final size:71
Alignment explanation
Indices: 556328--556559 Score: 302
Period size: 73 Copynumber: 3.2 Consensus size: 71
556318 ATCTCACTTG
*
556328 AGATTGTTTTTCTTAAAACATACTTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATT
1 AGATTGTTTTTCTTAAAACA-ACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATT
556393 TCACTCAA
65 TCACTC-A
* *
556401 AGTTTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGGAAGAAGATTTATT
1 AGATTGTTTTTCTTAAAACA-ACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATT
556466 TCACTCA
65 TCACTCA
* * * * *
556473 AGATTGTTTTTCTTAAAACAAGATTTGTCTCTCTTGGGACTATTTTCACTCGAAAAAAGGCATTT
1 AGATTGTTTTTCTTAAAACAA-CTTTGTCTCACTTGAGACTGTTTT-ACTCGAAAGAA-G-ATTT
*
556538 CGTTTCACTCA
62 -ATTTCACTCA
*
556549 AGACTGTTTTT
1 AGATTGTTTTT
556560 TAAAGAAGTT
Statistics
Matches: 141, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
71 1 0.01
72 40 0.28
73 76 0.54
74 1 0.01
75 4 0.03
76 19 0.13
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (71 bp):
AGATTGTTTTTCTTAAAACAACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTT
CACTCA
Found at i:556496 original size:36 final size:36
Alignment explanation
Indices: 556316--556503 Score: 128
Period size: 36 Copynumber: 5.2 Consensus size: 36
556306 ATGCAGATGA
** *
556316 TTATCTCACTTGAGATTGTTTTTCTTAAAACATA-CT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACA-AGAT
* ** * * * *
556352 TTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
* *
556388 TTATTTCACTCAAAGTTTGTTTTTCTTAAAAC-AGACT
1 TTATCTCACTC-AAGATTGTTTTTCTTAAAACAAGA-T
* ** * * *** *
556425 TTGTCTCACTTGAGACTGTTTTACTCGGAAGAAGAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
*
556461 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGAT
1 TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
*
556497 TTGTCTC
1 TTATCTC
556504 TCTTGGGACT
Statistics
Matches: 110, Mismatches: 38, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
35 1 0.01
36 83 0.75
37 26 0.24
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (36 bp):
TTATCTCACTCAAGATTGTTTTTCTTAAAACAAGAT
Found at i:556615 original size:21 final size:21
Alignment explanation
Indices: 556590--556639 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
556580 TGAGATAGTT
556590 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
556611 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
556632 TCCCTTGA
1 TCTCTTGA
556640 GACATTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:556765 original size:37 final size:37
Alignment explanation
Indices: 556705--556790 Score: 102
Period size: 37 Copynumber: 2.4 Consensus size: 37
556695 TTGAAAAAAT
** * *
556705 TTCCCTTGAAA-TTAATTTTGTCTCTCTTGAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGG
* *
556741 TTCCCTTGAAACAAAATTTTGTCTCCCTTGGGAAAGT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGG
*
556778 TTCTCTTGAAACA
1 TTCCCTTGAAACA
556791 TAAACATTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 11 0.26
37 31 0.74
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGG
Found at i:556866 original size:65 final size:66
Alignment explanation
Indices: 556741--556903 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 66
556731 TTGAGATAGG
*
556741 TTCCCTTGAAACAAAATTTTGTCTCCCTTGGGAAAGTTTCTCTTGAAACATAAACATTGAAAATG
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTGAAAATG
556806 T
66 T
** * * * ** *
556807 TTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATA-AAATTTTTGAATAT
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAA-CATTGAAAAT
556870 GT
65 GT
* * *
556872 TTCTCTTGAAAC-AAATTTCGTCTCCATTGAGA
1 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGA
556904 CATTTTCTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
64 3 0.04
65 67 0.83
66 11 0.14
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (66 bp):
TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTGAAAATG
T
Done.